diff --git a/.directory b/.directory
new file mode 100644
index 0000000..875ce20
--- /dev/null
+++ b/.directory
@@ -0,0 +1,4 @@
+[Dolphin]
+Timestamp=2015,7,11,17,31,9
+Version=3
+VisibleRoles=Icons_text
diff --git a/.gitignore b/.gitignore
index 691e5f6..0d72f4c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,4 +40,10 @@ Lobo/Tests/*.a
 Lobo/Tests/*.o
 tools/*.o
 tools/*.a
-tools/Depend
\ No newline at end of file
+tools/Depend
+Phylo/Sources/*.o
+Phylo/Sources/*.a
+Phylo/APPS/*.o
+Phylo/APPS/*.a
+Phylo/Tests/*.o
+Phylo/Test/*.a
diff --git a/Align2/APPS/Depend b/Align2/APPS/Depend
new file mode 100644
index 0000000..839cee9
--- /dev/null
+++ b/Align2/APPS/Depend
@@ -0,0 +1,168 @@
+subali.o: subali.cc /usr/include/stdc-predef.h \
+ ../../Align2/Sources/ScoringS2S.h ../../Align2/Sources/ScoringScheme.h \
+ ../../Align2/Sources/AlignmentData.h ../../Align2/Sources/Alignment.h \
+ ../../Align2/Sources/AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Align2/Sources/Structure.h \
+ ../../Align2/Sources/SubMatrix.h ../../Align2/Sources/Substitution.h \
+ ../../Align2/Sources/ScoringP2S.h ../../Align2/Sources/Profile.h \
+ ../../Biopool/Sources/AminoAcidCode.h ../../Align2/Sources/ScoringP2P.h \
+ ../../Align2/Sources/ScoringFunction.h \
+ ../../Align2/Sources/HenikoffProfile.h \
+ ../../Align2/Sources/PSICProfile.h \
+ ../../Align2/Sources/SeqDivergenceProfile.h \
+ ../../Align2/Sources/AGPFunction.h ../../Align2/Sources/GapFunction.h \
+ ../../Align2/Sources/NWAlign.h ../../Align2/Sources/Align.h \
+ ../../Align2/Sources/Traceback.h ../../Align2/Sources/SequenceData.h \
+ ../../Align2/Sources/CrossProduct.h ../../Align2/Sources/LogAverage.h \
+ ../../Align2/Sources/DotPFreq.h ../../Align2/Sources/DotPOdds.h \
+ ../../Align2/Sources/EDistance.h ../../Align2/Sources/Pearson.h \
+ ../../Align2/Sources/JensenShannon.h \
+ ../../Align2/Sources/AtchleyDistance.h \
+ ../../Align2/Sources/AtchleyCorrelation.h ../../Align2/Sources/SWAlign.h \
+ ../../Align2/Sources/FSAlign.h ../../Align2/Sources/VGPFunction.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ ../../Biopool/Sources/Identity.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Bond.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/SolvExpos.h ../../Align2/Sources/VGPFunction2.h \
+ ../../Align2/Sources/Sec.h ../../Align2/Sources/Ss2.h \
+ ../../Align2/Sources/Ss2Input.h ../../Align2/Sources/Prof.h \
+ ../../Align2/Sources/ProfInput.h ../../Align2/Sources/stringtools.h \
+ ../../Align2/Sources/SecSequenceData.h ../../tools/GetArg.h \
+ /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/ctime
diff --git a/Align2/Sources/Depend b/Align2/Sources/Depend
index e69de29..265882f 100644
--- a/Align2/Sources/Depend
+++ b/Align2/Sources/Depend
@@ -0,0 +1,5597 @@
+Alignment.o: Alignment.cc /usr/include/stdc-predef.h Alignment.h \
+ AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath stringtools.h
+AlignmentBase.o: AlignmentBase.cc /usr/include/stdc-predef.h \
+ AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
+Align.o: Align.cc /usr/include/stdc-predef.h Align.h Alignment.h \
+ AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h
+NWAlign.o: NWAlign.cc /usr/include/stdc-predef.h NWAlign.h Align.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h
+SWAlign.o: SWAlign.cc /usr/include/stdc-predef.h SWAlign.h Align.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h
+FSAlign.o: FSAlign.cc /usr/include/stdc-predef.h FSAlign.h Align.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h
+NWAlignNoTermGaps.o: NWAlignNoTermGaps.cc /usr/include/stdc-predef.h \
+ NWAlignNoTermGaps.h Align.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h
+AlignmentData.o: AlignmentData.cc /usr/include/stdc-predef.h \
+ AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h
+SequenceData.o: SequenceData.cc /usr/include/stdc-predef.h SequenceData.h \
+ AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h
+SecSequenceData.o: SecSequenceData.cc /usr/include/stdc-predef.h \
+ SecSequenceData.h AlignmentData.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h
+VGPFunction.o: VGPFunction.cc /usr/include/stdc-predef.h VGPFunction.h \
+ GapFunction.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/SolvExpos.h
+VGPFunction2.o: VGPFunction2.cc /usr/include/stdc-predef.h VGPFunction2.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc GapFunction.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h
+Substitution.o: Substitution.cc /usr/include/stdc-predef.h Substitution.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc
+SubMatrix.o: SubMatrix.cc /usr/include/stdc-predef.h SubMatrix.h \
+ Substitution.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc
+StructuralAlignment.o: StructuralAlignment.cc /usr/include/stdc-predef.h \
+ StructuralAlignment.h /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc AlignmentBase.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+ScoringScheme.o: ScoringScheme.cc /usr/include/stdc-predef.h \
+ ScoringScheme.h AlignmentData.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h
+ScoringS2S.o: ScoringS2S.cc /usr/include/stdc-predef.h ScoringS2S.h \
+ ScoringScheme.h AlignmentData.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h
+ScoringP2S.o: ScoringP2S.cc /usr/include/stdc-predef.h ScoringP2S.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringScheme.h AlignmentData.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h
+ScoringP2P.o: ScoringP2P.cc /usr/include/stdc-predef.h ScoringP2P.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h ScoringScheme.h \
+ AlignmentData.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h
+PssmInput.o: PssmInput.cc /usr/include/stdc-predef.h PssmInput.h \
+ Substitution.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc
+Profile.o: Profile.cc /usr/include/stdc-predef.h Profile.h Alignment.h \
+ AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/ctime
+HenikoffProfile.o: HenikoffProfile.cc /usr/include/stdc-predef.h \
+ HenikoffProfile.h Profile.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/ctime
+PSICProfile.o: PSICProfile.cc /usr/include/stdc-predef.h PSICProfile.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
+SeqDivergenceProfile.o: SeqDivergenceProfile.cc \
+ /usr/include/stdc-predef.h SeqDivergenceProfile.h AGPFunction.h \
+ GapFunction.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc NWAlign.h Align.h Alignment.h \
+ AlignmentBase.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ScoringScheme.h Structure.h \
+ SubMatrix.h Substitution.h Traceback.h Profile.h \
+ ../../Biopool/Sources/AminoAcidCode.h ScoringS2S.h SequenceData.h
+LogAverage.o: LogAverage.cc /usr/include/stdc-predef.h LogAverage.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h SubMatrix.h Substitution.h
+CrossProduct.o: CrossProduct.cc /usr/include/stdc-predef.h CrossProduct.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h SubMatrix.h Substitution.h
+DotPFreq.o: DotPFreq.cc /usr/include/stdc-predef.h DotPFreq.h Profile.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+DotPOdds.o: DotPOdds.cc /usr/include/stdc-predef.h DotPOdds.h Profile.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+Pearson.o: Pearson.cc /usr/include/stdc-predef.h Pearson.h Profile.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+JensenShannon.o: JensenShannon.cc /usr/include/stdc-predef.h \
+ JensenShannon.h Profile.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+EDistance.o: EDistance.cc /usr/include/stdc-predef.h EDistance.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+AtchleyDistance.o: AtchleyDistance.cc /usr/include/stdc-predef.h \
+ AtchleyDistance.h Profile.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+AtchleyCorrelation.o: AtchleyCorrelation.cc /usr/include/stdc-predef.h \
+ AtchleyCorrelation.h Profile.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath ScoringFunction.h
+Panchenko.o: Panchenko.cc /usr/include/stdc-predef.h Panchenko.h \
+ Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath PssmInput.h Substitution.h ScoringFunction.h
+Zhou.o: Zhou.cc /usr/include/stdc-predef.h Zhou.h Profile.h Alignment.h \
+ AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc \
+ ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath PssmInput.h Substitution.h ScoringFunction.h
+ThreadingInput.o: ThreadingInput.cc /usr/include/stdc-predef.h \
+ ThreadingInput.h Substitution.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc
+Ss2Input.o: Ss2Input.cc /usr/include/stdc-predef.h Ss2Input.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath Substitution.h
+ProfInput.o: ProfInput.cc /usr/include/stdc-predef.h ProfInput.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath stringtools.h Substitution.h
+Sec.o: Sec.cc /usr/include/stdc-predef.h Sec.h AlignmentData.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h
+Threading.o: Threading.cc /usr/include/stdc-predef.h Threading.h \
+ AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h ThreadingInput.h
+Ss2.o: Ss2.cc /usr/include/stdc-predef.h Ss2.h AlignmentData.h \
+ Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \
+ Substitution.h Ss2Input.h
+Prof.o: Prof.cc /usr/include/stdc-predef.h Prof.h ProfInput.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath stringtools.h Substitution.h Structure.h \
+ SubMatrix.h
+ThreadingSs2.o: ThreadingSs2.cc /usr/include/stdc-predef.h ThreadingSs2.h \
+ AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Ss2Input.h Substitution.h \
+ Structure.h SubMatrix.h ThreadingInput.h
+ThreadingProf.o: ThreadingProf.cc /usr/include/stdc-predef.h \
+ ThreadingProf.h AlignmentData.h Alignment.h AlignmentBase.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ProfInput.h stringtools.h \
+ Substitution.h Structure.h SubMatrix.h ThreadingInput.h
+ReverseScore.o: ReverseScore.cc /usr/include/stdc-predef.h ReverseScore.h \
+ Align.h Alignment.h AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \
+ Structure.h SubMatrix.h Substitution.h Traceback.h \
+ ../../tools/StatTools.h
+stringtools.o: stringtools.cc /usr/include/stdc-predef.h stringtools.h \
+ /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h
diff --git a/Biopool/APPS/Depend b/Biopool/APPS/Depend
new file mode 100644
index 0000000..1af4e12
--- /dev/null
+++ b/Biopool/APPS/Depend
@@ -0,0 +1,1008 @@
+PdbCorrector.o: PdbCorrector.cc /usr/include/stdc-predef.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/XyzSaver.h \
+ ../../Biopool/Sources/SeqSaver.h ../../Biopool/Sources/IntSaver.h
+PdbSecondary.o: PdbSecondary.cc /usr/include/stdc-predef.h \
+ ../../Biopool/Sources/Protein.h ../../Biopool/Sources/Component.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/XyzSaver.h \
+ ../../Biopool/Sources/SeqSaver.h ../../Biopool/Sources/IntSaver.h \
+ ../../tools/GetArg.h /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \
+ ../../tools/String2Number.h
+PdbEditor.o: PdbEditor.cc /usr/include/stdc-predef.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h
+Pdb2Seq.o: Pdb2Seq.cc /usr/include/stdc-predef.h \
+ ../../Biopool/Sources/Protein.h ../../Biopool/Sources/Component.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/SeqSaver.h ../../tools/GetArg.h \
+ /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \
+ ../../tools/String2Number.h
+pdb2secondary.o: pdb2secondary.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h
+pdbshifter.o: pdbshifter.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h
+pdbMover.o: pdbMover.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h
diff --git a/Biopool/Sources/Depend b/Biopool/Sources/Depend
index e69de29..f221352 100644
--- a/Biopool/Sources/Depend
+++ b/Biopool/Sources/Depend
@@ -0,0 +1,3622 @@
+Identity.o: Identity.cc /usr/include/stdc-predef.h Identity.h \
+ /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc
+SimpleBond.o: SimpleBond.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h SimpleBond.h \
+ /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc
+Bond.o: Bond.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h Bond.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h
+Component.o: Component.cc /usr/include/stdc-predef.h Component.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Loader.h Saver.h Visitor.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+Monomer.o: Monomer.cc /usr/include/stdc-predef.h Monomer.h Component.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Loader.h Saver.h Visitor.h
+Polymer.o: Polymer.cc /usr/include/stdc-predef.h Polymer.h Component.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Loader.h Saver.h Visitor.h AminoAcid.h Group.h Monomer.h SideChain.h \
+ AminoAcidCode.h IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath
+Atom.o: Atom.cc /usr/include/stdc-predef.h Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc Identity.h Group.h Monomer.h \
+ Component.h Bond.h Loader.h Saver.h Visitor.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath
+Group.o: Group.cc /usr/include/stdc-predef.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+SideChain.o: SideChain.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc SideChain.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h
+AminoAcid.o: AminoAcid.cc /usr/include/stdc-predef.h AminoAcid.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+Spacer.o: Spacer.cc /usr/include/stdc-predef.h Spacer.h Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \
+ Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ LigandSet.h Ligand.h NucleotideCode.h Protein.h \
+ /usr/include/c++/4.9/cassert /usr/include/assert.h
+IntSaver.o: IntSaver.cc /usr/include/stdc-predef.h IntSaver.h Spacer.h \
+ Bond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \
+ Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+IntLoader.o: IntLoader.cc /usr/include/stdc-predef.h IntLoader.h Spacer.h \
+ Bond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \
+ Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \
+ NucleotideCode.h
+SeqSaver.o: SeqSaver.cc /usr/include/stdc-predef.h SeqSaver.h SideChain.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h Ligand.h NucleotideCode.h
+PdbLoader.o: PdbLoader.cc /usr/include/stdc-predef.h PdbLoader.h \
+ /usr/include/string.h /usr/include/features.h \
+ /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h Loader.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc AminoAcid.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Saver.h Visitor.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath Spacer.h Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \
+ NucleotideCode.h Protein.h Nucleotide.h AminoAcidHydrogen.h \
+ /usr/include/c++/4.9/list /usr/include/c++/4.9/bits/stl_list.h \
+ /usr/include/c++/4.9/bits/list.tcc
+PdbSaver.o: PdbSaver.cc /usr/include/stdc-predef.h PdbSaver.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \
+ NucleotideCode.h Protein.h
+SeqLoader.o: SeqLoader.cc /usr/include/stdc-predef.h SeqLoader.h \
+ SideChain.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h RelLoader.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+IntCoordConverter.o: IntCoordConverter.cc /usr/include/stdc-predef.h \
+ IntCoordConverter.h /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc Atom.h AtomCode.h \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc Identity.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath AminoAcid.h \
+ Group.h Monomer.h Component.h Bond.h Loader.h Saver.h Visitor.h \
+ SideChain.h AminoAcidCode.h
+SeqConstructor.o: SeqConstructor.cc /usr/include/stdc-predef.h \
+ SeqConstructor.h Spacer.h Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \
+ Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h RelLoader.h
+Ligand.o: Ligand.cc /usr/include/stdc-predef.h Ligand.h Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h Group.h Monomer.h \
+ AminoAcidCode.h NucleotideCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+LigandSet.o: LigandSet.cc /usr/include/stdc-predef.h LigandSet.h Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h Ligand.h Group.h \
+ Monomer.h AminoAcidCode.h NucleotideCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+SolvExpos.o: SolvExpos.cc /usr/include/stdc-predef.h SolvExpos.h Spacer.h \
+ Bond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \
+ Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+AminoAcidHydrogen.o: AminoAcidHydrogen.cc /usr/include/stdc-predef.h \
+ AminoAcidHydrogen.h AminoAcid.h Group.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/list \
+ /usr/include/c++/4.9/bits/stl_list.h /usr/include/c++/4.9/bits/list.tcc
+Nucleotide.o: Nucleotide.cc /usr/include/stdc-predef.h Nucleotide.h \
+ Group.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h IntCoordConverter.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath NucleotideCode.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+RelLoader.o: RelLoader.cc /usr/include/stdc-predef.h RelLoader.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+XyzSaver.o: XyzSaver.cc /usr/include/stdc-predef.h XyzSaver.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h Ligand.h NucleotideCode.h
+RelSaver.o: RelSaver.cc /usr/include/stdc-predef.h RelSaver.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \
+ IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
+XyzLoader.o: XyzLoader.cc /usr/include/stdc-predef.h XyzLoader.h Group.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \
+ Bond.h Loader.h Saver.h Visitor.h Ligand.h Polymer.h AminoAcidCode.h \
+ NucleotideCode.h SideChain.h IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath AminoAcid.h \
+ Spacer.h /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h
diff --git a/Energy/APPS/Depend b/Energy/APPS/Depend
index e69de29..de1fa8e 100644
--- a/Energy/APPS/Depend
+++ b/Energy/APPS/Depend
@@ -0,0 +1,2197 @@
+frst.o: frst.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h \
+ ../../Energy/Sources/EffectiveSolvationPotential.h \
+ ../../Energy/Sources/RapdfPotential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h
+correlation.o: correlation.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h ../../tools/matrix3.h ../../tools/StatTools.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h
+energy2zscore.o: energy2zscore.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../tools/StatTools.h
+frstZscore.o: frstZscore.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h \
+ ../../Energy/Sources/EffectiveSolvationPotential.h \
+ ../../Energy/Sources/RapdfPotential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \
+ /usr/include/c++/4.9/numeric /usr/include/c++/4.9/bits/stl_numeric.h
+mutationGenerator.o: mutationGenerator.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h
+pdb2tor.o: pdb2tor.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h
+tap2plot.o: tap2plot.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h \
+ ../../Energy/Sources/EffectiveSolvationPotential.h \
+ ../../Energy/Sources/RapdfPotential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h
+pdb2solv.o: pdb2solv.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h \
+ ../../Energy/Sources/PolarSolvationPotential.h
+solv2energy.o: solv2energy.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h
+pdb2contact.o: pdb2contact.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h
+tapRef.o: tapRef.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmega.h \
+ ../Sources/TorsionPotential/PhiPsiPreAngle.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h
+pdb2energy.o: pdb2energy.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h \
+ ../../Energy/Sources/PolarSolvationPotential.h \
+ ../../Energy/Sources/RapdfPotential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \
+ ../../tools/StatTools.h
+taptable.o: taptable.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../tools/StatTools.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../Sources/TorsionPotential/PhiPsi.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/SimpleBond.h \
+ ../../Biopool/Sources/Identity.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../../Energy/Sources/Potential.h
+pdb2tap.o: pdb2tap.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h ../../Energy/Sources/Potential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiOmega.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h \
+ ../../tools/StatTools.h
+pdb2torenergy.o: pdb2torenergy.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h ../../Energy/Sources/Potential.h \
+ ../Sources/TorsionPotential/TorsionPotential.h \
+ ../Sources/TorsionPotential/PhiPsi.h \
+ ../Sources/TorsionPotential/PhiPsiPreAngle.h \
+ ../Sources/TorsionPotential/PhiPsiOmega.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaPreAngle.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1PreAngle.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h \
+ ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \
+ ../Sources/TorsionPotential/Omega.h \
+ ../Sources/TorsionPotential/Chi1Chi2.h
diff --git a/Energy/Sources/Depend b/Energy/Sources/Depend
index e69de29..8445bc3 100644
--- a/Energy/Sources/Depend
+++ b/Energy/Sources/Depend
@@ -0,0 +1,700 @@
+PolarSolvationPotential.o: PolarSolvationPotential.cc \
+ /usr/include/stdc-predef.h PolarSolvationPotential.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h Potential.h
+SolvationPotential.o: SolvationPotential.cc /usr/include/stdc-predef.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h SolvationPotential.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h Potential.h
+RapdfPotential.o: RapdfPotential.cc /usr/include/stdc-predef.h \
+ RapdfPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc Potential.h \
+ ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h /usr/include/c++/4.9/cstring \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h
+EnergyFeatures.o: EnergyFeatures.cc /usr/include/stdc-predef.h \
+ EnergyFeatures.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h RapdfPotential.h Potential.h \
+ SolvationPotential.h TorsionPotential/PhiPsi.h \
+ TorsionPotential/TorsionPotential.h \
+ TorsionPotential/PhiPsiOmegaChi1Chi2.h
+EffectiveSolvationPotential.o: EffectiveSolvationPotential.cc \
+ /usr/include/stdc-predef.h EffectiveSolvationPotential.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h Potential.h
diff --git a/Energy/Sources/TorsionPotential/Depend b/Energy/Sources/TorsionPotential/Depend
index e69de29..c29ca23 100644
--- a/Energy/Sources/TorsionPotential/Depend
+++ b/Energy/Sources/TorsionPotential/Depend
@@ -0,0 +1,1562 @@
+PhiPsi.o: PhiPsi.cc /usr/include/stdc-predef.h PhiPsi.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h TorsionPotential.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaChi1.o: PhiPsiOmegaChi1.cc /usr/include/stdc-predef.h \
+ PhiPsiOmegaChi1.h TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaChi1Chi2PreAngle.o: PhiPsiOmegaChi1Chi2PreAngle.cc \
+ /usr/include/stdc-predef.h PhiPsiOmegaChi1Chi2PreAngle.h \
+ TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiPreAngle.o: PhiPsiPreAngle.cc /usr/include/stdc-predef.h \
+ PhiPsiPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaPreAngle.o: PhiPsiOmegaPreAngle.cc /usr/include/stdc-predef.h \
+ PhiPsiOmegaPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaChi1Chi2.o: PhiPsiOmegaChi1Chi2.cc /usr/include/stdc-predef.h \
+ PhiPsiOmegaChi1Chi2.h TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmega.o: PhiPsiOmega.cc /usr/include/stdc-predef.h PhiPsiOmega.h \
+ TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h
+Chi1Chi2.o: Chi1Chi2.cc /usr/include/stdc-predef.h Chi1Chi2.h \
+ TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaPreAngle.o: PhiPsiOmegaPreAngle.cc /usr/include/stdc-predef.h \
+ PhiPsiOmegaPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+PhiPsiOmegaChi1PreAngle.o: PhiPsiOmegaChi1PreAngle.cc \
+ /usr/include/stdc-predef.h PhiPsiOmegaChi1PreAngle.h TorsionPotential.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
+Omega.o: Omega.cc /usr/include/stdc-predef.h Omega.h TorsionPotential.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \
+ ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \
+ ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \
+ ../../../tools/vglStd.h ../../../tools/vglEndian.h \
+ ../../../tools/vglCompilers.h ../../../tools/vglMath.h \
+ ../../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h \
+ ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \
+ ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \
+ ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \
+ ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \
+ ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \
+ ../../../Biopool/Sources/AminoAcidCode.h \
+ ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../../Energy/Sources/Potential.h
diff --git a/Lobo/APPS/Depend b/Lobo/APPS/Depend
index e69de29..fcbab73 100644
--- a/Lobo/APPS/Depend
+++ b/Lobo/APPS/Depend
@@ -0,0 +1,1273 @@
+loboLUT.o: loboLUT.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/LoopTable.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ ../../tools/matrix3.h ../../Lobo/Sources/RamachandranData.h \
+ ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \
+ /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h
+LoopTablePlot.o: LoopTablePlot.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc \
+ ../../Lobo/Sources/RamachandranData.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \
+ /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h ../../tools/GetArg.h \
+ /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \
+ ../../tools/String2Number.h
+ClusterLoopTable.o: ClusterLoopTable.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/LoopTable.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ ../../tools/matrix3.h ../../Lobo/Sources/RamachandranData.h \
+ ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \
+ /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h
+ClusterRama.o: ClusterRama.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/RamachandranData.h
+lobo.o: lobo.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Lobo/Sources/RamachandranData.h \
+ ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \
+ /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/SeqConstructor.h \
+ ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \
+ ../../Energy/Sources/TorsionPotential/PhiPsi.h \
+ ../../Energy/Sources/TorsionPotential/TorsionPotential.h \
+ ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \
+ ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \
+ ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \
+ ../../Lobo/Sources/LoboTools.h
+loop2torsion.o: loop2torsion.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Lobo/Sources/RamachandranData.h \
+ ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \
+ /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/SeqConstructor.h \
+ ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \
+ ../../Energy/Sources/TorsionPotential/PhiPsi.h \
+ ../../Energy/Sources/TorsionPotential/TorsionPotential.h \
+ ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \
+ ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \
+ ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \
+ ../../Biopool/Sources/XyzSaver.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \
+ /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/local_lim.h \
+ /usr/include/linux/limits.h \
+ /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/xopen_lim.h
+scatEdit.o: scatEdit.cc /usr/include/stdc-predef.h \
+ ../../Lobo/Sources/RankAnalyzer.h /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h ../../tools/matrix3.h
+backboneAnalyzer.o: backboneAnalyzer.cc /usr/include/stdc-predef.h \
+ ../../tools/GetArg.h /usr/include/c++/4.9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/IntSaver.h \
+ ../../tools/StatTools.h
+loboFull.o: loboFull.cc /usr/include/stdc-predef.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \
+ ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \
+ /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \
+ ../../Lobo/Sources/RamachandranData.h \
+ ../../Lobo/Sources/LoopTableEntry.h \
+ ../../Lobo/Sources/VectorTransformation.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \
+ /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/SeqConstructor.h \
+ ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \
+ ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \
+ ../../Energy/Sources/TorsionPotential/PhiPsi.h \
+ ../../Energy/Sources/TorsionPotential/TorsionPotential.h \
+ ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \
+ ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \
+ ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \
+ ../../tools/StatTools.h ../../Lobo/Sources/LoboTools.h
diff --git a/Lobo/Sources/Depend b/Lobo/Sources/Depend
index e69de29..ec7fdca 100644
--- a/Lobo/Sources/Depend
+++ b/Lobo/Sources/Depend
@@ -0,0 +1,1058 @@
+RamachandranData.o: RamachandranData.cc /usr/include/stdc-predef.h \
+ RamachandranData.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
+VectorTransformation.o: VectorTransformation.cc \
+ /usr/include/stdc-predef.h VectorTransformation.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
+LoopTableEntry.o: LoopTableEntry.cc /usr/include/stdc-predef.h \
+ LoopTableEntry.h VectorTransformation.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
+LoopTable.o: LoopTable.cc /usr/include/stdc-predef.h LoopTable.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/Debug.h /usr/include/stdlib.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc RamachandranData.h \
+ /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc LoopTableEntry.h \
+ VectorTransformation.h ../../Biopool/Sources/IntCoordConverter.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \
+ /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h
+LoopModel.o: LoopModel.cc /usr/include/stdc-predef.h LoopModel.h \
+ ../../tools/Debug.h /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h LoopTable.h \
+ ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \
+ ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \
+ /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ RamachandranData.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc LoopTableEntry.h \
+ VectorTransformation.h ../../Biopool/Sources/IntCoordConverter.h \
+ ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \
+ ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \
+ ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \
+ /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \
+ /usr/include/c++/4.9/bits/deque.tcc \
+ /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \
+ ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/SeqConstructor.h ranking_helper.h \
+ ranking_helper2.h ../../Energy/Sources/SolvationPotential.h \
+ ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \
+ ../../Energy/Sources/TorsionPotential/PhiPsi.h \
+ ../../Energy/Sources/TorsionPotential/TorsionPotential.h
+LoopExtractor.o: LoopExtractor.cc /usr/include/stdc-predef.h \
+ LoopExtractor.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h ranking_helper.h \
+ ranking_helper2.h
+ranking_helper.o: ranking_helper.cc /usr/include/stdc-predef.h \
+ ranking_helper.h
+ranking_helper2.o: ranking_helper2.cc /usr/include/stdc-predef.h \
+ ranking_helper2.h
+globalStatistic.o: globalStatistic.cc /usr/include/stdc-predef.h \
+ globalStatistic.h LoopExtractor.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h \
+ /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \
+ /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \
+ /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \
+ /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \
+ ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \
+ /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \
+ /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \
+ /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \
+ /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h ranking_helper.h \
+ ranking_helper2.h ranking_helper2.h
+RankAnalyzer.o: RankAnalyzer.cc /usr/include/stdc-predef.h RankAnalyzer.h \
+ /usr/include/c++/4.9/string \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/exception \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/cctype /usr/include/ctype.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/bits/locale_classes.h \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/iomanip \
+ /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \
+ /usr/include/c++/4.9/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \
+ ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \
+ ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc ../../tools/Debug.h \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath
diff --git a/Makefile b/Makefile
index c0f7aa4..0ef7082 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,8 @@
 # Path to project directory.
 UPDIR = .
 # Path to subdirectories.
-SUBDIRS =  tools Energy/Sources   Biopool/Sources  Align2/Sources Energy/Sources/TorsionPotential  Lobo/Sources Lobo/APPS Energy/APPS   Biopool/APPS   Align2/APPS
+SUBDIRS =  tools Energy/Sources   Biopool/Sources  Align2/Sources Energy/Sources/TorsionPotential  Lobo/Sources Lobo/APPS Energy/APPS   Biopool/APPS   Align2/APPS \
+           Phylo/Sources Phylo/APPS
 
 #
 # Libraries and paths (which are not defined globally).
diff --git a/Makefile.global b/Makefile.global
index 1f78a89..c9dfc08 100644
--- a/Makefile.global
+++ b/Makefile.global
@@ -106,11 +106,11 @@ SUBDIRS += _dummy_
 
 LIB_PATH += -L$(UPDIR)/lib
 
-INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources   -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential     -I$(UPDIR)/Lobo/Sources  -I$(UPDIR)/Align2/Sources  -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS  -I$(UPDIR)/Lobo/APPS
+INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential -I$(UPDIR)/Lobo/Sources -I$(UPDIR)/Align2/Sources  -I$(UPDIR)/Phylo/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS  -I$(UPDIR)/Lobo/APPS -I$(UPDIR)/Phylo/APPS
 
 ifdef test
-  INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests
-  SUBDIRS =  Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests
+  INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests -I$(UPDIR)/Phylo/Tests
+  SUBDIRS =  Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests Phylo/Tests
 endif
 
 ####### Implicit rules
@@ -196,4 +196,4 @@ subinstall:
 #
 # Include dependencies
 #
- 
\ No newline at end of file
+ 
diff --git a/Phylo/APPS/Makefile b/Phylo/APPS/Makefile
new file mode 100644
index 0000000..6bc40aa
--- /dev/null
+++ b/Phylo/APPS/Makefile
@@ -0,0 +1,57 @@
+#--*-makefile-*-----------------------------------------------------------------
+#
+#   Standard makefile - Phylo/APPS
+#
+#-------------------------------------------------------------------------------
+
+# Path to project directory
+PROJECT_ROOT = ../..
+BINPATH      = $(PROJECT_ROOT)/bin/
+LIBPATH      = $(PROJECT_ROOT)/lib/
+UPDIR        = $(PROJECT_ROOT)
+SUBDIR       = 
+
+
+
+#
+# Libraries and paths (which are not defined globally)
+#
+
+LIBS     = -lPhylo -lAlign2 -ltools
+INC_PATH = -I. -I $(PROJECT_ROOT)/Phylo/Sources
+LIB_PATH = -L. 
+
+
+
+#
+# Objects and headers
+#
+
+SOURCES = phyltree.cc clustalw.cc fengdoolittle.cc
+OBJECTS = phyltree.o clustalw.o fengdoolittle.o
+TARGETS = phyltree clustalw fengdoolittle
+EXECS   = phyltree clustalw fengdoolittle
+LIBRARY = APPSlibPhylo.a
+
+
+
+#
+# Install rule
+#
+
+compile: all
+
+all: install
+install: $(LIBRARY) $(TARGETS)
+	mv $(LIBRARY) $(LIBPATH)
+	mv $(EXECS) $(BINPATH)
+
+
+
+#
+# Call global Makefile to do the job
+#
+include ../../Makefile.global
+
+# Overriding to use C++11
+STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c
\ No newline at end of file
diff --git a/Phylo/APPS/clustalw.cc b/Phylo/APPS/clustalw.cc
new file mode 100644
index 0000000..2a59c13
--- /dev/null
+++ b/Phylo/APPS/clustalw.cc
@@ -0,0 +1,197 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <phylo.h>
+#include <SubMatrix.h>
+#include <AGPFunction.h>
+#include <Alignment.h>
+#include <AlignmentBase.h>
+#include <GetArg.h>
+#include <iostream>
+
+using namespace Victor::Phylo;
+using namespace Victor;
+
+
+
+/** @brief Shows a helper. */
+static void show_help() {
+    cout << "CLUSTALW - MULTIPLE SEQUENCE ALIGNMENT TOOL\n"
+         << "This program calculates a multiple sequence alignment.\n"
+         << "Options:\n"
+         << "--in <name>    \t Path to input FASTA file\n"
+         << "[--out <name>] \t Path to output ClustalW file (default: to screen)\n"
+         << "[-m <name>]    \t Path to substitution matrix file (default: blosum62.dat)\n"
+         << "[-o <double>]  \t Open gap penalty (default: 10.0)\n"
+         << "[-e <double>]  \t Extension gap penalty (default: 0.1)\n"
+         << "[-d <0|1|2>]   \t Distance matrix builder criterion (default: 0)\n"
+         << "               \t -d 0: Distance as 1 - percentage of identity\n"
+         << "               \t -d 1: Use Levenshtein distance\n"
+         << "               \t -d 2: Use Feng-Doolittle distance\n"
+         << "[-c <0|1|2>]   \t Clustering algorithm (default:2)\n"
+         << "               \t -c 0: UPGMA\n"
+         << "               \t -c 1: Fitch-Margoliash\n"
+         << "               \t -c 2: Neighbor Joining\n"
+         << "[-n <0|1>]     \t Substitution matrix family for multiple alignment (default: 1)\n"
+         << "               \t -w 0: PAM series\n"
+         << "               \t -w 1: BLOSUM series\n"
+         << "[-wo <double>] \t Initial open gap penalty for ClustalW (default: 10.0)\n"
+         << "[-we <double>] \t Initial extension gap penalty for ClustalW (default: 0.2)\n"
+         << "[-v]           \t Verbose (default: no)\n"
+         << "\n" << endl;
+}
+
+
+
+/** ClustalW multiple sequence alignment program. 
+ * @param[in]           argc      ARGument Counter
+ * @param[in]           argv      ARGument Vector
+ * @return 0 in case of success
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+int main(int argc, char *argv[]) {
+    string input_filename, output_filename, matrix_filename;
+    unsigned int distance_criterion, clustering, matrix_family;
+    double gap_open, gap_extension, clustalw_gop, clustalw_gep;
+    bool verbose;
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Reads options
+    if (getArg("h", argc, argv)) {
+        show_help();
+        return 0;
+    }
+
+    getArg("-in",  input_filename,     argc, argv, "!");
+    getArg("-out", output_filename,    argc, argv, "!");
+    getArg("m",    matrix_filename,    argc, argv, "blosum62.dat");
+    getArg("o",    gap_open,           argc, argv, 10.0);
+    getArg("e",    gap_extension,      argc, argv, 0.1);
+    getArg("d",    distance_criterion, argc, argv, 0);
+    getArg("c",    clustering,         argc, argv, 2);
+    getArg("n",    matrix_family,      argc, argv, 1);
+    getArg("wo",   clustalw_gop,       argc, argv, 10.0);
+    getArg("we",   clustalw_gep,       argc, argv, 0.2);
+    verbose = getArg("v", argc, argv);
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Loads and prepares data
+    // Alignment
+    if (verbose) cout << "Loading alignment data..." << endl;
+    Alignment alignment;
+    if (input_filename != "!") {
+        ifstream fasta_file(input_filename);
+        if (!fasta_file) {
+            ERROR("Error opening input FASTA file.", exception);
+        }
+        
+        alignment.loadFasta(fasta_file);
+        if (alignment.size() < 1) {
+            ERROR("Input FASTA file must contain two sequences.", exception);
+        }
+    } else {
+        ERROR("Missing input FASTA file.", exception);
+    }
+
+    // Substitution matrix
+    if (verbose) cout << "Loading substitution matrix..." << endl;
+    SubMatrix substitution_matrix;
+    if (matrix_filename != "!") {
+        ifstream matrix_file(matrix_filename);
+        if (!matrix_file) {
+            ERROR("Error opening substitution matrix file.", exception);
+        }
+        
+        substitution_matrix = SubMatrix(matrix_file);
+    } else {
+        ERROR("Missing substitution matrix file.", exception);
+    }
+
+    // Gap function
+    AGPFunction gap_function(gap_open, gap_extension);
+
+    // Distance builder
+    DistanceMatrixBuilder *build_matrix;
+    switch (distance_criterion) {
+        case 0:
+            build_matrix = new IdentityPercentage(substitution_matrix, gap_function);
+            break;
+        case 1:
+            build_matrix = new LevenshteinDistance();
+            break;
+        case 2:
+            build_matrix = new FengDoolittleDistance(substitution_matrix, gap_function);
+            break;
+        default:
+            ERROR("Invalid distance criterion", exception);
+            exit(-1);
+    }
+
+    // Clustering algorithm
+    ClusteringAlgorithm *build_tree;
+    switch (clustering) {
+        case 0:
+            build_tree = new UPGMA();
+            break;
+        case 1:
+            build_tree = new FitchMargoliash();
+            break;
+        case 2:
+            build_tree = new NJ();
+            break;
+        default:
+            ERROR("Invalid clustering algorithm", exception);
+            exit(-1);
+    }
+
+    // Substitution matrix family
+    ClustalW::WeightMatrix weight_family;
+    switch (matrix_family) {
+        case 0:
+            weight_family = ClustalW::PAM;
+            break;
+        case 1:
+            weight_family = ClustalW::BLOSUM;
+            break;
+        default:
+            ERROR("Invalid matrix family", exception);
+            exit(-1);
+    }
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Creates ClustalW object
+    if (verbose) cout << "Configuring ClustalW..." << endl;
+    ClustalW clustalw(*build_matrix, *build_tree, weight_family, clustalw_gop, clustalw_gep);
+    if (verbose) cout << "Generating multiple sequence alignment..." << endl;
+    MultipleAlignment MSA = clustalw(alignment);
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Saves output
+    if (verbose) cout << "Saving multiple sequence alignment..." << endl;
+    if (output_filename != "!") {
+        ofstream clustalw_file(output_filename);
+        MSA.saveClustalW(clustalw_file);
+    } else {
+        MSA.saveClustalW(cout);
+    }
+    if (verbose) cout << "done." << endl;
+
+    return 0;
+}
\ No newline at end of file
diff --git a/Phylo/APPS/fengdoolittle.cc b/Phylo/APPS/fengdoolittle.cc
new file mode 100644
index 0000000..e95d971
--- /dev/null
+++ b/Phylo/APPS/fengdoolittle.cc
@@ -0,0 +1,109 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <phylo.h>
+#include <AlignmentBase.h>
+#include <GetArg.h>
+#include <iostream>
+
+using namespace Victor::Phylo;
+using namespace Victor;
+
+
+
+/** @brief Shows a helper. */
+static void show_help() {
+    cout << "FENG DOOLITTLE - MULTIPLE SEQUENCE ALIGNMENT TOOL\n"
+         << "TThis program calculates a multiple sequence alignment.\n"
+         << "Options:\n"
+         << "--in <name>    \t Name of input FASTA file\n"
+         << "[--out <name>] \t Name of output alignment file (default: to screen)\n"
+         << "[-o <double>]  \t Open gap penalty (default: 10.0)\n"
+         << "[-e <double>]  \t Extension gap penalty (default: 0.1)\n"
+         << "[-v]           \t Verbose (default: no)\n"
+         << "\n" << endl;
+}
+
+
+
+/** @brief Feng-Doolittle multiple sequence alignment program.
+ * @param[in]           argc      ARGument Counter
+ * @param[in]           argv      ARGument Vector
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ * @return 0 in case of success
+ */
+int main(int argc, char *argv[]) {
+    string input_filename, output_filename;
+    double gap_open, gap_extension;
+    bool verbose;
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Reads options
+    if (getArg("h", argc, argv)) {
+        show_help();
+        return 0;
+    }
+
+    getArg("-in",  input_filename,  argc, argv, "!");
+    getArg("-out", output_filename, argc, argv, "!");
+    getArg("o",    gap_open,        argc, argv, 10.0);
+    getArg("e",    gap_extension,   argc, argv, 0.1);
+    verbose = getArg("v", argc, argv);
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Loads and prepares data
+    // Alignment
+    if (verbose) cout << "Loading alignment data..." << endl;
+    Alignment alignment;
+    if (input_filename != "!") {
+        ifstream fasta_file(input_filename);
+        if (!fasta_file) {
+            ERROR("Error opening input FASTA file.", exception);
+        }
+        
+        alignment.loadFasta(fasta_file);
+        if (alignment.size() < 1) {
+            ERROR("Input FASTA file must contain two sequences.", exception);
+        }
+    } else {
+        ERROR("Missing input FASTA file.", exception);
+    }
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Creates FengDoolittle object
+    if (verbose) cout << "Configuring Feng-Doolittle algorithm..." << endl;
+    FengDoolittle feng_doolittle(gap_open, gap_extension);
+    if (verbose) cout << "Generating multiple sequence alignment..." << endl;
+    MultipleAlignment MSA = feng_doolittle(alignment);
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Saves output
+    if (verbose) cout << "Saving multiple sequence alignment..." << endl;
+    if (output_filename != "!") {
+        ofstream clustalw_file(output_filename);
+        MSA.saveClustalW(clustalw_file);
+    } else {
+        MSA.saveClustalW(cout);
+    }
+    if (verbose) cout << "done." << endl;
+
+
+    return 0;
+}
\ No newline at end of file
diff --git a/Phylo/APPS/phyltree.cc b/Phylo/APPS/phyltree.cc
new file mode 100644
index 0000000..4a82526
--- /dev/null
+++ b/Phylo/APPS/phyltree.cc
@@ -0,0 +1,172 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <phylo.h>
+#include <SubMatrix.h>
+#include <AGPFunction.h>
+#include <Alignment.h>
+#include <AlignmentBase.h>
+#include <GetArg.h>
+#include <iostream>
+
+using namespace Victor::Phylo;
+using namespace Victor;
+
+
+
+/** @brief Shows an helper. */
+static void show_help() {
+    cout << "PHYLOGENETIC TREE GENERATOR\n"
+         << "This program calculates a phylogenetic tree for a given alignment.\n"
+         << "Options:\n"
+         << "--in <name>    \t Path to input FASTA file\n"
+         << "[--out <name>] \t Path to output Newick file (default: to screen\n"
+         << "[-m <name>]    \t Path to substitution matrix file (default: blosum62.dat)\n"
+         << "[-o <double>]  \t Open gap penalty (default: 10.0)\n"
+         << "[-e <double>]  \t Extension gap penalty (default: 0.1)\n"
+         << "[-d <0|1|2>]   \t Distance matrix builder criterion (default: 0)\n"
+         << "               \t -d 0: Distance as 1 - percentage of identity\n"
+         << "               \t -d 1: Use Levenshtein distance\n"
+         << "               \t -d 2: Use Feng-Doolittle distance\n"
+         << "[-c <0|1|2>]   \t Clustering algorithm (default:2)\n"
+         << "               \t -c 0: UPGMA\n"
+         << "               \t -c 1: Fitch-Margoliash\n"
+         << "               \t -c 2: Neighbor Joining\n"
+         << "[-v]           \t Verbose (default: no)\n"
+         << "\n" << endl;
+}
+
+
+
+/** @brief Builds a phylogenetic tree.
+ * @param[in]           argc      ARGument Counter
+ * @param[in]           argv      ARGument Vector
+ * @return 0 in case of success
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+int main(int argc, char *argv[]) {
+    string input_filename, output_filename, matrix_filename;
+    unsigned int distance_criterion, clustering;
+    double gap_open, gap_extension;
+    bool verbose;
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Reads options
+    if (getArg("h", argc, argv)) {
+        show_help();
+        return 0;
+    }
+
+    getArg("-in",  input_filename,     argc, argv, "!");
+    getArg("-out", output_filename,    argc, argv, "!");
+    getArg("m",    matrix_filename,    argc, argv, "blosum62.dat");
+    getArg("o",    gap_open,           argc, argv, 10.0);
+    getArg("e",    gap_extension,      argc, argv, 0.1);
+    getArg("d",    distance_criterion, argc, argv, 0);
+    getArg("c",    clustering,         argc, argv, 1);
+    verbose = getArg("v", argc, argv);
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Loads and prepares data
+    // Alignment
+    if (verbose) cout << "Loading alignment data..." << endl;
+    Alignment alignment;
+    if (input_filename != "!") {
+        ifstream fasta_file(input_filename);
+        if (!fasta_file) {
+            ERROR("Error opening input FASTA file.", exception);
+        }
+        
+        alignment.loadFasta(fasta_file);
+        if (alignment.size() < 1) {
+            ERROR("Input FASTA file must contain two sequences.", exception);
+        }
+    } else {
+        ERROR("Missing input FASTA file.", exception);
+    }
+
+    // Substitution matrix
+    if (verbose) cout << "Loading substitution matrix..." << endl;
+    SubMatrix substitution_matrix;
+    if (matrix_filename != "!") {
+        ifstream matrix_file(matrix_filename);
+        if (!matrix_file) {
+            ERROR("Error opening substitution matrix file.", exception);
+        }
+        
+        substitution_matrix = SubMatrix(matrix_file);
+    } else {
+        ERROR("Missing substitution matrix file.", exception);
+    }
+
+    // Gap function
+    AGPFunction gap_function(gap_open, gap_extension);
+
+    // Distance builder
+    DistanceMatrixBuilder *build_matrix;
+    switch (distance_criterion) {
+        case 0:
+            build_matrix = new IdentityPercentage(substitution_matrix, gap_function);
+            break;
+        case 1:
+            build_matrix = new LevenshteinDistance();
+            break;
+        case 2:
+            build_matrix = new FengDoolittleDistance(substitution_matrix, gap_function);
+            break;
+        default:
+            ERROR("Invalid distance criterion", exception);
+            exit(-1);
+    }
+
+    // Clustering algorithm
+    ClusteringAlgorithm *build_tree;
+    switch (clustering) {
+        case 0:
+            build_tree = new UPGMA();
+            break;
+        case 1:
+            build_tree = new NJ();
+            break;
+        default:
+            ERROR("Invalid clustering algorithm", exception);
+            exit(-1);
+    }
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Computes phylogenetic tree
+    if (verbose) cout << "Generating distance matrix..." << endl;
+    DistanceMatrix distance_matrix = (*build_matrix)(alignment);
+    if (verbose) cout << "Generating phylogenetic tree..." << endl;
+    RootedTree tree = (*build_tree)(distance_matrix).asRootedTree();
+
+
+    ////////////////////////////////////////////////////////////////////
+    // Saves output
+    if (verbose) cout << "Saving tree..." << endl;
+    if (output_filename != "!") {
+        ofstream newick_file(output_filename);
+        tree.saveNewick(newick_file);
+    } else {
+        tree.saveNewick(cout);
+    }
+    if (verbose) cout << "done." << endl;
+
+    return 0;
+}
\ No newline at end of file
diff --git a/Phylo/Sources/AminoAcid.cc b/Phylo/Sources/AminoAcid.cc
new file mode 100644
index 0000000..bebb028
--- /dev/null
+++ b/Phylo/Sources/AminoAcid.cc
@@ -0,0 +1,157 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <AminoAcid.h>
+
+namespace Victor {
+namespace Phylo {
+    typedef AminoAcid::Code Code;
+
+    const char AminoAcid::letter1s[] = {
+        'A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M',
+        'F', 'P', 'S', 'T', 'W', 'Y', 'V',
+        'U', 'O',
+        'B', 'Z', 'J', 'X'
+    };
+    const string AminoAcid::letter3s[] = {
+        "ALA", "ARG", "ASN", "ASP", "CYS", "GLU", "GLN", "GLY", "HIS",
+        "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP",
+        "TYR", "VAL",
+        "SEC", "PYL",
+        "ASX", "GLX", "XLE", "XAA"
+    };
+    const string AminoAcid::names[] = {
+        "Alanine", "Arginine", "Asparagine", "Aspartic acid", "Cysteine",
+        "Glutamic acid", "Glutamine", "Glycine", "Histeine", "Isoleucine",
+        "Leucine", "Lysine", "Methionine", "Phenylalanine", "Proline",
+        "Serine", "Threonine", "Tryptophan", "Tyrosine", "Valine",
+        "Selenocysteine", "Pyrrolisine",
+        "Asparagine / Aspartic acid", "Glutamine / Glutamic acid",
+        "Leucine / Isoleucine", "Unspecified / Unknown"
+    };
+
+
+
+    Code
+    AminoAcid::letter1ToCode(const char code) {
+        switch (code) {
+            case 'A': return A;
+            case 'R': return R;
+            case 'N': return N;
+            case 'D': return D;
+            case 'C': return C;
+            case 'E': return E;
+            case 'Q': return Q;
+            case 'G': return G;
+            case 'H': return H;
+            case 'I': return I;
+            case 'L': return L;
+            case 'K': return K;
+            case 'M': return M;
+            case 'F': return F;
+            case 'P': return P;
+            case 'S': return S;
+            case 'T': return T;
+            case 'W': return W;
+            case 'Y': return Y;
+            case 'V': return V;
+
+            case 'U': return U;
+            case 'O': return O;
+
+            case 'B': return B;
+            case 'Z': return Z;
+            case 'J': return J;
+            default:  return X;
+        }
+    }
+
+
+
+    Code
+    AminoAcid::letter3ToCode(const string &code) {
+        size_t index = 0;
+        bool found   = false;
+
+        while (!found && index < X) {
+            found = code == letter3s[index];
+            if (!found) {
+                index++;
+            }
+        }
+
+        return (Code) index;
+    }
+
+
+
+    AminoAcid::AminoAcid(const Code code)
+    : code(code) {
+    }
+
+
+
+    AminoAcid::AminoAcid(const char code)
+    : code(letter1ToCode(code)) {
+    }
+
+
+
+    AminoAcid::AminoAcid(const string &code)
+    : code(letter3ToCode(code)) {
+    }
+
+
+
+    AminoAcid::AminoAcid(const AminoAcid &origin)
+    : AminoAcid(origin.code) {
+    }
+
+
+
+    AminoAcid::~AminoAcid() {
+    }
+
+
+
+    Code
+    AminoAcid::getCode() const {
+        return code;
+    }
+
+
+
+    char
+    AminoAcid::getSingleLetter() const {
+        return letter1s[code];
+    }
+
+
+
+    string
+    AminoAcid::getThreeLetter() const {
+        return letter3s[code];
+    }
+
+
+
+    string
+    AminoAcid::getFullName() const {
+        return names[code];
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/AminoAcid.h b/Phylo/Sources/AminoAcid.h
new file mode 100644
index 0000000..30acb27
--- /dev/null
+++ b/Phylo/Sources/AminoAcid.h
@@ -0,0 +1,143 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_AMINOACID_H_
+#define _VICTOR_PHYLO_AMINOACID_H_
+
+/** Number of amino acids. */
+#define _AMINOACID_SIZE 26
+#include <string>
+
+using std::string;
+
+namespace Victor{
+namespace Phylo {
+
+/** @brief Implements an amino acid. 
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class AminoAcid {
+ public:
+    /** Hashed values for known amino acids. */
+    typedef enum {
+        A,    ///< Alanine
+        R,    ///< Arginine
+        N,    ///< Asparagine
+        D,    ///< Aspartic acid
+        C,    ///< Cysteine
+        E,    ///< Glutamic acid
+        Q,    ///< Glutamine
+        G,    ///< Glycine
+        H,    ///< Histidine
+        I,    ///< Isoleucine
+        L,    ///< Leucine
+        K,    ///< Lysine
+        M,    ///< Methionine
+        F,    ///< Phenylalanine
+        P,    ///< Proline
+        S,    ///< Serine
+        T,    ///< Threonine
+        W,    ///< Tryptophan
+        Y,    ///< Tyrosine
+        V,    ///< Valine
+
+        U,    ///< Selenocysteine
+        O,    ///< Pyrrolisine
+
+        B,    ///< Asparagine or aspartic acid
+        Z,    ///< Glutamine or glutamic acid
+        J,    ///< Leucine or isoleucine
+        X     ///< Unspecified or unknown
+    } Code;
+
+
+
+    /** @brief Returns code of given amino acid.
+     * @param[in]       code      Single letter code
+     * @return Hash value
+     */
+    static Code letter1ToCode(const char code);
+
+
+
+    /** @brief Returns code of given amino acid.
+     * @param[in]       code      Three letter code
+     * @return Hash value
+     */
+    static Code letter3ToCode(const string &code);
+
+
+
+    /** @brief Builds an amino acid of given code.
+     * @param[in]       code      Code of the amino acid
+     */
+    explicit AminoAcid(const Code code);
+
+    /** @brief Builds an amino acid of given code.
+     * @param[in]       code      Single letter code
+     */
+    explicit AminoAcid(const char code);
+
+    /** @brief Builds an amino acid of given code.
+     * @param[in]       code      Three letter code
+     */
+    explicit AminoAcid(const string &code);
+
+    /** @brief Copy constructor.
+     * @param[in]       origin    Original object
+     */
+    explicit AminoAcid(const AminoAcid &origin);
+
+    /** @brief Destructor. */
+    virtual ~AminoAcid();
+
+
+
+    /** @brief Returns code of this amino acid.
+     * @return Code of this amino acid
+     */
+    Code getCode() const;
+
+    /** @brief Returns single letter code of this amino acid.
+     * @return Single letter code
+     */
+    char getSingleLetter() const;
+
+    /** @brief Returns thre letters code of this amino acid.
+     * @return Three letters code
+     */
+    string getThreeLetter() const;
+
+    /** @brief Returns fullname of this amino acid.
+     * @return Full name of this amino acid
+     */
+    string getFullName() const;
+
+
+
+ private:
+    static const char   letter1s[_AMINOACID_SIZE]; ///< 1-letter codes of amino acids
+    static const string letter3s[_AMINOACID_SIZE]; ///< 3-letters code of amino acids
+    static const string names[_AMINOACID_SIZE];    ///< Full names of amino acids
+
+    const Code code;    ///< Code of this amino acid
+};
+
+}
+}
+
+#endif  // _VICTOR_PHYLO_AMINOACID_H_
\ No newline at end of file
diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc
new file mode 100644
index 0000000..4244189
--- /dev/null
+++ b/Phylo/Sources/ClustalW.cc
@@ -0,0 +1,569 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+/** Maximum distance to search gaps (position-specific GOP). */
+#define GAP_SEARCH_DISTANCE 8
+#include <ClustalW.h>
+
+using namespace std;
+using namespace Victor::Phylo;
+
+/** Direction for a traceback. */
+typedef enum {
+    NONE,     ///< No direction
+    UP,       ///< Up
+    LEFT,     ///< Left
+    DIAG      ///< Diagonal
+} Direction;
+
+/** @brief Pascarella and Argos residue specific gap modification factors.
+ * @return Map from residues to factors.
+ */
+static map<char, double> PascarellaArgos();
+
+/** @brief Selects best direction.
+ * @param[in]           diagonal  Score from the diagonal
+ * @param[in]           up        Score from top
+ * @param[in]           left      Score from bottom
+ * @return Best direction
+ */
+static inline Direction select_direction(
+    const double diagonal,
+    const double up,
+    const double left);
+
+/** @brief Performs the traceback operation.
+ * @param[in]           A         First MSA
+ * @param[in]           B         Second MSA
+ * @param[in]           direction Traceback matrix
+ * @return Vector of residues
+ */
+static vector<string> traceback(
+    const MultipleAlignment &A,
+    const MultipleAlignment &B,
+    vector<vector<Direction>> &direction);
+
+/** @brief Builds a vector of sequences.
+ *
+ * Joins sequences from two MSAs and a vector of residues.
+ * @param[in]           A         First MSA
+ * @param[in]           B         Second MSA
+ * @param[in]           residues  Vector of residues
+ * @return Vector of sequences
+ */
+static vector<Sequence> join(
+    const MultipleAlignment &A,
+    const MultipleAlignment &B,
+    vector<string> &residues);
+
+
+
+
+
+namespace Victor {
+namespace Phylo {
+    typedef map<string, double> Weights;
+    typedef vector<Sequence> Sequences;
+
+    map<char, double> ClustalW::gap_modifiers = PascarellaArgos();
+
+    ClustalW::ClustalW(
+        const DistanceMatrixBuilder &distance_matrix_builder,
+        const ClusteringAlgorithm &clustering_algorithm,
+        const WeightMatrix weight_matrix,
+        const double gap_open,
+        const double gap_extension)
+    : build_matrix(distance_matrix_builder),
+      build_tree(clustering_algorithm),
+      weight_matrix(weight_matrix),
+      gap_open(gap_open),
+      gap_extension(gap_extension) {
+    }
+
+
+
+    ClustalW::ClustalW(const ClustalW &origin)
+    : ClustalW(
+        origin.build_matrix,
+        origin.build_tree,
+        origin.weight_matrix,
+        origin.gap_open,
+        origin.gap_extension
+    ) {
+    }
+
+
+
+    ClustalW::~ClustalW() {
+    }
+
+
+
+    MultipleAlignment &
+    ClustalW::apply(const AlignmentBase &alignment) const {
+        // Reads sequences
+        Sequences sequences = Sequence::toMap(alignment);
+        
+        // Computes distance matrix (pairwise alignments)
+        DistanceMatrix d = build_matrix(alignment);
+
+        // Computes guide tree and weights
+        RootedTree guide_tree = build_tree(d).asRootedTree();
+        Weights weights = getWeights(guide_tree);
+
+        // Progressive alignments
+        return *align(sequences, guide_tree, weights);
+    }
+
+
+
+    Weights
+    ClustalW::getWeights(const RootedTree &guide_tree) const {
+        map<string, double> weights;
+
+        // Computes weighs for every sequence
+        double max_weight = 0.0;
+        for (auto &leaf : guide_tree.getLeaves()) {
+            RootedTree node = *leaf;
+            double weight   = node.getDistance();
+            const string id = node.getLabel();
+
+            while (!node.isRoot()) {
+                weight += node.getDistance() / node.getLeavesNumber();
+                node    = node.getParent();
+            }
+
+            weights[id] = weight;
+            max_weight  = max(weight, max_weight);
+        }
+
+        // Normalizes weights
+        for (auto &entry : weights) {
+            weights[entry.first] = entry.second / max_weight;
+        }
+
+        return weights;
+    }
+
+
+
+    MultipleAlignment *
+    ClustalW::align(
+        Sequences &sequences,
+        const RootedTree &node,
+        Weights &weights) const {
+
+        ////////////////////////////////////////////////////////////////
+        // Single sequence: just returns it
+        if (node.isLeaf()) {
+            const string identifier = node.getLabel();
+            const string residues   = sequences[identifier];
+            return new MultipleAlignment(Sequence(identifier, residues));
+        }
+
+
+        ////////////////////////////////////////////////////////////////
+        // Single inheritance: straightforward
+        if (node.getChildrenNumber() == 1) {
+            return align(sequences, node[0], weights);
+        }
+
+
+        ////////////////////////////////////////////////////////////////
+        // Two sequences: performs alignment
+        const MultipleAlignment *A   = align(sequences, node[0], weights),
+                                *B   = align(sequences, node[1], weights);
+        const SubstitutionMatrix ss(getSubstitutionMatrix(node));
+        const size_t M = A->getLength(),
+                     N = B->getLength();
+
+
+#if VERBOSE==1
+        cout << "Now aligning:" << endl;
+        for (size_t i = 0; i < A->getSize(); i++) {
+            cout << A->getSequence(i).getIdentifier() << endl;
+        }
+        cout << "---------- against ----------" << endl;
+        for (size_t j = 0; j < B->getSize(); j++) {
+            cout << B->getSequence(j).getIdentifier() << endl;
+        }
+        cout << endl << endl;
+#endif
+
+
+        // Allocates score and traceback matrices
+        vector<vector<double>> score(N + 1);
+        vector<vector<Direction>> direction(N + 1);
+        vector<vector<size_t>> hgaps(N + 1);
+        vector<vector<size_t>> vgaps(N + 1);
+        for (size_t i = 0; i <= N; i++) {
+            score[i]     = vector<double>(M + 1);
+            direction[i] = vector<Direction>(M + 1);
+
+            hgaps[i] = vector<size_t>(M + 1);
+            vgaps[i] = vector<size_t>(M + 1);
+        }
+
+
+        // Initializes first row
+        score[0][0]     = 0;
+        direction[0][0] = NONE;
+        for (size_t j = 1; j <= M; j++) {
+            const double GOP = getPositionSpecificGOP(*A, *B, ss, 0);
+            const double GEP = getPositionSpecificGEP(*A, *B, j - 1);
+            score[0][j]      = -(GOP + GEP * (j - 1));
+            direction[0][j]  = LEFT;
+            hgaps[0][j] = 0;
+            vgaps[0][j] = 1;
+        }
+
+
+        // Initializes first column
+        for (size_t i = 1; i <= N; i++) {
+            const double GOP = getPositionSpecificGOP(*B, *A, ss, 0),
+                         GEP = getPositionSpecificGEP(*B, *A, i - 1);
+            score[i][0]      = -(GOP + GEP * (i - 1));
+            direction[i][0]  = UP;
+            hgaps[i][0] = 1;
+            vgaps[i][0] = 0;
+        }
+
+
+        // Calculates score matrix
+        for (size_t i = 1; i <= N; i++) {
+            for (size_t j = 1; j <= M; j++) {
+                double vgap = 0.0;
+                double hgap = 0.0;
+
+                hgap = (direction[i][j - 1] != LEFT)
+                     ? getPositionSpecificGOP(*A, *B, ss, j - 1)
+                     : getPositionSpecificGEP(*A, *B, j - 1) * hgaps[i][j - 1];
+                vgap = (direction[i - 1][j] != UP)
+                     ? getPositionSpecificGOP(*B, *A, ss, i - 1)
+                     : getPositionSpecificGEP(*B, *A, i - 1) * vgaps[i - 1][j];
+
+                const double d = score[i-1][j-1] + S(*A, *B, i, j, ss, weights),
+                             u = score[i - 1][j] - vgap,
+                             l = score[i][j - 1] - hgap;
+
+                Direction dir   = select_direction(d, u, l);
+                score[i][j]     = max(d, max(u, l));
+                direction[i][j] = dir;
+
+                // Written in term of Linear programming for performance
+                hgaps[i][j] = 1 + (dir == LEFT) * hgaps[i][j - 1];
+                vgaps[i][j] = 1 + (dir == UP)   * vgaps[i - 1][j];
+            }
+        }
+
+
+        // Traceback
+        vector<string> residues = traceback(*A, *B, direction);
+
+
+        // Builds sequences
+        vector<Sequence> joint = join(*A, *B, residues);
+
+
+        // Returns multiple alignment
+        delete A;
+        delete B;
+        return new MultipleAlignment(joint);
+    }
+
+    
+
+    double
+    ClustalW::getInitialGOP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const SubstitutionMatrix &matrix) const {
+        const double M = A.getLength(),
+                     N = B.getLength(),
+                     avg = matrix.getAvgMismatchScore(),
+                     identity = A.getPercentIdentity();
+        return gap_open + log10(min(M, N)) * avg * identity;
+    }
+
+
+
+    double
+    ClustalW::getInitialGEP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B) const {
+        const double N = A.getLength(),
+                     M = B.getLength();
+        return gap_extension * (1.0 + abs(log10(N / M)));
+    }
+
+
+
+    double
+    ClustalW::getPositionSpecificGOP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const SubstitutionMatrix &matrix,
+        const size_t position) const {
+        double GOP = getInitialGOP(A, B, matrix);
+
+        // If there are sequences with gaps, ignore other rules
+        if (A.getGapNumber(position) > 0) {
+            return GOP * 0.3 * (1.0 - A.getGapNumber(position) / A.getSize());
+        }
+
+
+        // Checks for gaps within 8 spaces
+        size_t distance = 0;
+        bool gaps_nearby = false;
+        while (!gaps_nearby && distance <= GAP_SEARCH_DISTANCE) {
+            distance++;
+            const size_t gaps_before = A.getGapNumber(position - distance),
+                         gaps_after  = A.getGapNumber(position + distance);
+            gaps_nearby = (gaps_before + gaps_after) > 0;
+        }
+        if (gaps_nearby) {
+            GOP = GOP * (4.0 - distance / 4.0);
+        }
+
+
+        // Checks for hydrophilic stretches
+        if (A.hasHydrophilicStretch(position)) {
+            GOP = GOP * 2.0 / 3.0;
+        }
+
+
+        // Uses Pascarella-Argos table, if no hydropilic stretches
+        else {
+            const string &residues = A.getResidues(position);
+            double average = 0.0;
+
+            for (char residue : residues) {
+                average += gap_modifiers[residue];
+            }
+            average /= A.getSize();
+
+            GOP = GOP * average;
+        }
+
+        return GOP;
+    }
+
+
+
+    double
+    ClustalW::getPositionSpecificGEP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const size_t position) const {
+        const double GEP = getInitialGEP(A, B);
+
+        return (A.getGapNumber(position) > 0) ? GEP * 0.5 : GEP;
+    }
+
+
+
+    SubstitutionMatrix &
+    ClustalW::getSubstitutionMatrix(const RootedTree &guide_tree) const {
+        const double max_distance = guide_tree.getRoot().getMaxDistance();
+        const double raw_distance = guide_tree[0].getDistance(guide_tree[1]);
+        const double distance     = raw_distance / max_distance;
+        SubstitutionMatrix::Identifier identifier;
+
+        // PAM family
+        if (weight_matrix == PAM && distance >= 0.8)
+            identifier = SubstitutionMatrix::PAM20;
+        else if (weight_matrix == PAM && distance >= 0.6)
+            identifier = SubstitutionMatrix::PAM60;
+        else if (weight_matrix == PAM && distance >= 0.4)
+            identifier = SubstitutionMatrix::PAM120;
+        else if (weight_matrix == PAM)
+            identifier = SubstitutionMatrix::PAM350;
+
+        // BLOSUM family
+        else if (weight_matrix == BLOSUM && distance >= 0.8)
+            identifier = SubstitutionMatrix::BLOSUM80;
+        else if (weight_matrix == BLOSUM && distance >= 0.6)
+            identifier = SubstitutionMatrix::BLOSUM62;
+        else if (weight_matrix == BLOSUM && distance >= 0.3)
+            identifier = SubstitutionMatrix::BLOSUM45;
+        else if (weight_matrix == BLOSUM)
+            identifier = SubstitutionMatrix::BLOSUM30;
+
+        // Default
+        else
+            identifier = SubstitutionMatrix::BLOSUM62;
+
+
+        SubstitutionMatrix matrix(identifier);
+
+        // Shifts matrix so that minimum value is 0
+        return matrix - matrix.getMinScore();
+    }
+
+
+
+    double
+    ClustalW::S(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const size_t i,
+        const size_t j,
+        const SubstitutionMatrix &matrix,
+        Weights &weights) {
+        const size_t M = A.getSize(),
+                     N = B.getSize();
+        double score = 0.0;
+        
+        // Full version
+        for (size_t a = 0; a < M; a++) {
+            const Sequence seqA = A.getSequence(a);
+            const char rA       = seqA.getResidues()[j - 1];
+            const double wA     = weights[seqA.getIdentifier()];
+            for (size_t b = 0; b < N; b++) {
+                const Sequence seqB = B.getSequence(b);
+                const char rB       = seqB.getResidues()[i - 1];
+                const double wB     = weights[seqB.getIdentifier()];
+
+                score += (1 - (rA == '-' || rB == '-')) * matrix(rA, rB) * wA * wB;
+            }
+        }
+        score /= (M * N);
+
+        // Consensus only version
+        /*
+        const char a = A.getConsensus(i),
+                   b = B.getConsensus(j);
+        score = (1 - (a == '-' || b == '-')) * matrix(a, b);
+        */
+
+        return score;
+    }
+}  // namespace Phylo
+}  // namespace Victor
+
+
+
+
+
+////////////////////////////////////////////////////////////////////////
+// Support (local) functions.
+static map<char, double> PascarellaArgos() {
+    map<char, double> modifiers;
+
+    modifiers['A'] = 1.13;
+    modifiers['C'] = 1.13;
+    modifiers['D'] = 0.96;
+    modifiers['E'] = 1.31;
+    modifiers['F'] = 1.20;
+    modifiers['G'] = 0.61;
+    modifiers['H'] = 1.00;
+    modifiers['I'] = 1.32;
+    modifiers['K'] = 0.96;
+    modifiers['L'] = 1.21;
+    modifiers['M'] = 1.29;
+    modifiers['N'] = 0.63;
+    modifiers['P'] = 0.74;
+    modifiers['Q'] = 1.07;
+    modifiers['R'] = 0.72;
+    modifiers['S'] = 0.76;
+    modifiers['T'] = 0.89;
+    modifiers['V'] = 1.25;
+    modifiers['Y'] = 1.00;
+    modifiers['W'] = 1.23;
+
+    return modifiers;
+}
+
+
+
+static inline Direction select_direction(
+    const double diagonal,
+    const double up,
+    const double left) {
+    return (diagonal > up && diagonal > left)
+         ? DIAG
+         : ((up > left) ? UP : LEFT);
+}
+
+
+
+static vector<string> traceback(
+    const MultipleAlignment &A,
+    const MultipleAlignment &B,
+    vector<vector<Direction>> &direction) {
+    const size_t M = A.getSize(),
+                 N = B.getSize();
+    size_t i = B.getLength(),
+           j = A.getLength();
+    vector<string> residues(M + N);
+    Direction next = direction[i][j];
+
+    while (next != NONE) {
+        if (next == DIAG) {
+            i--; j--;
+            for (size_t k = 0; k < M; k++)
+                residues[k] = A.getResidues(j)[k] + residues[k];
+
+            for (size_t k = 0; k < N; k++)
+                residues[M + k] = B.getResidues(i)[k] + residues[M + k];
+        } else if (next == UP) {
+            i--;
+            for (size_t k = 0; k < M; k++)
+                residues[k] = "-" + residues[k];
+
+            for (size_t k = 0; k < N; k++)
+                residues[M + k] = B.getResidues(i)[k] + residues[M + k];
+        } else {
+            j--;
+            for (size_t k = 0; k < M; k++)
+                residues[k] = A.getResidues(j)[k] + residues[k];
+
+            for (size_t k = 0; k < N; k++)
+                residues[M + k] = "-" + residues[M + k];
+        }
+
+        next = direction[i][j];
+    }
+
+    return residues;
+}
+
+
+
+static vector<Sequence> join(
+    const MultipleAlignment &A,
+    const MultipleAlignment &B,
+    vector<string> &residues) {
+    const size_t M = A.getSize(),
+                 N = B.getSize();
+    vector<Sequence> sequences;
+
+    for (size_t i = 0; i < M; i++) {
+        sequences.push_back(Sequence(
+            A.getSequence(i).getIdentifier(),
+            residues[i]
+        ));
+    }
+
+    for (size_t j = 0; j < N; j++) {
+        sequences.push_back(Sequence(
+            B.getSequence(j).getIdentifier(),
+            residues[M + j]
+        ));
+    }
+
+    return sequences;
+}
diff --git a/Phylo/Sources/ClustalW.h b/Phylo/Sources/ClustalW.h
new file mode 100644
index 0000000..9486c22
--- /dev/null
+++ b/Phylo/Sources/ClustalW.h
@@ -0,0 +1,245 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_CLUSTALW_H_
+#define _VICTOR_PHYLO_CLUSTALW_H_
+
+#define _GLIBCXX_IOMANIP
+#include <DistanceMatrix.h>
+#include <ClusteringAlgorithm.h>
+#include <PhylogeneticTree.h>
+#include <RootedTree.h>
+#include <DistanceMatrixBuilder.h>
+#include <Sequence.h>
+#include <SubstitutionMatrix.h>
+#include <MultipleAlignmentAlgorithm.h>
+
+#include <AGPFunction.h>
+#include <AlignmentBase.h>
+#include <Alignment.h>
+#include <AlignmentData.h>
+#include <SequenceData.h>
+#include <Structure.h>
+#include <NWAlign.h>
+#include <ScoringS2S.h>
+
+using namespace Victor::Align2;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements the ClustalW algorithm.
+ *
+ * Implements ClustalW as a functor.
+ * ClustalW is a progressive multiple sequence alignment program. It is
+ * an improved version of the original Clustal which uses sequence
+ * weighting, position-specific gap penalties and weight matrix choice.
+ *
+ * For more information see:
+ * - CLUSTAL W: improving the sensitivity of progressive multiple sequence
+ *   alignment through sequence weighting, position-specific gap penalties
+ *   and weight matrix choice
+ *
+ * This class follows the Strategy and Facade Design Patterns.
+ *
+ * Please note that neither the original paper nor other available
+ * resources provide a good/serious description of the (many) implementation
+ * details. Moreover, the freely available source code of Clustal W is
+ * far too complex and too poorly documented. For these reason, this
+ * work (had to) follow a reverse-engeneering approach.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class ClustalW: public MultipleAlignmentAlgorithm {
+ public:
+    /** Available weight matrix families. */
+    typedef enum {
+        PAM,            ///< PAM series
+        BLOSUM          ///< BLOSUM series
+    } WeightMatrix;
+
+
+
+    /** @brief Builds a ClustalW aligner configured with given paramters.
+     * @param[in]       distance_matrix_builder  Distance matrix builder
+     * @param[in]       clustering_algorithm     Clustering algorithm
+     * @param[in]       weight_matrix            Weight matrix family (progressive alignment)
+     * @param[in]       gap_open                 Gap open penalty (progressive alignment)
+     * @param[in]       gap_extension            Gap extension penalty (progressive alignment)
+     */
+    explicit ClustalW(
+        const DistanceMatrixBuilder &distance_matrix_builder,
+        const ClusteringAlgorithm &clustering_algorithm,
+        const WeightMatrix weight_matrix,
+        const double gap_open = 10.0,
+        const double gap_extension = 0.1);
+
+    /** @brief Copy constructor.
+     * @param[in]       origin    Original object
+     */
+    explicit ClustalW(const ClustalW &origin);
+
+    /** @brief Destructor. */
+    virtual ~ClustalW();
+
+
+
+    /** @brief  Builds an MSA from an alignment.
+     * @param[in]       alignment The alignment
+     * @return Multiple sequence alignment
+     */
+    virtual MultipleAlignment &apply(const AlignmentBase &alignment) const;
+
+
+
+ private:
+    typedef map<string, double> Weights;    ///< Weight map
+    typedef map<string, string> Sequences;  ///< Set of sequences
+
+    /** Residue-specific gap modification factors (Pascarella and Argos). */
+    static map<char, double> gap_modifiers;
+
+    const DistanceMatrixBuilder &build_matrix;   ///< Distance matrix builder
+    const ClusteringAlgorithm &build_tree;  ///< Phylogenetic tree builder
+    const WeightMatrix weight_matrix;       ///< Weight matrix family
+    const double gap_open;                  ///< Gap open penalty
+    const double gap_extension;             ///< Gap extension penalty
+
+
+    /** @brief Returns weights.
+     *
+     * Weights are normalized.
+     * @param[in]       guide_tree Guide tree of the alignment
+     * @return Weights of the sequences
+     */
+    Weights getWeights(const RootedTree &guide_tree) const;
+
+
+
+    /** @brief Performs multiple sequence alignment.
+     *
+     * Order of alignments is determined by topology of guide tree.
+     * @param[in]       sequences Sequences to align
+     * @param[in]       node      Node on the guide tree
+     * @param[in]       weights   Weights
+     * @return Multiple sequence alignment
+     */
+    MultipleAlignment *align(
+        Sequences &sequences,
+        const RootedTree &node,
+        Weights &weights) const;
+
+
+
+    /** @brief Returns initial gap opening penalty.
+     * 
+     * Initial gap opening penalty is computed considering dependence on
+     * the weight matrix, dependence on the similarity of the sequences
+     * and dependences on the length of the sequences:
+     * GOP = GOP + log(min(N, M)) * (average mismatch score) * (percentage
+     * of identity)
+     * where M, N are the length of the sequences.
+     * @param[in]       A         First (group of) sequence
+     * @param[in]       B         Second (group of) sequence
+     * @param[in]       matrix    Substitution matrix
+     * @return Initial gap opening penalty
+     */
+    double getInitialGOP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const SubstitutionMatrix &matrix) const;
+
+    /** @brief Returns initial gap extension penalty.
+     *
+     * Initial gap extension penalty is computed considering dependence
+     * on the difference in the lengths of the sequences:
+     * GEP = GEP * (1.0 + |log(N/M)|)
+     * where M, N are the length of the sequences.
+     * @param[in]       A         First (group of) sequence
+     * @param[in]       B         Second (group of) sequence
+     * @return Initial gap extension penalty
+     */
+    double getInitialGEP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B) const;
+
+    /** @brief Returns position-specific gap open penalty.
+     * 
+     * Position-specific gap open penalty is computed considering
+     * presence of gaps, nearby gaps and hydrophilic stretches.
+     * @param[in]       A         First (group of) sequence
+     * @param[in]       B         Second (group of) sequence
+     * @param[in]       matrix    Substitution matrix
+     * @param[in]       position  Current position
+     * @return Position-specific gap open penalty
+     */
+    double getPositionSpecificGOP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const SubstitutionMatrix &matrix,
+        const size_t position) const;
+
+    /** @brief Returns position-specific gap extension penalty.
+     *
+     * Position specific gap extension penalty is computed considering
+     * presence of gaps: if there is a gap, GEP is halved.
+     * @param[in]       A         First (group of) sequence
+     * @param[in]       B         Second (group of) sequence
+     * @param[in]       position  Current positon
+     * @return Position-specific gap extension penalty
+     */
+    double getPositionSpecificGEP(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const size_t position) const;
+
+    /** @brief Returns a substitution matrix.
+     *
+     * Returns substitution matrix depending on the distance of the 
+     * (groups of) sequences to align. Substitution matrix is shifted so
+     * that its minimum value is 0.
+     * @param[in]       guide_tree Guide tree
+     * @return Substitution matrix
+     */
+    SubstitutionMatrix &getSubstitutionMatrix(const RootedTree &guide_tree) const;
+
+
+
+    /** @brief Returns match score.
+     *
+     * Computes match score between given MSAs, at given positions, using
+     * given substitutioin matrix and given weights for the sequences.
+     * @param[in]           A         First MSA
+     * @param[in]           B         Second MSA
+     * @param[in]           i         Row
+     * @param[in]           j         Column
+     * @param[in]           matrix    Substitution matrix
+     * @param[in]           weights   Weights of the sequences
+     * @return Score of the alignment.
+     */
+    static double S(
+        const MultipleAlignment &A,
+        const MultipleAlignment &B,
+        const size_t i,
+        const size_t j,
+        const SubstitutionMatrix &matrix,
+        Weights &weights);
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_CLUSTALW_H_
\ No newline at end of file
diff --git a/Phylo/Sources/ClusteringAlgorithm.h b/Phylo/Sources/ClusteringAlgorithm.h
new file mode 100644
index 0000000..b58ebf5
--- /dev/null
+++ b/Phylo/Sources/ClusteringAlgorithm.h
@@ -0,0 +1,60 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_CLUSTERINGALGORITHM_H_
+#define _VICTOR_PHYLO_CLUSTERINGALGORITHM_H_
+
+#include <PhylogeneticAlgorithm.h>
+#include <PhylogeneticTree.h>
+#include <DistanceMatrix.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief A clustering algorithm.
+ *
+ * Clustering algorithms are phylogenetic algorithms which produce
+ * phylogenetic trees by using information about distances among
+ * alignments.
+ *
+ * Clustering algorithms are implemented as functors from a distance matrix to
+ * a phylogenetic tree.
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class ClusteringAlgorithm: public PhylogeneticAlgorithm {
+ public:
+    /** @brief Builds a phylogenetic tree from given distance matrix.
+     * @param[in]       matrix    Distance matrix
+     * @return Phylogenetic tree
+     */
+    inline PhylogeneticTree &operator()(const DistanceMatrix &matrix) const {
+        return apply(matrix);
+    }
+
+    /** @brief Builds a phylogenetic tree from given distance matrix.
+     * @param[in]       matrix    Distance matrix
+     * @return Phylogenetic tree
+     */
+    virtual PhylogeneticTree &apply(const DistanceMatrix &matrix) const = 0;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_CLUSTERINGALGORITHM_
\ No newline at end of file
diff --git a/Phylo/Sources/DistanceMatrix.cc b/Phylo/Sources/DistanceMatrix.cc
new file mode 100644
index 0000000..5125d29
--- /dev/null
+++ b/Phylo/Sources/DistanceMatrix.cc
@@ -0,0 +1,225 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <DistanceMatrix.h>
+#include <limits>
+#include <iostream>
+
+namespace Victor {
+namespace Phylo {
+    typedef DistanceMatrix::key key;
+
+    const double DistanceMatrix::min_distance = 0.0;
+    const double DistanceMatrix::max_distance = std::numeric_limits<double>::max();
+
+
+    DistanceMatrix::~DistanceMatrix() {
+    }
+
+
+
+    double
+    DistanceMatrix::operator()(const string &a, const string &b) const {
+        return getElement(a, b);
+    }
+
+
+    DistanceMatrix &
+    DistanceMatrix::operator()(const string &a, const string &b, const double distance) {
+        return setDistance(a, b, distance);
+    }
+
+
+
+    bool
+    DistanceMatrix::isEmpty() const {
+        return getSize() <= 1;
+    }
+
+
+
+    bool
+    DistanceMatrix::isSet(const string &a, const string &b) const {
+        return isSetDirectional(a, b) || isSetDirectional(b, a);
+    }
+
+
+
+    bool
+    DistanceMatrix::hasOTU(const string &OTU) const {
+        for (auto &label : OTUs) {
+            if (label == OTU) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+
+
+    double
+    DistanceMatrix::getElement(const string &a, const string &b) const {
+        if (a == b) {
+            return min_distance;
+        } else if (isSetDirectional(a, b)) {
+            return find(make_pair(a, b))->second;
+        } else if (isSetDirectional(b, a)) {
+            return find(make_pair(b, a))->second;
+        } else {
+            return max_distance;
+        }
+    }
+
+
+
+    set<string>
+    DistanceMatrix::getOTUs() const {
+        return OTUs;
+    }
+
+
+
+    size_t
+    DistanceMatrix::getSize() const {
+        return OTUs.size();
+    }
+
+
+
+    double
+    DistanceMatrix::getMinimum() const {
+        double min = max_distance;
+
+        for (auto &entry : *this) {
+            if (entry.second <= min) {
+                min = entry.second;
+            }
+        }
+
+        return min;
+    }
+
+
+
+    key
+    DistanceMatrix::getMinimumPosition() const {
+        double min = max_distance;
+        key pos;
+        for (auto &entry : *this) {
+            if (entry.second <= min) {
+                min = entry.second;
+                pos = entry.first;
+            }
+        }
+
+        return pos;
+    }
+
+
+
+    double
+    DistanceMatrix::getMaximum() const {
+        double max = min_distance;
+
+        for (auto &entry : *this) {
+            if (entry.second >= max) {
+                max = entry.second;
+            }
+        }
+
+        return max;
+    }
+
+
+
+    key
+    DistanceMatrix::getMaximumPosition() const {
+        double max = min_distance;
+        key pos;
+
+        for (auto &entry : *this) {
+            if (entry.second >= max) {
+                max = entry.second;
+                pos = entry.first;
+            }
+        }
+
+        return pos;
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrix::setDistance(const string &a, const string &b, const double distance) {
+        key pos = (isSetDirectional(a, b)) ? make_pair(a, b) : make_pair(b, a);
+        (*this)[pos] = distance;
+        return *this;
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrix::unsetDistance(const string &a, const string &b) {
+        if (isSetDirectional(a, b))
+            this->erase(find(make_pair(a, b)));
+        if (isSetDirectional(b, a))
+            this->erase(find(make_pair(b, a)));
+        return *this;
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrix::unsetDistance(const string &OTU) {
+        for (auto &other : getOTUs()) {
+            unsetDistance(OTU, other);
+        }
+        return *this;
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrix::addOTU(const string &OTU) {
+        if (!hasOTU(OTU)) {
+            OTUs.insert(OTU);
+        }
+        return *this;
+    }
+
+
+    DistanceMatrix &
+    DistanceMatrix::removeOTU(const string &OTU) {
+        // Removes OTU from list
+        OTUs.erase(OTU);
+
+        // Removes OTU from distances
+        for (auto &i : OTUs) {
+            erase(make_pair(i, OTU));
+            erase(make_pair(OTU, i));
+        }
+
+        return *this;
+    }
+
+
+
+    bool
+    DistanceMatrix::isSetDirectional(const string &a, const string &b) const {
+        return find(make_pair(a, b)) != end();
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/DistanceMatrix.h b/Phylo/Sources/DistanceMatrix.h
new file mode 100644
index 0000000..9b3b981
--- /dev/null
+++ b/Phylo/Sources/DistanceMatrix.h
@@ -0,0 +1,220 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_DISTANCEMATRIX_H_
+#define _VICTOR_PHYLO_DISTANCEMATRIX_H_
+
+#include <string>
+#include <vector>
+#include <set>
+#include <map>
+
+using std::string;
+using std::pair;
+using std::vector;
+using std::set;
+using std::map;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a distance matrix.
+ *
+ * A distance matrix holds distances among OTUs.
+ * This class uses Method Cascading (through Method Chaining).
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class DistanceMatrix: public map<pair<string, string>, double> {
+ public:
+    /** Key to access an entry in the matrix. */
+    typedef pair<string, string> key;
+
+
+    /** @brief Destructor. */
+    virtual ~DistanceMatrix();
+
+
+
+    /** @brief Returns distance between given OTUs.
+     *
+     * If there is no recorded distance between given OTUs, returns
+     * maximum representable distance.
+     * Distance matrices are symmetric, hence order of indeces does not
+     * matter.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @return Distance between given OTUs
+     */
+    double operator()(const string &a, const string &b) const;
+
+    /** @brief Sets distance between given OTUs.
+     *
+     * If a distance was previously recorder for given OTUs, it is
+     * overwritten.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @param[in]       distance  Distance between a and b
+     * @return This matrix itself
+     */
+    DistanceMatrix &operator()(const string &a, const string &b, const double distance);
+
+
+
+    /** @brief Tells whether this matrix is empty.
+     *
+     * A distance matrix is empty when it contains 1 or less OTUs.
+     * @retval true     This distance matrix is empty
+     * @retval false    This distance matrix is not empty
+     */
+    bool isEmpty() const;
+
+    /** @brief Tells whether there is a distance recorder between given OTUs.
+     *
+     * Distance matrices are symmetric, hence order of indeces does not
+     * matter.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @retval true     There is a record for given OTUs
+     * @retval false    There is no record for given OTUs
+     */
+    bool isSet(const string &a, const string &b) const;
+
+    /** @brief Tells whether given OTU exists in this matrix.
+     * @param[in]       OTU       Given OTU
+     * @retval true     Given OTU exists in this matrix
+     * @retval false    Given OTU does not exist in this matrix
+     */
+    bool hasOTU(const string &OTU) const;
+
+
+
+    /** @brief Returns distance between given OTUs.
+     *
+     * If there is no recorded distance between given OTUs, returns
+     * maximum representable distance.
+     * Distance matrices are symmetric, hence order of indeces does not
+     * matter.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @return Distance between given OTUs
+     */
+    double getElement(const string &a, const string &b) const;
+
+    /** @brief Returns OTUs in this matrix.
+     * @return OTUs as vector<string>
+     */
+    set<string> getOTUs() const;
+
+    /** @brief Returns number of OTUs in this matrix.
+     * @return Number of OTUs in this matrix
+     */
+    size_t getSize() const;
+
+    /** @brief Returns minimum distance in this matrix.
+     * @return Minimum distance in this matrix
+     */
+    double getMinimum() const;
+
+    /** @brief Returns position of minimum distance in this matrix.
+     *
+     * Returns position as a pair<string, string>, where strings are
+     * the OTUs.
+     * @return Position of minimum distance
+     */
+    key getMinimumPosition() const;
+
+    /** @brief Returns maximum distance in this matrix.
+     * @return Maximum distance in this matrix
+     */
+    double getMaximum() const;
+
+    /** @brief Returns position of maximum distance in this matrix.
+     *
+     * Returns position as a pair<string, string>, where strings are
+     * the OTUs.
+     * @return Position of maximum distance
+     */
+    key getMaximumPosition() const;
+
+
+
+    /** @brief Sets distance between given OTUs.
+     *
+     * If a distance was previously recorder for given OTUs, it is
+     * overridden.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @param[in]       distance  Distance between a and b
+     * @return This matrix itself
+     */
+    DistanceMatrix &setDistance(const string &a, const string &b, const double distance);
+
+    /** @brief Unsets the distance between given OTUs.
+     *
+     * If no distance was set, nothing happens.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @return This matrix itself
+     */
+    DistanceMatrix &unsetDistance(const string &a, const string &b);
+
+    /** @brief Unsets every distance involving given OTU.
+     * @param[in]       OTU       OTU
+     * @return This matrix itself
+     */
+    DistanceMatrix &unsetDistance(const string &OTU);
+
+    /** @brief Adds a new OTU to this matrix.
+     *
+     * If given OTU already exists in this matrix, nothing happens.
+     * @param[in]       OTU       Given OTU
+     * @return This matrix itself
+     */
+    DistanceMatrix &addOTU(const string &OTU);
+
+    /** @brief Removes an OTU from this matrix.
+     *
+     * Data about given OTU (i.e. distances) is not removed.
+     * @param[in]       OTU       Given OTU
+     * @return This matrix itself
+     */
+    DistanceMatrix &removeOTU(const string &OTU);
+
+
+
+ private:
+    static const double min_distance;  ///< Minimum representable distance
+    static const double max_distance;  ///< Maximum representable distance
+
+    set<string> OTUs;   ///< OTUs in this matrix
+
+
+    /** @brief Tells whether there is a distance recorder between given OTUs.
+     *
+     * Order of OTUs matters.
+     * @param[in]       a         First OTU
+     * @param[in]       b         Second OTU
+     * @retval true     There is a record for given OTUs
+     * @retval false    There is no record for given OTUs
+     */
+    bool isSetDirectional(const string &a, const string &b) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_DISTANCEMATRIX_
\ No newline at end of file
diff --git a/Phylo/Sources/DistanceMatrixBuilder.cc b/Phylo/Sources/DistanceMatrixBuilder.cc
new file mode 100644
index 0000000..30b6cc5
--- /dev/null
+++ b/Phylo/Sources/DistanceMatrixBuilder.cc
@@ -0,0 +1,59 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <DistanceMatrixBuilder.h>
+#include <Sequence.h>
+
+namespace Victor {
+namespace Phylo {
+    DistanceMatrixBuilder::~DistanceMatrixBuilder() {
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrixBuilder::operator()(const AlignmentBase &alignment) const {
+        return apply(alignment);
+    }
+
+
+
+    DistanceMatrix &
+    DistanceMatrixBuilder::apply(const AlignmentBase &alignment) const {
+        const size_t n                   = alignment.size() + 1;
+        const vector<Sequence> sequences = Sequence::toSequences(alignment);
+        DistanceMatrix * const d         = new DistanceMatrix();
+        
+        // Adds OTUs to the matrix
+        for (auto &sequence : sequences) {
+            d->addOTU(sequence.getIdentifier());
+        }
+
+        // Computes distance matrix
+        for (size_t i = 0; i < n; i++) {
+            for (size_t j = i + 1; j < n; j++) {
+                (*d)(
+                    sequences[i].getIdentifier(),
+                    sequences[j].getIdentifier(),
+                    computeDistance(sequences[i].getResidues(), sequences[j].getResidues())
+                );
+            }
+        }
+
+        return *d;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/DistanceMatrixBuilder.h b/Phylo/Sources/DistanceMatrixBuilder.h
new file mode 100644
index 0000000..5a80465
--- /dev/null
+++ b/Phylo/Sources/DistanceMatrixBuilder.h
@@ -0,0 +1,69 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_
+#define _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_
+
+#define _GLIBCXX_IOMANIP
+#include <DistanceMatrix.h>
+#include <AlignmentBase.h>
+
+using namespace Victor::Align2;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements an algorithm for building a distance matrix.
+ *
+ * Builds a distance matrix from an alignment.
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+  */
+class DistanceMatrixBuilder {
+ public:
+    /** @brief Destructor. */
+    virtual ~DistanceMatrixBuilder();
+
+
+
+    /** @brief Builds a distance matrix from given alignment.
+     * @param[in]       alignment Alignment
+     * @return Distance matrix
+     */
+    DistanceMatrix &operator()(const AlignmentBase &alignment) const;
+
+    /** @brief Builds a distance matrix from given alignment.
+     * @param[in]      alignment  Alignment
+     * @return Distance matrix
+     */
+    DistanceMatrix &apply(const AlignmentBase &alignment) const;
+
+
+
+ private:
+    /** @brief Returns distance between two sequences.
+     * @param[in]       seq1      First sequence
+     * @param[in]       seq2      Second sequence
+     * @return Distance between seq1 and seq2
+     */
+    virtual double computeDistance(const string &seq1, const string &seq2) const = 0;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+#endif  // _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_
\ No newline at end of file
diff --git a/Phylo/Sources/FengDoolittle.cc b/Phylo/Sources/FengDoolittle.cc
new file mode 100644
index 0000000..2386240
--- /dev/null
+++ b/Phylo/Sources/FengDoolittle.cc
@@ -0,0 +1,195 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <FengDoolittle.h>
+#include <SubstitutionMatrix.h>
+#include <phylo.h>
+
+using namespace std;
+using namespace Victor::Phylo;
+
+/** @brief Replaces gaps in a sequence.
+ * @param[in]           sequence  Sequence
+ * @return Sequence where gaps have been replaced
+ */
+static string &replace_gaps(const string &sequence);
+
+/** @brief Returns the PAM 250 substitution matrix.
+ * @return PAM 250 matrix
+ */
+static SubMatrix &init_matrix();
+
+
+
+namespace Victor {
+namespace Phylo {
+    typedef map<string, string> Sequences;
+
+    // For some unknown reasons, matrix cannot be initialized statically (althought
+    // it is a static member). A good place is the constructor.
+    SubMatrix FengDoolittle::matrix;
+    const FitchMargoliash FengDoolittle::build_tree;
+
+
+    FengDoolittle::FengDoolittle(const double gap_open, const double gap_extension)
+    : gap_function(*new AGPFunction(gap_open, gap_extension)) {
+        matrix = init_matrix();
+    }
+
+
+
+    FengDoolittle::FengDoolittle(const FengDoolittle &origin)
+    : gap_function(origin.gap_function) {
+    }
+
+
+
+    FengDoolittle::~FengDoolittle() {
+    }
+
+
+
+    MultipleAlignment &
+    FengDoolittle::apply(const AlignmentBase &alignment) const {
+        // Reads sequences
+        Sequences sequences = Sequence::toMap(alignment);
+
+        // Computes distance matrix (pairwise alignment)
+        FengDoolittleDistance build_matrix(matrix, gap_function);
+        DistanceMatrix d = build_matrix(alignment);
+
+        // Computes guide tree
+        RootedTree guide_tree = build_tree(d).asRootedTree();
+
+        // Progressive alignments
+        return *align(sequences, guide_tree);
+    }
+
+
+
+    MultipleAlignment *
+    FengDoolittle::align(
+        Sequences &sequences,
+        const RootedTree &node) const {
+        ////////////////////////////////////////////////////////////////
+        // Single sequence: trivially aligned
+        if (node.isLeaf()) {
+            const string identifier = node.getLabel(),
+                         residues   = sequences[identifier];
+            return new MultipleAlignment(Sequence(identifier, residues));
+        }
+
+
+        ////////////////////////////////////////////////////////////////
+        // Single inheritance: straightforward
+        if (node.getChildrenNumber() == 1) {
+            return align(sequences, node[0]);
+        }
+
+
+        ////////////////////////////////////////////////////////////////
+        // Two MSAs: performs alignment
+        const MultipleAlignment *A = align(sequences, node[0]),
+                                *B = align(sequences, node[1]);
+        double max_score = -999999.0;
+        string horizontal, vertical;
+
+
+#if VERBOSE==1
+        cout << "Now aligning:" << endl;
+        for (size_t i = 0; i < A->getSize(); i++) {
+            cout << A->getSequence(i).getIdentifier() << endl;
+        }
+        cout << "---------- against ----------" << endl;
+        for (size_t j = 0; j < B->getSize(); j++) {
+            cout << B->getSequence(j).getIdentifier() << endl;
+        }
+        cout << endl << endl;
+#endif
+
+
+        // Finds best alignment
+        for (size_t i = 0; i < A->getSize(); i++) {
+            const string seqA = replace_gaps(A->getSequence(i).getResidues());
+            for (size_t j = 0; j < B->getSize(); j++) {
+                const string seqB = replace_gaps(B->getSequence(j).getResidues());
+
+                AlignmentData *data = new SequenceData(2, seqA, seqB, "", "");
+                ScoringS2S scoring_scheme(&matrix, data, nullptr, 1.0);
+                NWAlign nw_align(data, &gap_function, &scoring_scheme);
+                const double score = nw_align.getScore();
+
+                if (score > max_score) {
+                    max_score  = score;
+                    horizontal = nw_align.getMatch()[0];
+                    vertical   = nw_align.getMatch()[1];
+                }
+            }
+        }
+
+
+        // Builds a new MSA using best alignment
+        vector<Sequence> new_sequences;
+        for (size_t i = 0; i < A->getSize(); i++) {
+            const string identifier = A->getSequence(i).getIdentifier(),
+                         sequence   = A->getSequence(i).getResidues();
+            size_t cursor   = 0;
+            string residues = "";
+            for (char residue : horizontal) {
+                residues += (residue != '-') ? sequence[cursor++] : '-';
+            }
+            new_sequences.push_back(Sequence(identifier, residues));
+        }
+        
+        for (size_t i = 0; i < B->getSize(); i++) {
+            const string identifier = B->getSequence(i).getIdentifier(),
+                         sequence   = B->getSequence(i).getResidues();
+            size_t cursor   = 0;
+            string residues = "";
+            for (char residue : vertical) {
+                residues += (residue != '-') ? sequence[cursor++] : '-';
+            }
+            new_sequences.push_back(Sequence(identifier, residues));
+        }
+
+
+        // Returns multiple alignmnet
+        return new MultipleAlignment(new_sequences);
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
+
+
+
+////////////////////////////////////////////////////////////////////////
+// Support functions
+static string &replace_gaps(const string &sequence) {
+    string *new_sequence = new string();
+
+    for (char residue : sequence) {
+        (*new_sequence) += (residue != '-') ? residue : 'X';
+    }
+
+    return *new_sequence;
+}
+
+
+
+static SubMatrix &init_matrix() {
+    SubstitutionMatrix m(SubstitutionMatrix::PAM250);
+    return (m - m.getMinScore()).asSubMatrix();
+}
\ No newline at end of file
diff --git a/Phylo/Sources/FengDoolittle.h b/Phylo/Sources/FengDoolittle.h
new file mode 100644
index 0000000..ca0534c
--- /dev/null
+++ b/Phylo/Sources/FengDoolittle.h
@@ -0,0 +1,105 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_FENGDOOLITTLE_H_
+#define _VICTOR_PHYLO_FENGDOOLITTLE_H_
+
+#define _GLIBCXX_IOMANIP
+#include <FengDoolittleDistance.h>
+#include <DistanceMatrix.h>
+#include <FitchMargoliash.h>
+#include <RootedTree.h>
+#include <Sequence.h>
+#include <MultipleAlignmentAlgorithm.h>
+
+#include <AGPFunction.h>
+#include <AlignmentBase.h>
+#include <Alignment.h>
+#include <AlignmentData.h>
+#include <SequenceData.h>
+#include <Structure.h>
+#include <NWAlign.h>
+#include <ScoringS2S.h>
+
+using namespace Victor::Align2;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements the Feng and Doolittle multiple sequence
+ * alignment algorithm.
+ * 
+ * Implements Feng-Doolittle as a functor.
+ * Feng-Doolittle is a progressive multiple sequence alignment program.
+ * For more information see:
+ * - Progressive Sequence Alignment as a Prerequisite to Correct
+ *   Phylogenetic Trees
+ *
+ * This class follows the Strategy and the Facade Design Patterns.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class FengDoolittle: public MultipleAlignmentAlgorithm {
+ public:
+    /** @brief Builds a Feng-Doolittle aligner with given configuration.
+     * @param[in]       gap_open  Gap opening penalty (default: 10.0)
+     * @param[in]       gap_extension  Gap extension penalty (default: 0.1)
+     */
+    explicit FengDoolittle(
+        const double gap_open = 10.0,
+        const double gap_extension = 0.1);
+
+    /** @brief Copy constructor.
+     * @param[in]       origin    Original Feng-Doolittle aligner
+     */
+    explicit FengDoolittle(const FengDoolittle &origin);
+
+    /** @brief Destructor. */
+    ~FengDoolittle();
+
+
+
+    /** @brief Builds an MSA from a set of sequences.
+     * @param[in]       alignment Set of sequences
+     * @return Multiple sequence alignment
+     */
+    virtual MultipleAlignment &apply(const AlignmentBase &alignment) const;
+
+
+
+ private:
+    typedef map<string, string> Sequences;  ///< Set of sequences
+
+    static SubMatrix matrix;                ///< Substitution matix
+    static const FitchMargoliash build_tree; ///< Clustering algorithm
+
+    AGPFunction &gap_function;              ///< Gap function
+
+
+    /** @brief Aligns next nodes in the guide tree.
+     * @param[in]       sequences Sequences to align
+     * @param[in]       node      Next node of the guide tree
+     * @return Multiple sequence alignment
+     */
+    MultipleAlignment *align(
+        Sequences &sequences,
+        const RootedTree &node) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_FENGDOOLITTLE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/FengDoolittleDistance.cc b/Phylo/Sources/FengDoolittleDistance.cc
new file mode 100644
index 0000000..b7dc632
--- /dev/null
+++ b/Phylo/Sources/FengDoolittleDistance.cc
@@ -0,0 +1,74 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <FengDoolittleDistance.h>
+#include <algorithm>
+#include <SequenceData.h>
+#include <ScoringS2S.h>
+#include <NWAlign.h>
+#include <Sequence.h>
+
+namespace Victor {
+namespace Phylo {
+    FengDoolittleDistance::FengDoolittleDistance(
+        SubMatrix &matrix,
+        GapFunction &gap)
+    : substitution_matrix(matrix), gap_function(gap) {
+    }
+
+
+
+    FengDoolittleDistance::FengDoolittleDistance(const FengDoolittleDistance &origin)
+    : FengDoolittleDistance(origin.substitution_matrix, origin.gap_function) {
+    }
+
+
+
+    FengDoolittleDistance::~FengDoolittleDistance() {
+    }
+
+
+
+    double
+    FengDoolittleDistance::computeDistance(const string &seq1, const string &seq2) const {
+        string r1 = seq1, r2 = seq2;
+
+        std::random_shuffle(r1.begin(), r1.end());
+        std::random_shuffle(r2.begin(), r2.end());
+
+        const double S_x  = computeScore(seq1, seq1),
+                     S_y  = computeScore(seq2, seq2),
+                     S_xy = computeScore(seq1, seq2),
+                     S_r  = computeScore(r1, r2),
+                     d    = 2.0 * (S_xy - S_r) / (S_x + S_y + 2.0 * S_r);
+
+        return -log((d > 0.0) ? d : 1.0);
+    }
+
+
+
+    double
+    FengDoolittleDistance::computeScore(const string &seq1, const string &seq2) const {
+        AlignmentData *alignment_data = new SequenceData(2, seq1, seq2, "", "");
+        Structure     *structure      = nullptr;
+        const double  cSeq            = 1.0;
+        ScoringS2S    scoring_scheme(&substitution_matrix, alignment_data, structure, cSeq);
+        NWAlign align(alignment_data, &gap_function, &scoring_scheme);
+
+        return align.getScore();
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/FengDoolittleDistance.h b/Phylo/Sources/FengDoolittleDistance.h
new file mode 100644
index 0000000..3d9d3da
--- /dev/null
+++ b/Phylo/Sources/FengDoolittleDistance.h
@@ -0,0 +1,85 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_
+#define _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_
+
+#define _GLIBCXX_IOMANIP
+#include <DistanceMatrixBuilder.h>
+#include <SubMatrix.h>
+#include <GapFunction.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Builds a distance matrix using the Feng-Doolittle algorithm.
+ *
+ * Compute pairwise alignment for every pair of sequences, then creates
+ * the distance matrix using the formula proposed by Feng and Doolittle:
+ * D(x, y) = -log( ((S(x, y) - Srand) / (S(x, x)/2 + S(y, y)/2 - Srand) ).
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class FengDoolittleDistance: public DistanceMatrixBuilder {
+ public:
+ 	/** @brief Builds a Feng-Doolittle distance metrics with given paramters.
+ 	 *
+ 	 * Stores information about wich subsitution matrix to use (example:
+     * PAM260, BLOSUM50...) and which gap function to use.
+ 	 * @param[in]       matrix    Substitution matrix to use
+ 	 * @param[in]       gap       Gap function to use
+ 	 */
+ 	explicit FengDoolittleDistance(SubMatrix &matrix, GapFunction &gap);
+
+    /** @brief Copy constructor.
+     * @param[in]       origin    Original Feng-Doolittle object
+     */
+    explicit FengDoolittleDistance(const FengDoolittleDistance &origin);
+
+    /** @brief Destructor. */
+    ~FengDoolittleDistance();
+
+
+
+ private:
+ 	SubMatrix   &substitution_matrix;   ///< Substitution matrix
+ 	GapFunction &gap_function;          ///< Gap function
+
+
+    /** @brief Returns distance between two sequences.
+     * @param[in]       seq1      First sequence
+     * @param[in]       seq2      Second sequence
+     * @return Distance between seq1 and seq2
+     * @todo S_r is not computed due to complete lack of documentation
+     */
+    virtual double computeDistance(const string &seq1, const string &seq2) const;
+
+
+
+    /** @brief Performs alignment and returns score.
+     * @param[in]       seq1      First sequence
+     * @param[in]       seq2      Second sequence
+     * @return Score of the alignment
+     */
+    double computeScore(const string &seq1, const string &seq2) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/FitchMargoliash.cc b/Phylo/Sources/FitchMargoliash.cc
new file mode 100644
index 0000000..b84c993
--- /dev/null
+++ b/Phylo/Sources/FitchMargoliash.cc
@@ -0,0 +1,224 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <FitchMargoliash.h>
+#include <algorithm>
+#include <iterator>
+
+using Victor::Phylo::DistanceMatrix;
+
+/** @brief Returns distance between two clusters of nodes.
+ * @param[in]           in_X      Set of (names of) nodes in X
+ * @param[in]           in_O      Set of (names of) nodes in O
+ * @param[in]           d         Reference distance matrix
+ */
+static double d_XO(
+    const set<string> &in_X,
+    const set<string> &in_O,
+    const DistanceMatrix &d);
+
+/** @brief Returns union of sets.
+ * @param[in]       A         First set
+ * @param[in]       B         Second set
+ * @return Set union between A and B: A U B
+ */
+template <class T>
+set<T> set_union(const set<T> &A, const set<T> &B);
+
+/** @brief Returns difference of sets.
+ *
+ * This is a more comfortable inteface to the std set difference function
+ * which, unfortunately, does not seems a set difference function at all.
+ * @param[in]       A         First set
+ * @param[in]       B         Second set
+ * @return Set difference between A and B: A - B
+ */
+template <class T>
+set<T> set_difference(const set<T> &A, const set<T> &B);
+
+
+
+namespace Victor {
+namespace Phylo {
+    typedef UnrootedTree::Node Node;
+
+
+    FitchMargoliash::~FitchMargoliash() {
+    }
+
+
+
+    UnrootedTree &
+    FitchMargoliash::apply(const DistanceMatrix &matrix) const {
+        UnrootedTree *tree = new UnrootedTree();
+        DistanceMatrix d   = matrix;
+        set<string> OTUs   = matrix.getOTUs();
+        map<string, Node *> node_pool;
+        map<string, size_t> size_pool;
+        map<string, set<string>> sets_pool;
+
+
+        // Initializes leaves
+        for (auto &OTU : OTUs) {
+            Node *leaf = new Node(OTU);
+            node_pool[OTU] = leaf;
+            size_pool[OTU] = 1;
+            sets_pool[OTU].insert(OTU);
+            tree->addNode(*leaf);
+        }
+
+
+        // Repeats until only three nodes are left
+        while (d.getSize() > 3) {
+            OTUs = d.getOTUs();
+            set<string> others;
+
+            // Finds closest pair A and B, then join them into a new
+            // node R
+            const pair<string, string> min_pos = d.getMinimumPosition();
+            const string A = min_pos.first,
+                         B = min_pos.second,
+                         R = A + "+" + B;
+            Node *r      = new Node();
+            node_pool[R] = r;
+            size_pool[R] = size_pool[A] + size_pool[B];
+            sets_pool[R] = set_union(sets_pool[A], sets_pool[B]);
+            others       = set_difference(matrix.getOTUs(), sets_pool[R]);
+            tree->addNode(*r);
+
+
+            // Calculates distances among A, B and the other nodes (O)
+            const double d_AB = d(A, B),
+                         d_AO = d_XO(sets_pool[A], others, matrix),
+                         d_BO = d_XO(sets_pool[B], others, matrix);
+
+
+            // Calculates distances betwen R and A (a), R and B (b), R
+            // and the other nodes (c)
+            const double a = std::max(0.5 * (d_AO + d_AB - d_BO), 0.0),
+                         b = std::max(0.5 * (d_BO + d_AB - d_AO), 0.0);
+                         //c = abs(0.5 * (d_AO + d_BO - d_AB));
+
+
+            // Set distances among A, B, R
+            r->addNeighbor(*node_pool[A], a);
+            r->addNeighbor(*node_pool[B], b);
+
+
+            // Updates distance matrix
+            for (auto &K : OTUs) {
+                if (K == A || K == B) continue;
+                const double d_RK = 0.5 * (d(A, K) + d(B, K));
+                d(R, K, d_RK);
+            }
+
+
+            // Removes "consumed" OTUs and adds newly generated one
+            d.unsetDistance(A)
+             .unsetDistance(B)
+             .removeOTU(A)
+             .removeOTU(B)
+             .addOTU(R);
+        }
+
+
+        // If there are only three nodes left, the operation is trivial
+        if (d.getSize() == 3) {
+            vector<string> OTUs;
+            for (auto &OTU : d.getOTUs()) {
+                OTUs.push_back(OTU);
+            }
+
+            const string A = OTUs[0],
+                         B = OTUs[1],
+                         C = OTUs[2];
+            const double a = std::max(0.5 * (d(A, B) + d(A, C) - d(B, C)), 0.0),
+                         b = std::max(0.5 * (d(A, B) + d(B, C) - d(A, C)), 0.0),
+                         c = std::max(0.5 * (d(A, C) + d(B, C) - d(A, B)), 0.0);
+
+            Node *r = new Node();
+            tree->addNode(*r);
+            r->addNeighbor(*node_pool[A], a);
+            r->addNeighbor(*node_pool[B], b);
+            r->addNeighbor(*node_pool[C], c);
+        }
+
+        // If there were only two nodes in the matrix, operation is trivial
+        if (d.getSize() == 2) {
+            vector<string> OTUs;
+            for (auto &OTU : d.getOTUs()) {
+                OTUs.push_back(OTU);
+            }
+            
+            const string A = OTUs[0],
+                         B = OTUs[1];
+
+            Node *r = new Node();
+            tree->addNode(*r);
+            r->addNeighbor(*node_pool[A], d(A, B) / 2.0);
+            r->addNeighbor(*node_pool[B], d(A, B) / 2.0);
+        }
+
+        return *tree;
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
+
+
+
+////////////////////////////////////////////////////////////////////////
+// Support (local) functions
+static double d_XO(
+    const set<string> &in_X,
+    const set<string> &in_O,
+    const DistanceMatrix &d) {
+    const size_t N_X = in_X.size(),
+                 N_O = in_O.size();
+    double d_xo = 0.0;
+
+    for (auto &x : in_X) {
+        for (auto &o : in_O) {
+            d_xo += d(x, o);
+        }
+    }
+    d_xo /= (N_X * N_O);
+
+    return d_xo;
+}
+
+
+
+template <class T>
+set<T> set_union(const set<T> &A, const set<T> &B) {
+    set<T> C = A;
+    C.insert(B.begin(), B.end());
+    return C;
+}
+
+
+
+template <class T>
+set<T> set_difference(const set<T> &A, const set<T> &B) {
+    set<T> result;
+
+    std::set_difference(
+        A.begin(), A.end(), B.begin(), B.end(),
+        std::inserter(result, result.end())
+    );
+
+    return result;
+}
\ No newline at end of file
diff --git a/Phylo/Sources/FitchMargoliash.h b/Phylo/Sources/FitchMargoliash.h
new file mode 100644
index 0000000..dd06da8
--- /dev/null
+++ b/Phylo/Sources/FitchMargoliash.h
@@ -0,0 +1,58 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_FITCHMARGOLIASH_H_
+#define _VICTOR_PHYLO_FITCHMARGOLIASH_H_
+
+#include <ClusteringAlgorithm.h>
+#include <UnrootedTree.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements the Fitch-Margoliash clustering algorithm.
+ * 
+ * Implements Fitch-Margoliash as a functor.
+ * Fitch-Margoliash algorithm is a bottom-up agglomerative method for
+ * the creation of phylogenetic trees. This algorithm requires knowledge
+ * about the distance between each pair of taxa (e.g. species or
+ * sequences) in order to build the tree.
+ *
+ * For more information see:
+ * - Contruction of Phylogenetic Trees (Fitch and Margoliash)
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class FitchMargoliash: public ClusteringAlgorithm {
+ public:
+    /** @brief Destructor. */
+    ~FitchMargoliash();
+
+
+    
+    /** @brief Builds a phylogenetic tree from given distance matrix.
+     * @param[in]       matrix    Distance matrix
+     * @return Phylogenetic tree
+     */
+    virtual UnrootedTree &apply(const DistanceMatrix &matrix) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_FITCHMARGOLIASH_H_
\ No newline at end of file
diff --git a/Phylo/Sources/IdentityPercentage.cc b/Phylo/Sources/IdentityPercentage.cc
new file mode 100644
index 0000000..5c9ac3d
--- /dev/null
+++ b/Phylo/Sources/IdentityPercentage.cc
@@ -0,0 +1,64 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <IdentityPercentage.h>
+#include <Sequence.h>
+#include <SequenceData.h>
+#include <ScoringS2S.h>
+#include <NWAlign.h>
+
+namespace Victor {
+namespace Phylo {
+    IdentityPercentage::IdentityPercentage(
+        SubMatrix &matrix,
+        GapFunction &gap)
+    : substitution_matrix(matrix), gap_function(gap) {
+    }
+
+
+
+    IdentityPercentage::IdentityPercentage(const IdentityPercentage &origin)
+    : IdentityPercentage(origin.substitution_matrix, origin.gap_function) {
+    }
+
+
+
+    IdentityPercentage::~IdentityPercentage() {
+    }
+
+
+
+    double
+    IdentityPercentage::computeDistance(const string &seq1, const string &seq2) const {
+        return 1.0 - identityPercentage(seq1, seq2);
+    }
+
+
+
+    double
+    IdentityPercentage::identityPercentage(const string &seq1, const string &seq2) const {
+        AlignmentData *alignment_data = new SequenceData(2, seq1, seq2, "", "");
+        ScoringS2S    scoring_scheme(&substitution_matrix, alignment_data, nullptr, 1.0);
+        AlignmentBase alignment;
+
+        NWAlign align(alignment_data, &gap_function, &scoring_scheme);
+
+        vector<string> result = align.getMatch();
+
+        return alignment.calculatePairwiseIdentity(result[0], result[1]);
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/IdentityPercentage.h b/Phylo/Sources/IdentityPercentage.h
new file mode 100644
index 0000000..6192aba
--- /dev/null
+++ b/Phylo/Sources/IdentityPercentage.h
@@ -0,0 +1,87 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_
+#define _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_
+
+#define _GLIBCXX_IOMANIP
+#include <DistanceMatrixBuilder.h>
+#include <SubMatrix.h>
+#include <GapFunction.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Builds a distance matrix by considering percentage of identity.
+ *
+ * Compute pairwise alignment for every pair of sequences, then creates
+ * the distance matrix using percentage of identity. The distance is
+ * estimated as 1 - % of identity.
+ * Percentage of identity is defined as the number of identical residues
+ * (not considering gaps) divided by the length of the longest sequence
+ * (not considering gaps).
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class IdentityPercentage: public DistanceMatrixBuilder {
+ public:
+ 	/** @brief Builds an identity percentage metrics with given configuration.
+ 	 *
+ 	 * Stores information about wich subsitution matrix to use (example:
+     * PAM260, BLOSUM50...) and which gap function to use.
+ 	 * @param[in]       matrix    Substitution matrix to use
+ 	 * @param[in]       gap       Gap function to use
+ 	 */
+ 	explicit IdentityPercentage(SubMatrix &matrix, GapFunction &gap);
+
+    /** @brief Copy constructor.
+     * @param[in]       origin    Original object
+     */
+    explicit IdentityPercentage(const IdentityPercentage &origin);
+
+    /** @brief Destructor. */
+    virtual ~IdentityPercentage();
+
+
+
+ private:
+ 	SubMatrix   &substitution_matrix;   ///< Substitution matrix
+ 	GapFunction &gap_function;          ///< Gap function
+
+
+    /** @brief Returns distance between two sequences.
+     * @param[in]       seq1      First sequence
+     * @param[in]       seq2      Second sequence
+     * @return Distance between seq1 and seq2
+     */
+    virtual double computeDistance(const string &seq1, const string &seq2) const;
+
+ 	/** @brief Returns percentage of identity between two sequences.
+ 	 *
+ 	 * Percentage of identity is returned as a number in [0; 1].
+ 	 * @param[in]       seq1      First sequence
+ 	 * @param[in]       seq2      Second sequence
+ 	 * @return Percentage of identity between seq1 and seq2
+ 	 */
+ 	double identityPercentage(const string &seq1, const string &seq2) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/LevenshteinDistance.cc b/Phylo/Sources/LevenshteinDistance.cc
new file mode 100644
index 0000000..d3b141f
--- /dev/null
+++ b/Phylo/Sources/LevenshteinDistance.cc
@@ -0,0 +1,62 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <LevenshteinDistance.h>
+
+namespace Victor {
+namespace Phylo {
+    LevenshteinDistance::~LevenshteinDistance() {
+    }
+
+
+
+    double
+    LevenshteinDistance::computeDistance(const string &seq1, const string &seq2) const {
+        const size_t m = seq1.size();
+        const size_t n = seq2.size();
+
+        if (m == 0) return n;
+        if (n == 0) return m;
+
+        size_t *costs = new size_t[n + 1];
+
+        // Initializes cost vector
+        for (size_t k = 0; k <= n; k++)
+            costs[k] = k;
+
+        // Computes distances
+        for (size_t i = 0; i < m; i++) {
+            size_t corner = i;
+            costs[0] = i + 1;
+
+            for (size_t j = 0; j < n; j++) {
+                size_t upper = costs[j + 1];
+
+                costs[j + 1] = (seq1[i] == seq2[j])
+                             ? corner
+                             : min(costs[j], min(upper, corner)) + 1;
+                
+                corner = upper;
+            }
+        }
+
+        double distance = (double) costs[n];
+        delete [] costs;
+
+        return distance;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/LevenshteinDistance.h b/Phylo/Sources/LevenshteinDistance.h
new file mode 100644
index 0000000..cf310a1
--- /dev/null
+++ b/Phylo/Sources/LevenshteinDistance.h
@@ -0,0 +1,53 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_
+#define _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_
+
+#include <DistanceMatrixBuilder.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Builds a distance matrix by considering Levenshtein distance.
+ *
+ * Compute pairwise alignment for every pair of sequences, then creates
+ * the distance matrix using Levenshtein distance.
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class LevenshteinDistance: public DistanceMatrixBuilder {
+ public:
+    /** @brief Destructor. */
+    virtual ~LevenshteinDistance();
+
+
+
+ private:
+    /** @brief Returns distance between two sequences.
+     * @param[in]       seq1      First sequence
+     * @param[in]       seq2      Second sequence
+     * @return Distance between seq1 and seq2
+     */
+    virtual double computeDistance(const string &seq1, const string &seq2) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/Makefile b/Phylo/Sources/Makefile
new file mode 100644
index 0000000..4a75531
--- /dev/null
+++ b/Phylo/Sources/Makefile
@@ -0,0 +1,68 @@
+#--*-makefile-*-----------------------------------------------------------------
+#
+#   Standard makefile - Phylo
+#
+#-------------------------------------------------------------------------------
+
+# Path to project directory
+PROJECT_ROOT = ../..
+BINPATH      = $(PROJECT_ROOT)/bin/
+LIBPATH      = $(PROJECT_ROOT)/lib/
+UPDIR        = $(PROJECT_ROOT)
+SUBDIR       = 
+
+
+
+#
+# Libraries and paths (which are not defined globally)
+#
+
+LIBS     =
+INC_PATH = -I.
+LIB_PATH = -L.
+
+
+
+#
+# Objects and headers
+#
+
+SOURCES = PhylogeneticTree.cc RootedTree.cc UnrootedTree.cc NewickParser.cc \
+          Sequence.cc AminoAcid.cc SubstitutionMatrix.cc \
+          DistanceMatrix.cc DistanceMatrixBuilder.cc \
+          IdentityPercentage.cc LevenshteinDistance.cc FengDoolittleDistance.cc \
+          FitchMargoliash.cc UPGMA.cc NJ.cc \
+          MultipleAlignment.cc \
+          FengDoolittle.cc ClustalW.cc
+OBJECTS = PhylogeneticTree.o RootedTree.o UnrootedTree.o NewickParser.o \
+          Sequence.o AminoAcid.o SubstitutionMatrix.o \
+          DistanceMatrix.o DistanceMatrixBuilder.o \
+          IdentityPercentage.o LevenshteinDistance.o FengDoolittleDistance.o \
+          FitchMargoliash.o UPGMA.o NJ.o \
+          MultipleAlignment.o \
+          FengDoolittle.o ClustalW.o
+TARGETS = 
+EXECS   = 
+LIBRARY = libPhylo.a
+
+
+
+#
+# Install rule
+#
+
+compile: all
+
+all: install
+install: $(LIBRARY) $(TARGETS)
+	mv $(LIBRARY) $(LIBPATH)
+
+
+
+#
+# Call global Makefile to do the job
+#
+include ../../Makefile.global
+
+# Overriding to use C++11
+STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c
diff --git a/Phylo/Sources/MultipleAlignment.cc b/Phylo/Sources/MultipleAlignment.cc
new file mode 100644
index 0000000..a3ffa61
--- /dev/null
+++ b/Phylo/Sources/MultipleAlignment.cc
@@ -0,0 +1,360 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#define HYDROPHILIC_RANGE 5
+#define HYDROPHILIC_RESIDUES "DEGKNQPRS"
+#include <MultipleAlignment.h>
+#include <algorithm>
+
+/** @brief Tells whether a residue is a hydrophiic residue.
+ * @param[in]           residue   Residue to check
+ * @retval true         Residue is hydrophilic
+ * @retval false        Residue is not hydrophilic
+ */
+static bool is_hydrophiic_residue(const char residue) {
+    for (char r : HYDROPHILIC_RESIDUES) {
+        if (residue == r) {
+            return true;
+        }
+    }
+
+    return false;
+}
+
+
+
+/** @brief Tells whether a sequence has a hydrophilic stretch.
+ * @param[in]           sequence  Sequence to check
+ * @param[in]           position  Position to check
+ * @retval true         The sequence has a hydrophilic stretch
+ * @retval false        The sequence has not hydrophilic stretches
+ */
+static bool has_hydrophilic_stretch(const string &sequence, const size_t position) {
+    size_t start = position - HYDROPHILIC_RANGE,
+           end   = position + HYDROPHILIC_RANGE;
+    bool found = false;
+
+    if (start > sequence.size()) start = 0;
+    if (end   > sequence.size()) end   = 0;
+
+    bool previous = false;
+    size_t p = start, consecutives = 0;
+    while (!found && p < end) {
+        if (is_hydrophiic_residue(sequence[p])) {
+            if (previous) {
+                consecutives++;
+            }
+            previous = true;
+        } else {
+            consecutives = 0;
+            previous = false;
+        }
+
+        found = consecutives == HYDROPHILIC_RANGE;
+        p++;
+    }
+
+    return found;
+}
+
+
+
+namespace Victor {
+namespace Phylo {
+    const string MultipleAlignment::residues = "ARNDCQEGHILKMFPSTWYVUBZX-";
+
+
+    MultipleAlignment::MultipleAlignment(const vector<Sequence> &sequences)
+    : sequences(sequences) {
+    }
+
+
+
+    MultipleAlignment::MultipleAlignment(const Sequence &sequence) {
+        sequences.push_back(sequence);
+    }
+
+
+
+    MultipleAlignment::MultipleAlignment() {
+        MultipleAlignment(vector<Sequence>());
+    }
+
+
+
+    MultipleAlignment::~MultipleAlignment() {
+    }
+
+
+
+    void
+    MultipleAlignment::operator=(const MultipleAlignment &other) {
+        sequences = other.sequences;
+    }
+
+
+
+    bool
+    MultipleAlignment::isEmpty() const {
+        return getSize() == 0;
+    }
+
+
+
+    bool
+    MultipleAlignment::hasSequence(const string &identifier) const {
+        return getSequence(identifier) < getSize();
+    }
+
+
+
+    bool
+    MultipleAlignment::hasHydrophilicStretch(const size_t position) const {
+        bool found = false;
+
+        size_t i = 0;
+        while (!found && i < getSize()) {
+            const string &sequence = getSequence(i).getResidues();
+            found = has_hydrophilic_stretch(sequence, position);
+            i++;
+        }
+
+        return found;
+    }
+
+
+
+    size_t
+    MultipleAlignment::getSize() const {
+        return sequences.size();
+    }
+
+
+
+    size_t
+    MultipleAlignment::getLength() const {
+        return (!isEmpty()) ? getSequence(0).getResidues().size() : 0;
+    }
+
+
+
+    Sequence
+    MultipleAlignment::getSequence(const size_t index) const {
+        return (index < getSize()) ? sequences[index] : Sequence("", "");
+    }
+
+
+
+    size_t
+    MultipleAlignment::getSequence(const string &identifier) const {
+        size_t index = 0;
+
+        for (index = 0; index < getSize(); index++) {
+            if (getSequence(index).getIdentifier() == identifier) {
+                return index;
+            }
+        }
+
+        return index;
+    }
+
+
+
+    string
+    MultipleAlignment::getResidues(const size_t position) const {
+        char *s = new char[getSize()];
+        size_t idx = 0;
+
+        if (position < getLength()) {
+            for (auto &sequence : sequences) {
+                s[idx++] = sequence.getResidue(position);
+            }
+        }
+
+        string result(s);
+        delete [] s;
+        return result;
+    }
+
+
+
+    size_t
+    MultipleAlignment::getResiduesNumber(const size_t position) const {
+        return getResidues(position).size();
+    }
+
+
+
+    size_t
+    MultipleAlignment::getNonGapNumber(const size_t position) const {
+        return getResiduesNumber(position) - getGapNumber(position);
+    }
+
+
+
+    size_t
+    MultipleAlignment::getGapNumber(const size_t position) const {
+        return getCount('-', position);
+    }
+
+
+
+    size_t
+    MultipleAlignment::getCount(
+        const char residue,
+        const size_t position) const {
+        size_t count = 0;
+        
+        for (auto &sequence : sequences) {
+            count += sequence.getResidue(position) == residue;
+        }
+        
+        return count;
+    }
+
+
+
+    double
+    MultipleAlignment::getFrequency(
+        const char residue,
+        const size_t position) const {
+        return (getResiduesNumber(position) != 0)
+             ? (double) getCount(residue, position) / (double) getResiduesNumber(position)
+             : 0.0;
+    }
+
+
+
+    map<char, double> &
+    MultipleAlignment::getFrequencies(const size_t position) const {
+        map<char, double> *frequencies = new map<char, double>();
+
+        for (char residue : residues) {
+            (*frequencies)[residue] = getFrequency(residue, position);
+        }
+
+        return *frequencies;
+    }
+
+
+
+    double
+    MultipleAlignment::getPercentIdentity() const {
+        size_t conserved = 0;
+
+        for (size_t j = 0; j < getSize(); j++) {
+            const string column = getResidues(j);
+            size_t i            = 1;
+            bool is_conserved   = true;
+            while (is_conserved && i < getSize()) {
+                is_conserved &= column[i] == column[0];
+                i++;
+            }
+            conserved += is_conserved ? 1 : 0;
+        }
+
+        return (double) conserved / getLength();
+    }
+
+
+
+    char
+    MultipleAlignment::getConsensus(const size_t position) const {
+        char consensus   = '-';
+        size_t max_count = 0;
+
+        for (char residue : residues) {
+            if (residue == '-') continue;
+            const size_t count = getCount(residue, position);
+
+            if (count > max_count) {
+                max_count = count;
+                consensus = residue;
+            }
+        }
+
+        return consensus;
+    }
+
+    
+
+    string &
+    MultipleAlignment::getConsensus() const {
+        string *consensus = new string();
+
+        for (size_t i = 0; i < getLength(); i++) {
+            (*consensus) += getConsensus(i);
+        }
+
+        return *consensus;
+    }
+
+
+
+    string &
+    MultipleAlignment::asString() const {
+        size_t longest_name = 0;
+        string *result = new string();
+        vector<string> names(getSize());
+        vector<size_t> positions(getSize());
+
+        // Finds longest name of sequence
+        for (size_t i = 0; i < getSize(); i++) {
+            const size_t length = getSequence(i).getIdentifier().size();
+            longest_name = std::max(longest_name, length);
+        }
+
+        // Pads names
+        for (size_t i = 0; i < getSize(); i++) {
+            const string identifier = getSequence(i).getIdentifier();
+            string name             = identifier;
+            for (size_t j = identifier.size(); j < longest_name; j++) {
+                name += " ";
+            }
+            name += "    ";
+            names[i] = name;
+        }
+
+        // Prints data
+        for (size_t j = 0; j < getLength(); j += 50) {
+            for (size_t i = 0; i < getSize(); i++) {
+                bool print_positions = false;
+                (*result) += names[i];
+                for (size_t k = 0; k < 50 && j + k < getLength(); k++) {
+                    const char symbol = getSequence(i).getResidues()[j + k];
+                    (*result)       += symbol;
+                    positions[i]    += (symbol != '-');
+                    print_positions |= (symbol != '-');
+                }
+                if (print_positions) {
+                    (*result) += " " + to_string(positions[i]);
+                }
+                (*result) += "\n";
+            }
+            (*result) += "\n\n";
+        }
+
+        return *result;
+    }
+
+
+
+    void
+    MultipleAlignment::saveClustalW(ostream &output) const {
+        output << asString() << endl;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/MultipleAlignment.h b/Phylo/Sources/MultipleAlignment.h
new file mode 100644
index 0000000..ad6538e
--- /dev/null
+++ b/Phylo/Sources/MultipleAlignment.h
@@ -0,0 +1,225 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_
+#define _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_
+
+#include <string>
+#include <vector>
+#include <map>
+#include <Sequence.h>
+
+using std::string;
+using std::pair;
+using std::vector;
+using std::map;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief A multiple sequence alignment (MSA).
+ *
+ * MSAs holds information about alignments of a set of sequences.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class MultipleAlignment {
+public:
+    /** @brief Builds an MSA from a set of sequences.
+     * @param[in]       sequences Sequences in the MSA
+     */
+    explicit MultipleAlignment(const vector<Sequence> &sequences);
+
+    /** @brief Builds an MSA from a single sequence.
+     * @param[in]       sequence  Sequence
+     */
+    explicit MultipleAlignment(const Sequence &sequence);
+
+    /** @brief Default constructor.
+     *
+     * Produces an empty MSA.
+     */
+    MultipleAlignment();
+
+    /** @brief Destructor. */
+    ~MultipleAlignment();
+
+
+
+    /** @brief Assignment operator.
+     * @param[in]       other     MultipleAlignment to copy
+     */
+    void operator=(const MultipleAlignment &other);
+
+
+
+    /** @brief Tells whether the MSA is empty.
+     *
+     * An MSA is empty when it contains no sequences.
+     * @retval true     This MSA is empty
+     * @retval false    This MSA is not empty
+     */
+    bool isEmpty() const;
+
+    /** @brief Tells whether this MSA contains a sequence with given identifier.
+     * @param[in]       identifier An identifier
+     * @retval true     This MSA contains data about given sequence
+     * @retval false    This MSA does not contain data about given sequence
+     */
+    bool hasSequence(const string &identifier) const;
+
+    /** @brief Tells whether this MSA has a hydrophilic stretch.
+     * @param[in]       position  Position to check
+     * @retval true     This MSA contains a hydrophilic stretch
+     * @retval false     This MSA does not contain a hydrophilic stretch
+     */
+    bool hasHydrophilicStretch(const size_t position) const;
+
+
+
+    /** @brief Returns number of sequences in this MSA.
+     * @return Number of sequences in this MSA.
+     */
+    size_t getSize() const;
+
+    /** @brief Returns length of the MSA.
+     *
+     * The length of an MSA is the length of its sequences (including gaps).
+     * Every sequence has the same length, by construction.
+     * @return Length of this multiple alignment
+     */
+    size_t getLength() const;
+
+    /** @brief Returns sequence at given index.
+     * 
+     * If index is invalid, returns an empty sequence.
+     * @param[in]       index     Index of the sequence
+     * @return Sequence at given index
+     */
+    Sequence getSequence(const size_t index) const;
+
+    /** @brief Returns index of given sequence.
+     *
+     * Searches a sequence with given identifier and returns its index in this
+     * MSA. If sequence is not found, returns an invalid index (greater than
+     * or equal to the size of this MSA).
+     * @param[in]       identifier Identifier of the sequence
+     * @return Index of the found sequence, or an invalid position
+     */
+    size_t getSequence(const string &identifier) const;
+
+    /** @brief Returns residues at given position.
+     *
+     * Returns a string containing residues (or gaps) at given column of this
+     * MSA.
+     *
+     * If position is invalid, returns an empty string.
+     * @param[in]       position  Index of the columng.
+     * @return Residues at given position
+     */
+    string getResidues(const size_t position) const;
+
+    /** @brief Returns number of residues (or gaps) at given position.
+     *
+     * If position is invalid, returns 0.
+     * @param[in]       position  Index of the column
+     * @return Number of residues at given column of this MSA
+     */
+    size_t getResiduesNumber(const size_t position) const;
+
+    /** @brief Returns number of non-gaps at given position.
+     *
+     * If position is invalid, returns 0.
+     * @param[in]       position  Index of the column
+     * @return Number of non-gaps at given column of this MSA
+     */
+    size_t getNonGapNumber(const size_t position) const;
+
+    /** @brief Returns number of gaps at given position.
+     *
+     * If position is invalid, returns 0.
+     * @param[in]       position  Index of the column
+     * @return Number of gaps at given column of this MSA
+     */
+    size_t getGapNumber(const size_t position) const;
+
+    /** @brief Returns number of occurencies of given residues at given position.
+     *
+     * If residue or position are invalid, returns 0.
+     * @param[in]       residue  Residue to find
+     * @param[in]       position  Index of the column
+     * @return Number of occurencies of given residue at given position
+     */
+    size_t getCount(const char residue, const size_t position) const;
+
+    /** @brief Returns frequency of given residue at given position.
+     *
+     * If residue or position are invalid, returns 0.
+     * @param[in]       residue  Residue to find
+     * @param[in]       position  Index of the column
+     * @return Frequency of given residue at given position
+     */
+    double getFrequency(const char residue, const size_t position) const;
+
+    /** @brief Returns the map of frequencies for given position.
+     *
+     * Keys of the map are residues (or gap), values are their frequencies.
+     * 
+     * If position is invalid, frequencies in the map are 0.
+     * @param[in]       position  Index of the column
+     * @return Map of frequencies
+     */
+    map<char, double> &getFrequencies(const size_t position) const;
+
+    /** @brief Returns percent identity of this multiple alignment.
+     * @return Percent identity
+     */
+    double getPercentIdentity() const;
+
+    /** @brief Returns consensus residue.
+     * @param[in]       position  Position to use
+     * @return Consensus
+     */
+    char getConsensus(const size_t position) const;
+
+    /** @brief Returns consensus sequence.
+     * @return Consensus
+     */
+    string &getConsensus() const;
+
+
+
+    /** @brief Returns a string version of this multiple alignment.
+     * @return This multiple sequence alignment as a string
+     */
+    string &asString() const;
+
+    /** @brief Exports this multiple sequence alignment.
+     * @param[out]      output    Stream to write output to
+     */
+    void saveClustalW(ostream &output) const;
+
+
+
+private:
+    static const string residues;     ///< Every possible residue
+    vector<Sequence> sequences;  ///< Sequences in the MSA
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_
\ No newline at end of file
diff --git a/Phylo/Sources/MultipleAlignmentAlgorithm.h b/Phylo/Sources/MultipleAlignmentAlgorithm.h
new file mode 100644
index 0000000..bdf9b78
--- /dev/null
+++ b/Phylo/Sources/MultipleAlignmentAlgorithm.h
@@ -0,0 +1,61 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_
+#define _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_
+
+#include <MultipleAlignment.h>
+#include <AlignmentBase.h>
+
+using namespace Victor::Align2;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a multiple sequence alignment algorithm.
+ *
+ * Multiple sequence alignment (MSA) algorithms produce MSAs by considering
+ * a set of sequences.
+ *
+ * MSA algorithms are implemented as functors from an alignment to a MSA.
+ *
+ * This class follows the Strategy and the Facade Design Patterns.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class MultipleAlignmentAlgorithm {
+ public:
+    /** @brief  Builds an MSA from an alignment.
+     * @param[in]       alignment The alignment
+     * @return Multiple sequence alignment
+     */
+    inline MultipleAlignment &operator()(const AlignmentBase &alignment) {
+        return apply(alignment);
+    }
+
+
+    
+    /** @brief  Builds an MSA from an alignment.
+     * @param[in]       alignment The alignment
+     * @return Multiple sequence alignment
+     */
+    virtual MultipleAlignment &apply(const AlignmentBase &alignment) const = 0;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_
\ No newline at end of file
diff --git a/Phylo/Sources/NJ.cc b/Phylo/Sources/NJ.cc
new file mode 100644
index 0000000..d52ed0b
--- /dev/null
+++ b/Phylo/Sources/NJ.cc
@@ -0,0 +1,115 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+                        
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <NJ.h>
+
+using std::max;
+
+namespace Victor {
+namespace Phylo {
+    typedef UnrootedTree::Node Node;
+
+
+    NJ::~NJ() {
+    }
+
+    
+    
+    UnrootedTree &
+    NJ::apply(const DistanceMatrix &matrix) const {
+        UnrootedTree *tree = new UnrootedTree();
+        DistanceMatrix d = matrix;
+        set<string> OTUs = matrix.getOTUs();
+        map<string, Node *> node_pool;
+
+
+        // Initializes leaves
+        for (auto OTU : OTUs) {
+            Node *leaf = new Node(OTU);
+            node_pool[OTU] = leaf;
+            tree->addNode(*leaf);
+        }
+
+
+        // Repeats until every element in the matrix is consumed
+        while (!d.isEmpty()) {
+            // Calculates matrix Q, based on current distance matrix
+            DistanceMatrix Q;
+            OTUs = d.getOTUs();
+            const size_t n = OTUs.size();
+            for (auto i : OTUs) {
+                Q.addOTU(i);
+                for (auto j : OTUs) {
+                    if (i == j) continue;
+                    double q_ij, d_ik = 0.0, d_jk = 0.0;
+                    for (auto k : OTUs){
+                        d_ik += d(i, k);
+                        d_jk += d(j, k);
+                    }
+
+                    q_ij = (n - 2) * d(i, j) - d_ik - d_jk;
+                    q_ij = q_ij;
+                    Q(i, j, q_ij);
+                }
+            }
+
+
+            // Finds f, g such that Q(f, g) is minimum (i != j), then
+            // joins them to a new node u
+            const pair<string, string> min_pos = Q.getMinimumPosition();
+            const string f = min_pos.first,
+                         g = min_pos.second,
+                         u = f  + "+" + g;
+            Node *node = new Node();
+            node_pool[u] = node;
+            tree->addNode(*node);
+
+
+            // Calculates distances between new node and merged ones. If
+            // there are only two nodes left, operation is trivial
+            if (2 == n) {
+                node->addNeighbor(*node_pool[f], d(f, g) / 2.0);
+                node->addNeighbor(*node_pool[g], d(f, g) / 2.0);
+            } else {
+                double delta_fu, delta_gu, d_fk = 0.0, d_gk = 0.0;;
+                for (auto k : OTUs) {
+                    d_fk += d(f, k);
+                    d_gk += d(g, k);
+                }
+                delta_fu = max(0.5 * d(f, g) + (1.0 / (2.0 * (n - 2))) * (d_fk - d_gk), 0.0);
+                delta_gu = max(d(f, g) - delta_fu, 0.0);
+                node->addNeighbor(*node_pool[f], delta_fu);
+                node->addNeighbor(*node_pool[g], delta_gu);
+            }
+
+
+            // Calculates distances from each OTU to the new node
+            for (auto k : OTUs) {
+                double d_uk = 0.5 * (d(f, k) + d(g, k) - d(f, g));
+                d(u, k, d_uk);
+            }
+
+
+            // Removes "consumed" OTUs and adds newly generated one
+            d.removeOTU(f)
+             .removeOTU(g)
+             .addOTU(u);
+        }
+
+        return *tree;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/NJ.h b/Phylo/Sources/NJ.h
new file mode 100644
index 0000000..f8cc86c
--- /dev/null
+++ b/Phylo/Sources/NJ.h
@@ -0,0 +1,59 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_NJ_H_
+#define _VICTOR_PHYLO_NJ_H_
+
+#include <ClusteringAlgorithm.h>
+#include <UnrootedTree.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements the NJ algorithm.
+ *
+ * Implements NJ as a functor.
+ * NJ (Neighbor Joining) is a bottom-up agglomerative clustering method
+ * for the creation of phylogenetic trees. This algorithm requires
+ * knowledge about the distance between each pair of taxa (e.g., species
+ * or sequences) to form the tree.
+ * 
+ * For more information see:
+ * - The Neighbor-joining Method: A New Method for Reconstructing
+ *   Phylogenetic Trees (Saitou and Nei)
+ * 
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class NJ: public ClusteringAlgorithm {
+ public:
+    /** @brief Destructor. */
+    virtual ~NJ();
+
+
+    
+    /** @brief Builds a phylogenetic tree from given distance matrix.
+     * @param[in]       matrix    Distance matrix
+     * @return Phylogenetic tree
+     */
+    virtual UnrootedTree &apply(const DistanceMatrix &matrix) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_NJ_
\ No newline at end of file
diff --git a/Phylo/Sources/NewickParser.cc b/Phylo/Sources/NewickParser.cc
new file mode 100644
index 0000000..b0c8afc
--- /dev/null
+++ b/Phylo/Sources/NewickParser.cc
@@ -0,0 +1,261 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <NewickParser.h>
+
+#define SYNTAX_ERROR -1
+
+using std::stringstream;
+
+namespace Victor {
+namespace Phylo {
+    static const double NA = -1.0;
+
+
+    NewickParser::~NewickParser() {
+    }
+
+
+    
+    bool
+    NewickParser::isEmpty() const {
+        return input.empty();
+    }
+
+
+
+    bool
+    NewickParser::isNext(string character_set) const {
+        bool is_next = false;
+
+        if (isEmpty()) {
+            return false;
+        }
+
+        for (auto c : character_set) {
+            is_next |= c == input[0];
+        }
+
+        return is_next;
+    }
+
+
+
+    char
+    NewickParser::getNext() const {
+        return (!isEmpty()) ? input[0] : '\0';
+    }
+
+
+
+    char
+    NewickParser::shift() {
+        char c = getNext();
+
+        if (!isEmpty()){
+            input = input.substr(1);
+        }
+
+        return c;
+    }
+
+
+
+    void
+    NewickParser::error(const string &message) const {
+        std::cerr << "[Victor::Phylo::NewickParser Syntax error]: "
+                  << message
+                  << " near: \"" << input << "\""
+                  << std::endl;
+        exit(SYNTAX_ERROR);
+    }
+
+
+
+    RootedTree &
+    NewickParser::parse(const string &input) {
+        this->input = input;
+        return parseNewick();
+    }
+
+
+
+    RootedTree &
+    NewickParser::parseNewick() {
+        RootedTree *newick;
+
+        // Empty Newick file
+        if (isNext(";")) {
+            newick = new RootedTree();
+        }
+
+        // Recursvely parses file
+        else {
+            newick = parseTree();
+        }
+
+        // Consumes ";" and checks for errors.
+        shift();
+        if (!isEmpty()) {
+            error("Stray character after last character");
+        }
+
+        return *newick;
+    }
+
+
+
+    RootedTree *
+    NewickParser::parseTree() {
+         RootedTree *node;
+
+        // Subtree
+        if (isNext("(")) {
+            vector<RootedTree *> children;
+
+            shift();
+            children.push_back(parseTree());
+            parseSiblings(&children);
+            shift();
+            node = parseNode();
+            
+            for (auto child : children) {
+                node->addChild(*child);
+            }
+        }
+
+        // Length only
+        else if (isNext(":")) {
+            double length = parseLength();
+            node = new RootedTree(length);
+        }
+
+        // Label and length
+        else {
+            string label = parseString();
+            double length = parseLength();
+
+            node = (length != NA)
+                 ? new RootedTree(length, label)
+                 : new RootedTree(label);
+        }
+
+        return node;
+    }
+
+
+
+    void
+    NewickParser::parseSiblings(vector<RootedTree *> *siblings) {
+        // No more siblings
+        if (isNext(")")) {
+            return;
+        }
+
+        // One more sibling
+        else if (isNext(",")) {
+            shift();
+            siblings->push_back(parseTree());
+            parseSiblings(siblings);
+            return;
+        }
+
+        // Syntax error
+        else {
+            error("Error while parsing siblings");
+        }
+    }
+
+
+
+    RootedTree *
+    NewickParser::parseNode() {
+        string label = parseLabel();
+        double length = parseLength();
+        RootedTree *node = (length != NA)
+                         ? new RootedTree(length, label)
+                         : new RootedTree(label);
+        return node;
+    }
+
+
+
+    string
+    NewickParser::parseLabel() {
+        return (!isNext(";):,")) ? parseString() : "";
+    }
+
+
+
+    double
+    NewickParser::parseLength() {
+        // A length is specified
+        if (isNext(":")) {
+            shift();
+            return parseNumber();
+        }
+
+        // No length is specified
+        else if (isNext(";),")) {
+            return NA;
+        }
+
+        // Syntax error
+        else {
+            error("Error while parsing number");
+            return NA;
+        }
+    }
+
+
+
+    string
+    NewickParser::parseString() {
+        string buffer = "";
+
+        // String is enclosed by double quotes
+        if (isNext("\"")) {
+            shift();
+            while (!isEmpty() && !isNext("\"")) {
+                buffer += shift();
+            }
+            shift();
+        }
+
+        // String is not enclosed by double quotes
+        else {
+            while (!isEmpty() && !isNext("):, ;")) {
+                buffer += shift();
+            }
+        }
+
+        return buffer;
+    }
+
+
+
+    double
+    NewickParser::parseNumber() {
+        char *ptr;
+        double length = strtod(input.c_str(), &ptr);
+
+        input = string(ptr);
+
+        return length;
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/NewickParser.h b/Phylo/Sources/NewickParser.h
new file mode 100644
index 0000000..8a5ab5f
--- /dev/null
+++ b/Phylo/Sources/NewickParser.h
@@ -0,0 +1,145 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_NEWICKPARSER_H_
+#define _VICTOR_PHYLO_NEWICKPARSER_H_
+
+#include <RootedTree.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a parser for the Newick format.
+ * 
+ * This parser recognizes the following LL(1) grammar:
+ * \verbatim
+ Newick   ::= Tree;
+            | ;
+ Tree     ::= (Tree Siblings) Node
+            | string Length
+            | :number
+ Siblings ::= , Tree Siblings
+            | 
+ Node     ::= Label Length
+ Label    ::= string
+            | 
+ Length   ::= :number
+            |
+ \endverbatim
+ * Where string represents any alphanumeric sequence or any sequence
+ * of characters enclosed by double quotes, and number represents a
+ * floating point number.
+ * 
+ * @note There is no official newick grammar. The one proposed here was
+ * built with reverse engeneering techniques.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class NewickParser {
+ public:
+    /** @brief Destructor. */
+    virtual ~NewickParser();
+
+
+    
+    /** @brief Parses a Newick string.
+     * @param[in]       input     Input string
+     * @return Rooted tree
+     */
+    RootedTree &parse(const string &input);
+
+
+
+ private:
+    string input;       ///< Input string
+
+
+    /** @brief Tells whether input string is empty.
+     * @retval true     Input string is empty
+     * @retval false    Input string is not empty
+     */
+    bool isEmpty() const;
+
+    /** @brief tells whether next input character belong to given set.
+     * @param[in]       character_set Set of characters (as string)
+     * @retval True if next character belongs to given set
+     * @retval False if next character does not belong to given set
+     */
+    bool isNext(string character_set = "") const;
+
+    /** @brief Returns next character in the input string.
+     * @retval Next character from input string
+     */
+    char getNext() const;
+
+    /** @brief Consumes first input character.
+     *
+     * Removes first character from input and returns it.
+     * @retval Next input character
+     */
+    char shift();
+
+    /** @brief Reports a parsing error and exits. */
+    void error(const string &message = "Unknown error") const;
+
+    /** @brief Parses a Newick file.
+     * @return Rooted tree encoded by the Newick file
+     */
+    RootedTree &parseNewick();
+
+    /** @brief Parses a tree.
+     * @return Rooted tree
+     */
+    RootedTree *parseTree();
+
+    /** @brief Parses siblings (sub)trees.
+     * @param[in, out]  siblings  Siblings parsed so far
+     */
+    void parseSiblings(vector<RootedTree *> *siblings);
+
+    /** @brief Parses a node.
+     * @return Node of a rooted tree
+     */
+    RootedTree *parseNode();
+
+    /** @brief Parses a label.
+     * @return Label of the node
+     */
+    string parseLabel();
+
+    /** @brief Parses an arc length.
+     * @return Arc length
+     */
+    double parseLength();
+
+    /** @brief Parses a string.
+     *
+     * Strings may be either spaces-free sequences of character or any
+     * sequence of character enclosed by double quotes.
+     * @return String
+     */
+    string parseString();
+
+    /** @brief Parses a number.
+     * @return Number (floating point)
+     */
+    double parseNumber();
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_NEWICKPARSER_H_
\ No newline at end of file
diff --git a/Phylo/Sources/PhylogeneticAlgorithm.h b/Phylo/Sources/PhylogeneticAlgorithm.h
new file mode 100644
index 0000000..7ed353b
--- /dev/null
+++ b/Phylo/Sources/PhylogeneticAlgorithm.h
@@ -0,0 +1,37 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_PHYLOGENETICALGORITHM_H_
+#define _VICTOR_PHYLO_PHYLOGENETICALGORITHM_H_
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a phylogenetic algorithm.
+ *
+ * Phylogenetic algorithms produce phylogenetic trees by aggregating,
+ * clustering and/or optimizing informations about alignments, profiles,
+ * etc..
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class PhylogeneticAlgorithm {
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_PHYLOGENETICALGORITHM_
\ No newline at end of file
diff --git a/Phylo/Sources/PhylogeneticTree.cc b/Phylo/Sources/PhylogeneticTree.cc
new file mode 100644
index 0000000..9f6c9b5
--- /dev/null
+++ b/Phylo/Sources/PhylogeneticTree.cc
@@ -0,0 +1,51 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <PhylogeneticTree.h>
+#include <sstream>
+
+using std::stringstream;
+
+namespace Victor {
+namespace Phylo {
+    PhylogeneticTree::~PhylogeneticTree() {
+    }
+
+
+
+    void
+    PhylogeneticTree::loadNewick(const istream &input) {
+        stringstream buffer;
+        buffer << input.rdbuf();
+        parseNewick(buffer.str());
+    }
+
+
+
+    void
+    PhylogeneticTree::saveNewick(ostream &output) const {
+        output << asNewick() << ";";
+    }
+
+
+
+    PhylogeneticTree &
+    PhylogeneticTree::accept(Visitor &visitor) {
+        visitor.visit(*this);
+        return *this;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/PhylogeneticTree.h b/Phylo/Sources/PhylogeneticTree.h
new file mode 100644
index 0000000..383558a
--- /dev/null
+++ b/Phylo/Sources/PhylogeneticTree.h
@@ -0,0 +1,104 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_PHYLOGENETICTREE_H_
+#define _VICTOR_PHYLO_PHYLOGENETICTREE_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>
+#include <DistanceMatrix.h>
+#include <Visitor.h>
+
+using std::istream;
+using std::ostream;
+using std::string;
+using std::vector;
+
+namespace Victor {
+namespace Phylo {
+
+// Forward declaration
+class RootedTree;
+class UnrootedTree;
+
+/** @brief A phylogenetic tree.
+ *
+ * A phylogenetic tree is a tree where every node may have a label, and
+ * arcs have a length.
+ * 
+ * This class follows the Visitor Design Pattern and uses Method
+ * Cascading (through Method Chaining).
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class PhylogeneticTree {
+ public:
+    /** @brief Destructor. */
+    virtual ~PhylogeneticTree();
+
+
+    
+    /** @brief Returns matrix of distances among leaves.
+     * @return Distance matrix
+     */
+    virtual DistanceMatrix &getDistanceMatrix() const = 0;
+
+    /** @brief Returns a rooted version of this tree.
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &asRootedTree() const = 0;
+
+    /** @brief Returns an unrooted version of this tree.
+     * @return An unrooted version of this tree
+     */
+    virtual UnrootedTree &asUnrootedTree() const = 0;
+
+    /** @brief Parses a string in Newick format.
+     * @param[in]       input     String in Newick format
+     * @return This tree itself
+     */
+    virtual PhylogeneticTree &parseNewick(const string &input) = 0;
+
+    /** @brief Returns a Newick version of this tree.
+     * @return String representing this tree in Newick format
+     */
+    virtual string asNewick() const = 0;
+
+    /** @brief Loads a phylogenetic tree in Newick format.
+     * @param[in]       input     Stream to read input from
+     */
+    void loadNewick(const istream &input);
+
+    /** @brief Saves a phylogenetic tree in Newick format.
+     * @param[out]      output    Stream to write output to
+     */
+    void saveNewick(ostream &output) const;
+
+
+
+    /** @brief Accepts a visitor.
+     * @param[in, out]  visitor   Visitor to accept
+     * @return This tree itself
+     */
+    virtual PhylogeneticTree &accept(Visitor &visitor);
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_PHYLOGENETICTREE_
\ No newline at end of file
diff --git a/Phylo/Sources/RootedTree.cc b/Phylo/Sources/RootedTree.cc
new file mode 100644
index 0000000..6fffe28
--- /dev/null
+++ b/Phylo/Sources/RootedTree.cc
@@ -0,0 +1,485 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <sstream>
+#include <limits>
+#include <RootedTree.h>
+#include <UnrootedTree.h>
+#include <NewickParser.h>
+
+using std::stringstream;
+
+namespace Victor {
+namespace Phylo {
+    typedef RootedTree::Node Node;
+    typedef RootedTree::Subtree Subtree;
+
+    RootedTree RootedTree::emptyTree;
+    const double RootedTree::NA = -1.0;
+
+    RootedTree::RootedTree(Node *parent, const double distance, const string &label) 
+    : parent(parent), label(label), distance(distance) {
+        this->previous = nullptr;
+        this->next     = nullptr;
+        if (nullptr != parent) {
+            parent->addChild(*this);
+        }
+    }
+
+    RootedTree::RootedTree(const double distance, const string &label):
+        RootedTree(nullptr, distance, label) {}
+
+    RootedTree::RootedTree(const string &label):
+        RootedTree(nullptr, NA, label) {}
+
+
+
+    RootedTree::~RootedTree() {
+    }
+
+
+
+    bool
+    RootedTree::operator==(const Subtree &other) const {
+        bool equal = true;
+        size_t i = 0;
+
+        // If trees point the same memory area, they are equal.
+        if (this == &other) {
+            return true;
+        }
+
+        // If trees have different labels, number of children or distance,
+        // they are not equal.
+        if (label != other.label
+            || getChildrenNumber() != other.getChildrenNumber()
+            || getDistance() != other.getDistance()) {
+            return false;
+        }
+
+        // If children of trees are equal, trees are equal.
+        while (equal && i < getChildrenNumber()) {
+            equal &= getChild(i) == other.getChild(i);
+            i++;
+        }
+
+        return equal;
+    }
+
+
+
+    bool
+    RootedTree::operator!=(const Subtree &other) const {
+        return !(*this == other);
+    }
+
+
+
+    bool
+    RootedTree::operator<(const Node &other) const {
+        return isAncestor(other);
+    }
+
+
+
+    bool
+    RootedTree::operator>(const Node &other) const {
+        return isDescendant(other);
+    }
+
+
+
+    RootedTree &
+    RootedTree::operator+(Node &child) {
+        return addChild(child);
+    }
+
+
+
+    Subtree &
+    RootedTree::operator[](const size_t index) const {
+        return getChild(index);
+    }
+
+
+
+    bool
+    RootedTree::isLeaf() const {
+        return children.size() == 0;
+    }
+
+
+
+    bool
+    RootedTree::hasSiblings() const {
+        return nullptr != previous || nullptr != next;
+    }
+
+
+
+    bool
+    RootedTree::hasChildren() const {
+        return !isLeaf();
+    }
+
+
+
+    bool
+    RootedTree::isRoot() const {
+        return nullptr == parent;
+    }
+
+
+
+    bool
+    RootedTree::isAncestor(const Node &node) const {
+        if (node.isRoot()) {
+            return false;
+        } else if (node.parent == this) {
+            return true;
+        } else {
+            return isAncestor(node.getParent());
+        }
+    }
+
+
+
+    bool
+    RootedTree::isDescendant(const Node &node) const {
+        return node.isAncestor(*this);
+    }
+
+
+
+    bool
+    RootedTree::hasDistance() const {
+        return distance != NA;
+    }
+
+
+
+
+    size_t
+    RootedTree::getSize() const {
+        size_t size = 0;
+
+        for (Node *child : children) {
+            size += child->getSize();
+        }
+
+        return size + 1;
+    }
+
+
+
+    vector<Node *>
+    RootedTree::getLeaves() const {
+        vector<Node *> leaves;
+
+        if (isLeaf()) {
+            leaves.push_back(const_cast<Node *>(this));
+        }
+        else {
+            for (Node *child : children) {
+                vector<Node *> child_leaves = child->getLeaves();
+                leaves.reserve(leaves.size() + child_leaves.size());
+                leaves.insert(leaves.end(), child_leaves.begin(), child_leaves.end());
+            }
+        }
+
+        return leaves;
+    }
+
+
+
+    size_t
+    RootedTree::getLeavesNumber() const {
+        size_t leaves = (isLeaf()) ? 1 : 0;
+        
+        for (Node *child : children) {
+            leaves += child->getLeavesNumber();
+        }
+
+        return leaves;
+    }
+
+
+
+    size_t
+    RootedTree::getSiblingsNumber() const {
+        return isRoot() ? 0 : getParent().getChildrenNumber() - 1;
+    }
+
+
+
+    size_t
+    RootedTree::getChildrenNumber() const {
+        return children.size();
+    }
+
+
+
+    Node &
+    RootedTree::getChild(const size_t index) const {
+        return (index < getChildrenNumber())
+             ? *(children[index]) : emptyTree;
+    }
+
+
+
+    Node &
+    RootedTree::getRoot() const {
+        return isRoot()
+             ? *const_cast<RootedTree *>(this)
+             : getParent().getRoot();
+    }
+
+
+
+    size_t
+    RootedTree::getDepth() const {
+        return isRoot() ? 0 : getParent().getDepth() + 1;
+    }
+
+
+
+    size_t
+    RootedTree::getHeight() const {
+        if (isLeaf()) {
+            return 0;
+        } else {
+            size_t height = 0, max_height = 0;
+            for (Node *child : children) {
+                height = child->getHeight();
+                if (height > max_height) {
+                    max_height = height;
+                }
+            }
+            return height + 1;
+        }
+    }
+
+
+
+    Node &
+    RootedTree::getParent() const {
+        return isRoot() ? emptyTree : *parent;
+    }
+
+
+
+    double
+    RootedTree::getDistance() const {
+        return distance;
+    }
+
+
+
+    double
+    RootedTree::getDistance(const Node &node) const {
+        if (isAncestor(node)) {
+            return node.getTotalDistance() - getTotalDistance();
+        } else if (isDescendant(node)) {
+            return getTotalDistance() - node.getTotalDistance();
+        } else {
+            Node *ancestor = parent;
+            while (!ancestor->isAncestor(node)) {
+                ancestor = ancestor->parent;
+            }
+            return getDistance(*ancestor) + node.getDistance(*ancestor);
+        }
+    }
+
+
+
+    double
+    RootedTree::getTotalDistance() const {
+        return isRoot()
+             ? getDistance()
+             : getDistance() + getParent().getTotalDistance();
+    }
+
+
+
+    double
+    RootedTree::getMaxDistance() const {
+        double max_distance = 0.0;
+
+        for (auto &leaf : getLeaves()) {
+            max_distance = std::max(max_distance, leaf->getTotalDistance());
+        }
+
+        return max_distance;
+    }
+
+
+
+    string
+    RootedTree::getLabel() const {
+        return label;
+    }
+
+
+
+    Node &
+    RootedTree::getPreviousSibling() const {
+        return (nullptr != previous) ? *previous : emptyTree;
+    }
+
+
+
+    Node &
+    RootedTree::getNextSibling() const {
+        return (nullptr != next) ? *next : emptyTree;
+    }
+
+
+
+    DistanceMatrix &
+    RootedTree::getDistanceMatrix() const {
+        DistanceMatrix *d = new DistanceMatrix();
+        vector<Node *> leaves = getLeaves();
+
+        for (auto i : leaves) {
+            d->addOTU(i->getLabel());
+            for (auto j : leaves) {
+                if (i == j) {
+                    continue;
+                }
+                (*d)(i->getLabel(), j->getLabel(), i->getDistance(*j));
+            }
+        }
+
+        return *d;
+    }
+
+
+
+    RootedTree &
+    RootedTree::setDistance(const double distance) {
+        this->distance = distance;
+        return *this;
+    }
+
+
+
+    RootedTree &
+    RootedTree::setLabel(const string &label) {
+        this->label = label;
+        return *this;
+    }
+
+
+
+    Subtree &
+    RootedTree::addChild(RootedTree::Subtree &child) {
+        if (hasChildren()) {
+            children[getChildrenNumber() - 1]->next = &child;
+            child.previous = children[getChildrenNumber() - 1];
+        }
+        children.push_back(&child);
+        child.parent = this;
+        return *this;
+    }
+
+
+
+    RootedTree &
+    RootedTree::asRootedTree() const {
+        return *(const_cast<RootedTree *>(this));
+    }
+
+
+
+    /** @brief Recursively builds an unrooted tree.
+     * @param[in]       root      Current node
+     * @param[in]       tree      Pointer to unrooted tree built so far
+     * @return Unrooted version of this node
+     * @note This local utility function must be implemented out of the
+     * RootedTree class, because UnrootedTree::Node is not available
+     * in the class definition. This is due to a missing feature in C++:
+     * no forward declarations for nested class.
+     */
+    static UnrootedTree::Node &
+    _buildNode(const RootedTree &root, UnrootedTree *tree = nullptr) {
+        // Creates tree if null
+        if (nullptr == tree) {
+            tree = new UnrootedTree();
+        }
+
+        // Adds current node to the tree
+        UnrootedTree::Node *node =
+            new UnrootedTree::Node(tree, root.getLabel());
+
+        // Recursively adds children of current node to the tree as neighbors
+        for (size_t i = 0; i < root.getChildrenNumber(); i++) {
+            const RootedTree child = root.getChild(i);
+            node->addNeighbor(_buildNode(child, tree), child.getDistance());
+        }
+
+        return *node;
+    }
+
+    UnrootedTree &
+    RootedTree::asUnrootedTree() const {
+        return _buildNode(*this).getTree();
+    }
+
+
+
+    RootedTree &
+    RootedTree::parseNewick(const string &input) {
+        NewickParser parser;
+
+        *this = parser.parse(input);
+
+        return *this;
+    }
+
+    string
+    RootedTree::asNewick() const {
+        stringstream output;
+
+        // Saves data about children
+        if (hasChildren()) {
+            output << "(" << getChild(0).asNewick() << ")";
+        }
+
+        // Saves label of this node
+        output << getLabel();
+
+        // Saves data about distance
+        if (hasDistance()) {
+            output << ":" << getDistance();
+        }
+
+        // Saves data about sibling
+        if (next != nullptr) {
+            output << "," << next->asNewick();
+        }
+
+        return output.str();
+    }
+
+
+
+    RootedTree &
+    RootedTree::accept(Visitor &visitor) {
+        visitor.visit(*this);
+        return *this;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/RootedTree.h b/Phylo/Sources/RootedTree.h
new file mode 100644
index 0000000..df8e889
--- /dev/null
+++ b/Phylo/Sources/RootedTree.h
@@ -0,0 +1,353 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_ROOTEDTREE_H_
+#define _VICTOR_PHYLO_ROOTEDTREE_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <PhylogeneticTree.h>
+
+using std::string;
+using std::vector;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a rooted phylogenetic tree
+ *
+ * A rooted tree is a phylogenetic tree where every node may have a
+ * label, arcs have a length and every node has a parent (except the
+ * root node).
+ *
+ * A rooted tree is implemented using a recursive structure, and a
+ * (sub)tree is represented by its root node.
+ *
+ * This class follows the Visitor Design Pattern and uses Method
+ * Cascading (through Method Chaining).
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class RootedTree: public PhylogeneticTree {
+ public:
+    /** Subtree is an alias for RootedTree. */
+    typedef RootedTree Subtree;
+
+    /** Node is an alias for RootedTree. */
+    typedef RootedTree Node;
+
+
+    /** Distance from parent node Not Available. */
+    static const double NA;
+
+
+    /** @brief Default constructor.
+     * @param[in,out]   parent    Pointer to parent node
+     * @param[in]       distance  Distance from parent node
+     * @param[in]       label     Label of this node
+     */
+    RootedTree(
+        Node *parent = nullptr,
+        const double distance = NA,
+        const string &label = "");
+
+    /** @brief Constructor.
+     * @param[in]       distance  Distance from parent node
+     * @param[in]       label     Label of this node
+     */
+    explicit RootedTree(const double distance, const string &label = "");
+
+    /** @brief Constructor.
+     * @param[in]       label     Label of this node
+     */
+    explicit RootedTree(const string &label);
+
+    /** @brief Destructor. */
+    virtual ~RootedTree();
+
+
+
+    /** @brief Equality test for rooted trees.
+     *
+     * Two rooted trees are equal if (they point to the same
+     * memory area, or) they have identical labels, distance and children.
+     * @param[in]       other     Other tree
+     * @retval true     Trees are equal
+     * @retval false    Trees are not equal
+     */
+    bool operator==(const Subtree &other) const;
+
+    /** @brief Inequality test for rooted trees.
+     *
+     * Two rooted trees are equal if (they point to the same
+     * memory area, or) they have identical labels, distance and children.
+     * @param[in]       other     Other tree
+     * @retval true     Trees are not equal
+     * @retval false    Trees are equal
+     */
+    bool operator!=(const Subtree &other) const;
+
+    /** @brief Tells whether this node is an ancestor of given node.
+     * @param[in]       other     Given node
+     * @retval true     This node is an ancestor of given one
+     * @retval false    This node is not an ancestor of given one
+     */
+    bool operator<(const Node &other) const;
+
+    /** @brief Tells whether this node is a descendant of given node.
+     * @param[in]       other     Given node
+     * @retval true     This node is a descendant of given one
+     * @retval false    This node is not a descendant of given one
+     */
+    bool operator>(const Node &other) const;
+
+    /** @brief Adds a child to this node.
+     * @param[in, out]  child     Child to be added
+     * @return This node itself
+     */
+    RootedTree &operator+(Node &child);
+
+    /** @brief Returns child at given index.
+     *
+     * If index is invalid, returns an empty tree.
+     * @param[in]       index     Index of the child
+     * @return Child at given index
+     */
+    Subtree &operator[](const size_t index) const;
+
+
+
+    /** @brief Tells whether this node is a leaf.
+     * @retval true     This node is a leaf
+     * @retval false    This node has at least one child
+     */
+    bool isLeaf() const;
+
+    /** @brief Tells whether this node has siblings.
+     * @retval true     This node has at least one sibling
+     * @retval false    This node does not have any siblings
+     */
+    bool hasSiblings() const;
+
+    /** @brief Tells whether this node has children.
+     * @retval true     This node has at least one child
+     * @retval false    This node does not have any child
+     */
+    bool hasChildren() const;
+
+    /** @brief Tells whether this node is a root node.
+     * @retval true     This node is a root node
+     * @retval false    This node is not a root node
+     */
+    bool isRoot() const;
+
+    /** @brief Tells whether this node is an ancestor of given node.
+     * @param[in]       node      Given node
+     * @retval true     This node is an ancestor of giiven node
+     * @retval false    This node is not an ancestor of given node
+     */
+    bool isAncestor(const Node &node) const;
+
+    /** @brief Tells whether this node is a descendant of given node.
+     * @param[in]       node      Given node
+     * @retval true     This node is a descendant of given node
+     * @retval false    This node is not a descendant of given node
+     */
+    bool isDescendant(const Node &node) const;
+
+    /** @brief Tells whether this node has the distance from parent node set.
+     * @retval true     A distance was set for this node
+     * @retval false    A distance was not set for this node
+     */
+    bool hasDistance() const;
+
+
+
+    /** @brief Returns number of nodes in this (sub)tree.
+     * @return Number of nodes in this (sub)tree
+     */
+    size_t getSize() const;
+
+    /** @brief Returns leaves of this (sub)tree.
+     * @return Leaves as a vector
+     */
+    vector<Node *> getLeaves() const;
+
+    /** @brief Returns number of leaves in this (sub)tree.
+     * @return Number of leaves in this (sub)tree
+     */
+    size_t getLeavesNumber() const;
+
+    /** @brief Returns number of siblings of this node.
+     * @return Number of siblings
+     */
+    size_t getSiblingsNumber() const;
+
+    /** @brief Return number of children of this node.
+     * @return Number of children
+     */
+    size_t getChildrenNumber() const;
+
+    /** @brief Returns child at given index.
+     *
+     * By default, returns first child.
+     * If index is invalid, returns an empty tree.
+     * @param[in]       index     Index of the child to be returned
+     * @return Child node
+     */
+    Subtree &getChild(const size_t index = 0) const;
+
+    /** @brief Returns root node of the tree this node belongs to.
+     * @return Root node
+     */
+    Node &getRoot() const;
+
+    /** @brief Returns depth of this node.
+     * @return Depth of this node
+     */
+    size_t getDepth() const;
+
+    /** @brief Returns height of this node.
+     * @return Height of this node
+     */
+    size_t getHeight() const;
+
+    /** @brief Returns parent of this node.
+     *
+     * If this node is a root node, returns an empty tree.
+     * @return Parent node
+     */
+    Node &getParent() const;
+
+    /** @brief Returns distance from this node to its parent.
+     *
+     * Equivalently, returns the length of the arc.
+     * @return Distance from this node to its parent
+     */
+    double getDistance() const;
+
+    /** @brief Returns distance from this node to given one.
+     *
+     * @param[in]       node      Node
+     * @return Distance from this node to given one.
+     */
+    double getDistance(const Node &node) const;
+
+    /** @brief Returns total distance from this node to its root.
+     * @return Cumulative distance from this node to the root
+     */
+    double getTotalDistance() const;
+
+    /** @brief Returns maximum distance in this tree.
+     * @return Maximum cumulative distance
+     */
+    double getMaxDistance() const;
+
+    /** @brief Returns label of this node.
+     * @return Label of this node
+     */
+    string getLabel() const;
+
+    /** @brief Returns previous sibling of this node.
+     *
+     * If this node has no previous sibling, returns an empty tree.
+     * @return Previous sibling
+     */
+    Node &getPreviousSibling() const;
+
+    /** @brief Returns next sibling of this node.
+     *
+     * If this node has no next sibling, returns an empty tree.
+     * @return Next sibling
+     */
+    Node &getNextSibling() const;
+
+    /** @brief Returns matrix of distances among leaves.
+     * @return Distance matrix
+     */
+    virtual DistanceMatrix &getDistanceMatrix() const;
+
+
+
+    /** @brief Sets distance from this node to its parent.
+     *
+     * Equivalently, sets the length of the arc.
+     * @param[in]       distance  New distance from this node to its parent
+     * @return This node
+     */
+    RootedTree &setDistance(const double distance = NA);
+
+    /** @brief Sets label of this node.
+     * @param[in]       label     New label of this node
+     * @return This node
+     */
+    RootedTree &setLabel(const string &label = "");
+
+
+
+    /** @brief Adds a new child to this node.
+     *
+     * New child become the last child of this node.
+     * @param[in, out]  child     New child
+     * @return This node
+     */
+    Subtree &addChild(Subtree &child);
+
+    /** @brief Returns a rooted version of this tree.
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &asRootedTree() const;
+
+    /** @brief Returns an unrooted version of this tree.
+     * @return An unrooted version of this tree
+     */
+    virtual UnrootedTree &asUnrootedTree() const;
+
+    /** @brief Parses a string in Newick format.
+     * @param[in]       input     String in Newick format
+     * @return This tree itself
+     */
+    virtual RootedTree &parseNewick(const string &input);
+
+    /** @brief Returns a Newick version of this tree.
+     * @return String representing this tree in Newick format
+     */
+    virtual string asNewick() const;
+
+
+
+    /** @brief Accepts a visitor.
+     * @param[in, out]  visitor   Visitor to accept
+     * @return This tree itself
+     */
+    virtual RootedTree &accept(Visitor &visitor);
+
+ private:
+    static RootedTree emptyTree;  ///< Empty tree
+
+    string label;                 ///< Label of this node
+    double distance;              ///< Distance from parent node
+    Node *parent;                 ///< Parent of this node
+    vector<Subtree *> children;   ///< Children of this node
+    Node *previous;               ///< Pointer to Previous sibling
+    Node *next;                   ///< Pointer to next sibling
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_ROOTEDTREE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/Sequence.cc b/Phylo/Sources/Sequence.cc
new file mode 100644
index 0000000..524ac43
--- /dev/null
+++ b/Phylo/Sources/Sequence.cc
@@ -0,0 +1,112 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <Sequence.h>
+
+namespace Victor {
+namespace Phylo {
+    Sequence::Sequence(const string &identifier, const string &residues)
+    : residues(residues) {
+        this->identifier = Sequence::formatIdentifier(identifier);
+    }
+
+
+    Sequence::~Sequence() {
+    }
+
+
+
+    vector<Sequence> &
+    Sequence::toSequences(const AlignmentBase &alignment) {
+        string identifier, residues;
+        vector<Sequence> *sequences = new vector<Sequence>();
+
+        // Inserts "target" sequence
+        identifier = alignment.getTargetName();
+        residues  = AlignmentBase::getPureSequence(alignment.getTarget());
+        sequences->push_back(Sequence(identifier, residues));
+
+        // Inserts every template sequence
+        for (size_t i = 0; i < alignment.size(); i++) {
+            identifier = alignment.getTemplateName(i);
+            residues  = AlignmentBase::getPureSequence(alignment.getTemplate(i));
+            sequences->push_back(Sequence(identifier, residues));            
+        }
+
+        return *sequences;
+    }
+
+
+
+    map<string, string> &
+    Sequence::toMap(const AlignmentBase &alignment) {
+        vector<Sequence> list = toSequences(alignment);
+        map<string, string> *sequences = new map<string, string>;
+
+        for (auto &sequence : list) {
+            (*sequences)[sequence.getIdentifier()] = sequence.getResidues();
+        }
+
+        return *sequences;
+    }
+
+
+
+    bool
+    Sequence::isEmpty() const {
+        return residues.empty();
+    }
+
+
+
+    string
+    Sequence::getIdentifier() const {
+        return identifier;
+    }
+
+
+
+    string
+    Sequence::getID() const {
+        return getIdentifier();
+    }
+
+
+
+    char
+    Sequence::getResidue(const size_t position) const {
+        return (position < residues.size()) ? residues[position] : '\0';
+    }
+
+
+
+    string
+    Sequence::getResidues() const {
+        return residues;
+    }
+
+
+
+    string
+    Sequence::formatIdentifier(const string &identifier) {
+        const string::size_type pos = identifier.find(' ', 0);
+        return (pos < identifier.size())
+             ? identifier.substr(0, pos)
+             : identifier;
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
diff --git a/Phylo/Sources/Sequence.h b/Phylo/Sources/Sequence.h
new file mode 100644
index 0000000..5ea7851
--- /dev/null
+++ b/Phylo/Sources/Sequence.h
@@ -0,0 +1,116 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_SEQUENCE_H_
+#define _VICTOR_PHYLO_SEQUENCE_H_
+
+#define _GLIBCXX_IOMANIP
+#include <string>
+#include <map>
+#include <AlignmentBase.h>
+
+using std::string;
+using std::map;
+using Victor::Align2::AlignmentBase;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief A sequence.
+ *
+ * Contains information about a sequence.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class Sequence {
+ public:
+    /** @brief Builds a sequence with given identifier and residues
+     * @param[in]       identifier Idenfifier of this sequence
+     * @param[in]       residues Residues in this sequence
+     */
+    explicit Sequence(const string &identifier, const string &residues);
+
+    /** @brief Destructor. */
+    ~Sequence();
+
+
+
+    /** Converts an alignment into a list of sequences.
+     * @param[in]       alignment Alignment
+     * @return Vector of Sequence
+     */
+    static vector<Sequence> &toSequences(const AlignmentBase &alignment);
+
+
+
+    /** Converts an alignment into a map of sequences.
+     * @param[in]       alignment Alignment
+     * @return Map of sequences: identifier => residues
+     */
+    static map<string, string> &toMap(const AlignmentBase &alignment);
+
+
+
+    /** @brief Tells whether this sequence is empty.
+     * @retval true     This sequence is empty
+     * @retval false    This sequence is not empty
+     */
+    bool isEmpty() const;
+
+
+
+    /** @brief Returns identifier of this sequence.
+     * @return Identifier of this sequence.
+     */
+    string getIdentifier() const;
+
+    /** @brief Returns identifier of this sequence.
+     * @return Identifier of this sequence.
+     */
+    string getID() const;
+
+    /** @brief Returns residue at given position.
+     * @param[in]       position  Position of the residue to return
+     * @return Residue
+     */
+    char getResidue(const size_t position) const;
+
+    /** @brief Returns residues in this sequence.
+     * @return Residues in this sequence
+     */
+    string getResidues() const;
+
+
+    
+ private:
+    string identifier;  ///< Identifier of this sequence
+    string residues;   ///< Residues in this sequence
+
+
+
+    /** @brief Returns a compact version of an identifier.
+     *
+     * Strips spaces and keeps only the first word of the identifier.
+     * @param[in]       identifier Identifier
+     * @return Compact identifier
+     */
+    static string formatIdentifier(const string &identifier);
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_SEQUENCE_H_
diff --git a/Phylo/Sources/SubstitutionMatrix.cc b/Phylo/Sources/SubstitutionMatrix.cc
new file mode 100644
index 0000000..37bbbe4
--- /dev/null
+++ b/Phylo/Sources/SubstitutionMatrix.cc
@@ -0,0 +1,405 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <SubstitutionMatrix.h>
+#include <iostream>
+#include <sstream>
+#include <string.h>
+#include <AminoAcid.h>
+#include <precalculated_matrices.h>
+
+namespace Victor {
+namespace Phylo {
+    typedef SubstitutionMatrix::Identifier Identifier;
+
+    /** @brief Returns a precalculate matrix as a map.
+     * @param[in]           identifier Identifier of the matrix
+     * @return Precalculated matrix
+     */
+    static map<char, map<char, int>> &precalculated_matrices(const Identifier identifier);
+    
+    const string SubstitutionMatrix::residues = "ARNDCEQGHILKMFPSTWYVUOBZJX";
+
+
+    SubstitutionMatrix::SubstitutionMatrix(const map<char, map<char, int>> &scores) {
+        const size_t size = 26;
+        int new_scores[26 * 26],
+            max_score = 0,
+            min_score = 0;
+        double avg_mismatch_score = 0.0;
+        map<char, map<char, int>> scores_map = scores;
+
+        for (size_t i = 0; i < size; i++) {
+            const char r1 = residues[i];
+            for (size_t j = 0; j < size; j++) {
+                const char r2 = residues[j];
+                const int score = scores_map[r1][r2];
+
+                new_scores[hash(r1) * size + hash(r2)]  = score;
+                min_score           = std::min(score, min_score);
+                max_score           = std::max(score, max_score);
+                avg_mismatch_score += score;
+            }
+        }
+        avg_mismatch_score /= (size * size);
+
+        memcpy(&this->scores, &new_scores, size * size * sizeof(int));
+        this->min_score          = min_score;
+        this->max_score          = max_score;
+        this->avg_mismatch_score = avg_mismatch_score;
+    }
+
+
+
+    SubstitutionMatrix::SubstitutionMatrix(const Identifier identifier)
+    : SubstitutionMatrix(precalculated_matrices(identifier)) {
+    }
+
+
+
+    SubstitutionMatrix::SubstitutionMatrix(const SubMatrix &matrix)
+    : SubstitutionMatrix(SubMatrixToMap(matrix)) {
+    }
+
+
+
+    SubstitutionMatrix::SubstitutionMatrix(const SubstitutionMatrix &matrix)
+    : min_score(matrix.min_score), max_score(matrix.max_score),
+    avg_mismatch_score(matrix.avg_mismatch_score) {
+        memcpy(&scores, &matrix.scores, matrix.getScoresNumber() * sizeof(int));
+    }
+
+
+
+    SubstitutionMatrix::~SubstitutionMatrix() {
+    }
+
+
+
+    bool
+    SubstitutionMatrix::operator==(const SubstitutionMatrix &other) const {
+        return isEqual(other);
+    }
+
+
+
+    int
+    SubstitutionMatrix::operator()(const char a, const char b) const {
+        return getScore(a, b);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::operator+(const int value) const {
+        return add(value);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::operator-(const int value) const {
+        return add(-value);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::operator-() const {
+        return multiply(-1);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::operator*(const int value) const {
+        return multiply(value);
+    }
+
+
+
+    bool
+    SubstitutionMatrix::isEqual(const SubstitutionMatrix &other) const {
+        const size_t size = getScoresNumber();
+        bool is_equal = true;
+        size_t i = 0;
+
+        // If matrices differ in sizes, they are not equal
+        if (size != other.getScoresNumber()) {
+            return false;
+        }
+
+        // Checks whether every score is equal
+        while (is_equal && i < size) {
+            is_equal &= scores[i] == other.scores[i];
+            i++;
+        }
+
+        return is_equal;
+    }
+
+
+
+    size_t
+    SubstitutionMatrix::getSize() const {
+        return getResidues().size();
+    }
+
+
+
+    size_t
+    SubstitutionMatrix::getScoresNumber() const {
+        return getSize() * getSize();
+    }
+
+
+
+    string
+    SubstitutionMatrix::getResidues() const {
+        return residues;
+    }
+
+
+
+    int
+    SubstitutionMatrix::getScore(const char a, const char b) const {
+        return scores[hash(a) * getSize() + hash(b)];
+    }
+
+
+
+    int
+    SubstitutionMatrix::getMinScore() const {
+        return min_score;
+    }
+
+
+
+    int
+    SubstitutionMatrix::getMaxScore() const {
+        return max_score;
+    }
+
+
+
+    double
+    SubstitutionMatrix::getAvgMismatchScore() const {
+        return avg_mismatch_score;
+    }
+
+
+
+    map<char, map<char, int>> &
+    SubstitutionMatrix::getScoresAsMap() const {
+        map<char, map<char, int>> *scores_map = new map<char, map<char, int>>();
+
+        for (char r1 : residues) {
+            for (char r2: residues) {
+                (*scores_map)[r1][r2] = getScore(r1, r2);
+            }
+        }
+
+        return *scores_map;
+    }
+
+
+
+    SubMatrix &
+    SubstitutionMatrix::asSubMatrix() const {
+        stringstream stream;
+
+        // Saves matrix into a stream
+        stream << getResidues() << "\n" << getSize() << "\n";
+        for (char r1 : getResidues()) {
+            stream << getSize();
+            for (char r2 : getResidues()) {
+                if (getScore(r1, r2) >= 0 && getScore(r1, r2) < 10) {
+                    stream << " ";
+                }
+                stream << " " << getScore(r1, r2) << " ";
+            }
+            stream << "\n";
+        }
+        stream << "#" << "\n";
+
+        // Build SubMatrix from the stream
+        return *(new SubMatrix(stream));
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::add(const int value) const {
+        return fma(value, 1);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::multiply(const int value) const {
+        return fma(0, value);
+    }
+
+
+
+    SubstitutionMatrix &
+    SubstitutionMatrix::fma(const int addend, const int factor) const {
+        map<char, map<char, int>> scores_map;
+
+        for (char r1 : residues) {
+            for (char r2: residues) {
+                scores_map[r1][r2] = addend + factor * getScore(r1, r2);
+            }
+        }
+
+        return *(new SubstitutionMatrix(scores_map));
+    }
+
+
+
+    Identifier
+    SubstitutionMatrix::stringToIdentifier(const string &identifier) {
+        if (identifier == "BLOSUM30") return BLOSUM30;
+        if (identifier == "BLOSUM35") return BLOSUM35;
+        if (identifier == "BLOSUM40") return BLOSUM40;
+        if (identifier == "BLOSUM45") return BLOSUM45;
+        if (identifier == "BLOSUM50") return BLOSUM50;
+        if (identifier == "BLOSUM55") return BLOSUM55;
+        if (identifier == "BLOSUM62") return BLOSUM62;
+        if (identifier == "BLOSUM65") return BLOSUM65;
+        if (identifier == "BLOSUM70") return BLOSUM70;
+        if (identifier == "BLOSUM75") return BLOSUM75;
+        if (identifier == "BLOSUM80") return BLOSUM80;
+        if (identifier == "BLOSUM90") return BLOSUM90;
+
+        if (identifier == "PAM20")  return PAM20;
+        if (identifier == "PAM60")  return PAM60;
+        if (identifier == "PAM120") return PAM120;
+        if (identifier == "PAM160") return PAM160;
+        if (identifier == "PAM250") return PAM250;
+        if (identifier == "PAM350") return PAM350;
+
+        if (identifier == "MD40")  return MD40;
+        if (identifier == "MD120") return MD120;
+        if (identifier == "MD250") return MD250;
+        if (identifier == "MD350") return MD350;
+
+        if (identifier == "IDENTITY") return IDENTITY;
+
+        if (identifier == "GON40")  return GON40;
+        if (identifier == "GON80")  return GON80;
+        if (identifier == "GON120") return GON120;
+        if (identifier == "GON160") return GON160;
+        if (identifier == "GON250") return GON250;
+        if (identifier == "GON300") return GON300;
+        if (identifier == "GON350") return GON350;
+
+        return IDENTITY;
+    }
+
+
+
+    size_t
+    SubstitutionMatrix::hash(const char amino) {
+        return (size_t) AminoAcid::letter1ToCode(amino);
+    }
+
+
+
+    map<char, map<char, int>> &
+    SubstitutionMatrix::SubMatrixToMap(const SubMatrix &submatrix) {
+        map<char, map<char, int>> *scores_map = new map<char, map<char, int>>();
+
+        for (char r1 : residues) {
+            for (char r2 : residues) {
+                (*scores_map)[r1][r2] = submatrix.score[r1][r2];
+            }
+        }
+
+        return *scores_map;
+    }
+
+
+
+////////////////////////////////////////////////////////////////////////
+// Precalculated matrices
+static map<char, map<char, int>> &precalculated_matrices(const Identifier identifier) {
+    const string residues = _residues;;
+    const size_t size     = residues.size();
+    map<char, map<char, int>> *matrix = new map<char, map<char, int>>();
+    int *ptr;
+
+    // Finds correct matrix
+    switch (identifier) {
+        // BLOSUM family
+        case SubstitutionMatrix::BLOSUM30: ptr = _blosum30; break;
+        case SubstitutionMatrix::BLOSUM35: ptr = _blosum35; break;
+        case SubstitutionMatrix::BLOSUM40: ptr = _blosum40; break;
+        case SubstitutionMatrix::BLOSUM45: ptr = _blosum45; break;
+        case SubstitutionMatrix::BLOSUM50: ptr = _blosum50; break;
+        case SubstitutionMatrix::BLOSUM55: ptr = _blosum55; break;
+        case SubstitutionMatrix::BLOSUM62: ptr = _blosum62; break;
+        case SubstitutionMatrix::BLOSUM65: ptr = _blosum65; break;
+        case SubstitutionMatrix::BLOSUM70: ptr = _blosum70; break;
+        case SubstitutionMatrix::BLOSUM75: ptr = _blosum75; break;
+        case SubstitutionMatrix::BLOSUM80: ptr = _blosum80; break;
+        case SubstitutionMatrix::BLOSUM90: ptr = _blosum90; break;
+
+        // PAM family
+        case SubstitutionMatrix::PAM20:  ptr = _pam20;  break;
+        case SubstitutionMatrix::PAM60:  ptr = _pam60;  break;
+        case SubstitutionMatrix::PAM120: ptr = _pam120; break;
+        case SubstitutionMatrix::PAM160: ptr = _pam160; break;
+        case SubstitutionMatrix::PAM250: ptr = _pam250; break;
+        case SubstitutionMatrix::PAM350: ptr = _pam350; break;
+
+        // MD family
+        case SubstitutionMatrix::MD40:  ptr = _md40;  break;
+        case SubstitutionMatrix::MD120: ptr = _md120; break;
+        case SubstitutionMatrix::MD250: ptr = _md250; break;
+        case SubstitutionMatrix::MD350: ptr = _md350; break;
+
+        // Identity
+        case SubstitutionMatrix::IDENTITY: ptr = _idmat; break;
+
+        // GON family
+        case SubstitutionMatrix::GON40:  ptr = _gon40;  break;
+        case SubstitutionMatrix::GON80:  ptr = _gon80;  break;
+        case SubstitutionMatrix::GON120: ptr = _gon120; break;
+        case SubstitutionMatrix::GON160: ptr = _gon160; break;
+        case SubstitutionMatrix::GON250: ptr = _gon250; break;
+        case SubstitutionMatrix::GON300: ptr = _gon300; break;
+        case SubstitutionMatrix::GON350: ptr = _gon350; break;
+
+        // Default: identity
+        default: ptr = _idmat;
+    }
+
+    // Converts raw matrix to map
+    for (size_t i = 0; i < size; i++) {
+        const char r_i = residues[i];
+        for (size_t j = 0; j <= i; j++) {
+            const char r_j = residues[j];
+            (*matrix)[r_i][r_j] = ptr[(i * i + i) / 2 + j];
+            (*matrix)[r_j][r_i] = ptr[(i * i + i) / 2 + j];
+        }
+    }
+
+    return *matrix;
+}
+
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/SubstitutionMatrix.h b/Phylo/Sources/SubstitutionMatrix.h
new file mode 100644
index 0000000..c1908ef
--- /dev/null
+++ b/Phylo/Sources/SubstitutionMatrix.h
@@ -0,0 +1,274 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_
+#define _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_
+
+#include <map>
+#include <SubMatrix.h>
+
+using std::map;
+using Victor::Align2::SubMatrix;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements a substitution matrix.
+ *
+ * This class is similar to SubMatrix in the Align2 package. This class
+ * can interoperate with SubMatrix, since it offers methods to convert
+ * a SubMatrix to a SubstitutionMatrix and vice-versa.
+ *
+ * This class uses Method Cascading (thought Method Chaining) for its
+ * setter member functions.
+ *
+ * Most common substitution matrices are hardcoded, so that it is no
+ * longer necessary to read from a stream.
+ *
+ * Values for the precalculated matrices are taken from the official
+ * ClustalW implementation.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class SubstitutionMatrix {
+ public:
+    /** Identifiers of hardcoded substitution matrices. */
+    typedef enum {
+        BLOSUM30,       ///< BLOSUM 30
+        BLOSUM35,       ///< BLOSUM 35
+        BLOSUM40,       ///< BLOSUM 40
+        BLOSUM45,       ///< BLOSUM 45
+        BLOSUM50,       ///< BLOSUM 50
+        BLOSUM55,       ///< BLOSUM 55
+        BLOSUM62,       ///< BLOSUM 62
+        BLOSUM65,       ///< BLOSUM 65
+        BLOSUM70,       ///< BLOSUM 70
+        BLOSUM75,       ///< BLOSUM 75
+        BLOSUM80,       ///< BLOSUM 80
+        BLOSUM90,       ///< BLOSUM 90
+
+        PAM20,          ///< PAM 20
+        PAM60,          ///< PAM 60
+        PAM120,         ///< PAM 120
+        PAM160,         ///< PAM 160
+        PAM250,         ///< PAM 250
+        PAM350,         ///< PAM 350
+
+        MD40,           ///< MD 40
+        MD120,          ///< MD 120
+        MD250,          ///< MD 250
+        MD350,          ///< MD 350
+
+        IDENTITY,       ///< Identity matrix
+
+        GON40,          ///< GON 40
+        GON80,          ///< GON 80
+        GON120,         ///< GON 120
+        GON160,         ///< GON 160
+        GON250,         ///< GON 250
+        GON300,         ///< GON 300
+        GON350          ///< GON 350
+    } Identifier;
+
+
+
+    /** @brief Builds a subsitution matrix from a map.
+     * @param[in]       scores    Scores among residues
+     */
+    explicit SubstitutionMatrix(const map<char, map<char, int>> &scores);
+
+    /** @brief Builds a pre-calculated substitution matrix.
+     * @param[in]       identifer Identifier of the matrix
+     */
+    explicit SubstitutionMatrix(const Identifier identifer);
+
+    /** @brief Builds a substitution matrix from a SubMatrix.
+     * 
+     * Converts a SubMatrix to a SubstitutionMatrix.
+     * @param[in]       matrix    SubMatrix object
+     */
+    explicit SubstitutionMatrix(const SubMatrix &matrix);
+
+    /** @brief Copy constructor.
+     * @param[in]       matrix    Substitution matrix
+     */
+    explicit SubstitutionMatrix(const SubstitutionMatrix &matrix);
+
+    /** @brief Destructor. */
+    virtual ~SubstitutionMatrix();
+
+
+
+    /** @brief Tells whether this matrix is equal to given one.
+     * @param[in]       other     Other substitution matrix
+     */
+    bool operator==(const SubstitutionMatrix &other) const;
+
+    /** @brief Returns score between given residues.
+     * @param[in]       a         First amino acid
+     * @param[in]       b         Second amino acid
+     * @return Score between a and b
+     */
+    int operator()(const char a, const char b) const;
+
+    /** @brief Computes sum of scores and a given constant.
+     * @param[in]       value     Value to be added
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &operator+(const int value) const;
+
+    /** @brief Computes difference between scores and a given constant.
+     * @param[in]       value     Value to be subtracted
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &operator-(const int value) const;
+
+    /** @brief Changes signess of scores.
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &operator-() const;
+
+    /** @brief Computes product of scores and a given constant.
+     * @param[in]       value     Value to be multiplied
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &operator*(const int value) const;
+
+
+
+    /** @brief Tells whether this matrix is equal to given one.
+     * @param[in]       other     Other substitution matrix
+     */
+    bool isEqual(const SubstitutionMatrix &other) const;
+
+
+
+    /** @brief Returns size of this subsitution matrix.
+     * @return Size of this matrix
+     */
+    size_t getSize() const;
+
+    /** @brief Returns number of elements in this matrix.
+     * @return Number of scores in this matrix.
+     */
+    size_t getScoresNumber() const;
+
+    /** @brief Returns residues in this substitution matrix.
+     * @return Residues
+     */
+    string getResidues() const;
+
+    /** @brief Returns score between given residues.
+     * @param[in]       a         First amino acid
+     * @param[in]       b         Second amino acid
+     * @return Score between a and b
+     */
+    int getScore(const char a, const char b) const;
+
+    /** @brief Returns minimum score in this matrix.
+     * @return Minimum score
+     */
+    int getMinScore() const;
+
+    /** @brief Returns maximum score in this matrix.
+     * @return Maximum score
+     */
+    int getMaxScore() const;
+
+    /** @brief Returns average mismatch score.
+     * @return Average mismatch score
+     */
+    double getAvgMismatchScore() const;
+
+    /** @brief Returns scores as a map.
+     * @return Scores as a map
+     */
+    map<char, map<char, int>> &getScoresAsMap() const;
+
+    /** @brief Returns a SubMatrix reference.
+     *
+     * Converts this substitution matrix to a SubMatrix object.
+     * @return This substitution matrix as a SubMatrix
+     */
+    SubMatrix &asSubMatrix() const;
+
+
+
+    /** @brief Computes sum of scores and a given constant.
+     * @param[in]       value     Value to be added
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &add(const int value) const;
+
+    /** @brief Computes product of scores and a given constant.
+     * @param[in]       value     Value to be multiplied
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &multiply(const int value) const;
+
+    /** @brief Performs a fused multiply-add (fma) operation.
+     *
+     * Multiplies this matrix by given factor, then adds given addend to
+     * the result at once. This is more efficient than a + b * M.
+     * @param[in]       addend    Value to be added
+     * @param[in]       factor    Value to be multiplied
+     * @return A new substitution matrix
+     */
+    SubstitutionMatrix &fma(const int addend, const int factor) const;
+
+
+
+ private:
+    static const string residues;      ///< Residues
+
+    int scores[26 * 26];         ///< Scores
+    double avg_mismatch_score;   ///< Average mismatch score
+    int min_score;               ///< Minimum score
+    int max_score;               ///< Maximum score
+
+
+    /** @brief Converts a string into an identifier.
+     * 
+     * If conversion fails, returns the identity identifier.
+     * @param[in]       identifier Identifier as a string
+     * @return Identifier
+     */
+    static Identifier stringToIdentifier(const string &identifier);
+
+    /** @brief Returns an hased version of an amino acid.
+     * 
+     * Hash function maps amino acids into the interval [0, 25], minimizing
+     * entropy.
+     * @param[in]       amino     Amino acid
+     * @return Hash value
+     */
+    static size_t hash(const char amino);
+
+    /** @brief Returns a SubMatrix as a map.
+     *
+     * Converts a SubMatrix object into a map of scores.
+     * @param[in]       submatrix SubMatrix object
+     * @return Score map
+     */
+    static map<char, map<char, int>> &SubMatrixToMap(const SubMatrix &submatrix);
+};
+
+
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_
\ No newline at end of file
diff --git a/Phylo/Sources/UPGMA.cc b/Phylo/Sources/UPGMA.cc
new file mode 100644
index 0000000..14a2fd5
--- /dev/null
+++ b/Phylo/Sources/UPGMA.cc
@@ -0,0 +1,111 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <UPGMA.h>
+
+/** Returns union of sets.
+ * @param[in]       A         First set
+ * @param[in]       B         Second set
+ * @return Set union between A and B: A U B
+ */
+template <class T>
+set<T> set_union(const set<T> &A, const set<T> &B) {
+    set<T> C = A;
+    C.insert(B.begin(), B.end());
+    return C;
+}
+
+
+
+namespace Victor {
+namespace Phylo {
+    UPGMA::~UPGMA() {
+    }
+
+
+    
+    RootedTree &
+    UPGMA::apply(const DistanceMatrix &matrix) const {
+        map<string, RootedTree *> node_pool;
+        map<string, double> cumulative;
+        map<string, set<string>> components;
+        RootedTree *tree;
+        DistanceMatrix DM = matrix;
+        set<string> OTUs = matrix.getOTUs();
+
+
+        // Initializes auxilary data structures
+        for (auto &label : OTUs) {
+            node_pool[label] = new RootedTree(label);
+            cumulative[label] = 0.0;
+            components[label].insert(label);
+        }
+
+        while (!DM.isEmpty()) {
+            // Takes minimum from distance matrix and computes new label and
+            // distance
+            pair<string, string> min = DM.getMinimumPosition();
+            string i = min.first,
+                   j = min.second,
+                   new_label = i + "+" + j;
+            double new_distance = DM(i, j) / 2.0;
+
+            // Creates a new node for this joining
+            tree = new RootedTree();
+            tree->addChild(*node_pool[i]);
+            tree->addChild(*node_pool[j]);
+
+            // Sets distance between new joining node and children
+            node_pool[i]->setDistance(new_distance - cumulative[i]);
+            node_pool[j]->setDistance(new_distance - cumulative[j]);
+
+            // Updates auxiliary data structures
+            node_pool[new_label] = tree;
+            cumulative[new_label] = new_distance;
+            components[new_label] = set_union(components[i], components[j]);
+
+
+            // Updates distance matrix with new distances
+            OTUs = DM.getOTUs();
+            for (auto &l : OTUs) {
+                // Does not update entries about consumed labels
+                if (l == i || l == j) {
+                    continue;
+                }
+
+                // Computes average distance
+                double average_distance = 0.0;
+                for (auto &a : components[new_label]) {
+                    for (auto &b : components[l]) {
+                        average_distance += matrix(a, b);
+                    }
+                }
+                average_distance /= (components[new_label].size() * components[l].size());
+
+                // Updates matrix
+                DM(l, new_label, average_distance);
+            }
+
+            // Adds new OTU to the distance matrix, and removes consumed ones
+            DM.addOTU(new_label)
+              .removeOTU(i)
+              .removeOTU(j);
+        }
+        return *tree;
+    }
+
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/UPGMA.h b/Phylo/Sources/UPGMA.h
new file mode 100644
index 0000000..288ceb5
--- /dev/null
+++ b/Phylo/Sources/UPGMA.h
@@ -0,0 +1,60 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_UPGMA_H_
+#define _VICTOR_PHYLO_UPGMA_H_
+
+#include <ClusteringAlgorithm.h>
+#include <RootedTree.h>
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements the UPGMA algorithm.
+ *
+ * Implements UPGMA as a functor.
+ * UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is an
+ * agglomerative, bottom-up hierarchical clustering method.
+ * The UPGMA algorithm constructs a rooted tree (dendrogram) that
+ * reflects the structure present in a pairwise similarity matrix
+ * (or a dissimilarity matrix).
+ * 
+ * For more information see:
+ * - A quantitative approach to a problem in classification
+ *   (Michanel and Sockal)
+ *
+ * This class follows the Strategy Design Pattern.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class UPGMA: public ClusteringAlgorithm {
+ public:
+    /** @brief Destructor. */
+    virtual ~UPGMA();
+
+
+    
+    /** @brief Builds a phylogenetic tree from given distance matrix.
+     * @param[in]       matrix    Distance matrix
+     * @return Phylogenetic tree
+     */
+    virtual RootedTree &apply(const DistanceMatrix &matrix) const;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_UPGMA_
\ No newline at end of file
diff --git a/Phylo/Sources/UnrootedTree.cc b/Phylo/Sources/UnrootedTree.cc
new file mode 100644
index 0000000..0ac2bdb
--- /dev/null
+++ b/Phylo/Sources/UnrootedTree.cc
@@ -0,0 +1,608 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <sstream>
+#include <limits>
+#include <UnrootedTree.h>
+#include <RootedTree.h>
+
+using std::stringstream;
+
+namespace Victor {
+namespace Phylo {
+    typedef UnrootedTree::Node Node;
+
+    UnrootedTree UnrootedTree::emptyTree;
+    Node Node::emptyNode;
+    const double Node::NA = -1.0;
+    size_t Node::next_ID = 0;
+
+    ////////////////////////////////////////////////////////////////////
+    // UnrootedTree::Node
+    Node::Node(UnrootedTree *tree, const string &label)
+    : tree(tree), label(label) {
+        this->ID = getNextIdentifier();
+
+        if (nullptr != tree) {
+            tree->addNode(*this);
+        }
+    }
+
+
+
+    Node::Node(const string &label) : Node(nullptr, label) {
+    }
+
+
+
+    bool
+    Node::operator==(const Node &other) const {
+        return getIdentifier() == other.getIdentifier();
+    }
+
+
+    bool
+    Node::operator!=(const Node &other) const {
+        return !(*this == other);
+    }
+
+
+
+    bool
+    Node::isLeaf() const {
+        return getSize() < 2;
+    }
+
+
+
+    bool
+    Node::hasNeighbors() const {
+        return !neighbors.empty();
+    }
+
+
+
+    bool
+    Node::isNeighbor(const size_t identifier) const {
+        return neighbors.find(identifier) != neighbors.end();
+    }
+
+
+
+    bool
+    Node::isNeighbor(const Node &node) const {
+        return isNeighbor(node.getIdentifier());
+    }
+
+
+
+    bool
+    Node::hasPath(const size_t identifier, const Node *previous) const {
+        if (isNeighbor(identifier)) {
+            return true;
+        }
+
+        bool has_path = false;
+        for (auto neighbor : getNeighbors()) {
+            if (neighbor == previous) {
+                continue;
+            }
+
+            has_path |= neighbor->hasPath(identifier, this);
+        }
+
+        return has_path;
+    }
+
+
+
+    bool
+    Node::hasPath(const Node &node) const {
+        return hasPath(node.getIdentifier());
+    }
+
+
+
+    bool
+    Node::belongsTo(const UnrootedTree &tree) const {
+        return this->tree == &tree || getTree() == tree;
+    }
+
+
+
+    size_t
+    Node::getIdentifier() const {
+        return ID;
+    }
+
+
+
+    size_t
+    Node::getID() const {
+        return getIdentifier();
+    }
+
+
+
+    size_t
+    Node::getSize() const {
+        return neighbors.size();
+    }
+
+
+
+    size_t
+    Node::getNeighborsNumber() const {
+        return getSize();
+    }
+
+
+
+    Node &
+    Node::getNeighbor(const size_t identifier) const {
+        return (isNeighbor(identifier))
+             ? *(neighbors.find(identifier)->second.first)
+             : emptyNode;
+    }
+
+
+
+    Node &
+    Node::getClosestNeighbor() const {
+        Node *closest   = const_cast<Node *>(this);
+        double distance = std::numeric_limits<double>::max();
+
+        for (auto neighbor : getNeighbors()) {
+            if (getDistance(*neighbor) < distance) {
+                distance = getDistance(*neighbor);
+                closest  = neighbor;
+            }
+        }
+
+        return *closest;
+    }
+
+
+
+    Node &
+    Node::getNeighborClosestTo(const Node &target, const Node *avoid) const {
+        Node *closest   = const_cast<Node *>(this);
+        double distance = std::numeric_limits<double>::max();
+
+        for (auto neighbor : getNeighbors()) {
+            if (avoid != nullptr && *avoid == *neighbor) continue;
+            if (neighbor->getDistance(target) < distance) {
+                distance = neighbor->getDistance(target);
+                closest  = neighbor;
+            }
+        }
+
+        return *closest;
+    }
+
+
+
+    vector<Node *>
+    Node::getNeighbors() const {
+        vector<Node *> neighbors;
+
+        for (auto entry : this->neighbors) {
+            neighbors.push_back(entry.second.first);
+        }
+
+        return neighbors;
+    }
+
+
+
+    double
+    UnrootedTree::Node::getDistance(const size_t identifier, const Node *previous) const {
+        // If nodes are neighbors, returns distance directly
+        if (isNeighbor(identifier)) {
+            return neighbors.find(identifier)->second.second;
+        }
+        
+        // If nodes are not neighbors, finds a path
+        double distance = NA;
+        vector<Node *> neighbors = getNeighbors();
+
+        for (auto neighbor : neighbors) {
+            double to_neighbor = getDistance(*neighbor),
+                   path_length;
+
+            // Avoids infinite loops
+            if (previous == neighbor || NA == to_neighbor) {
+                continue;
+            }
+
+            path_length = neighbor->getDistance(identifier, this);
+
+            // Exits the loop if the path was found
+            if (path_length != NA) {
+                distance = to_neighbor + path_length;
+                break;
+            }
+        }
+
+        return distance;
+    }
+
+
+
+    double
+    UnrootedTree::Node::getDistance(const Node &node) const {
+        return getDistance(node.getIdentifier());
+    }
+
+
+
+    UnrootedTree &
+    Node::getTree() const {
+        return (nullptr != tree) ? *tree : emptyTree;
+    }
+
+
+
+    string
+    Node::getLabel() const {
+        return label;
+    }
+
+
+
+    Node &
+    Node::setLabel(const string &label) {
+        this->label = label;
+        return *this;
+    }
+
+
+    Node &
+    Node::setDistance(const size_t identifier, const double distance) {
+        if (isNeighbor(identifier)) {
+             neighbors.find(identifier)->second.second = distance;
+        }
+        return *this;
+    }
+
+
+    Node &
+    Node::setDistance(Node &node, const double distance) {
+        return setDistance(node.getIdentifier(), distance);
+    }
+
+
+
+    Node &
+    Node::addNeighbor(Node &node, const double distance) {
+        // If nodes do not belong to the same tree, nothing happens
+        if (!node.belongsTo(getTree())) {
+            return *this;
+        }
+
+        neighbors[node.getIdentifier()] = make_pair(&node, distance);
+        node.neighbors[getIdentifier()] = make_pair(this, distance);
+
+        return *this;
+    }
+
+
+
+    Node &
+    Node::addBetween(Node &neighbor, Node &node, const double distance) {
+        // If node do not belong to the same tree, or are not neighbors,
+        // nothing happens
+        if (!node.belongsTo(getTree()) || !isNeighbor(neighbor)) {
+            return *this;
+        }
+
+        const double d_ac = distance,
+                     d_bc = getDistance(neighbor) - d_ac;
+
+        addNeighbor(node, d_ac);
+        neighbor.addNeighbor(node, d_bc);
+        removeNeighbor(neighbor);
+
+        return *this;
+    }
+
+
+
+    Node &
+    Node::removeNeighbor(Node &node) {
+        neighbors.erase(node.getIdentifier());
+        node.neighbors.erase(getIdentifier());
+
+        return *this;
+    }
+
+
+    RootedTree &
+    Node::asRootedTree() const {
+        return getTree().asRootedTree(getIdentifier());
+    }
+
+
+
+    size_t
+    Node::getNextIdentifier() {
+        return next_ID++;
+    }
+
+
+
+
+
+    ////////////////////////////////////////////////////////////////////
+    // UnrootedTree
+    UnrootedTree::UnrootedTree() {
+    }
+
+
+
+    UnrootedTree::~UnrootedTree() {
+    }
+
+
+
+    bool
+    UnrootedTree::operator==(const UnrootedTree &other) const {
+        // If trees point the same memory area, they are trivially equal
+        if (this == &other) {
+            return true;
+        }
+
+        // If trees have a different number of nodes, they cannot be equal
+        if (getSize() != other.getSize()) {
+            return false;
+        }
+
+        // Trees are equal if their nodes are equal
+        bool equal = true;
+        for (auto &entry : nodes) {
+            equal &= getNode(entry.first) == other.getNode(entry.first);
+        }
+
+        return equal;
+    }
+
+
+
+    bool
+    UnrootedTree::operator!=(const UnrootedTree &other) const {
+        return !(*this == other);
+    }
+
+
+
+    UnrootedTree &
+    UnrootedTree::operator+(Node &node) {
+        return addNode(node);
+    }
+
+
+
+    Node &
+    UnrootedTree::operator[](const size_t identifier) const {
+        return getNode(identifier);
+    }
+
+
+
+    bool
+    UnrootedTree::isEmpty() const {
+        return getSize() == 0;
+    }
+
+
+
+    bool
+    UnrootedTree::hasNode(const size_t ID) const {
+        return nodes.find(ID) != nodes.end();
+    }
+
+
+
+    bool
+    UnrootedTree::hasNode(const Node &node) const {
+        return hasNode(node.getIdentifier());
+    }
+
+
+
+    size_t
+    UnrootedTree::getSize() const {
+        return nodes.size();
+    }
+
+
+
+    Node &
+    UnrootedTree::getNode(const size_t identifier) const {
+        return hasNode(identifier)
+             ? *(nodes.find(identifier)->second)
+             : Node::emptyNode;
+    }
+
+
+
+    vector<Node *>
+    UnrootedTree::getNodes() const {
+        vector<Node *> nodes;
+
+        for (auto entry : this->nodes) {
+            nodes.push_back(entry.second);
+        }
+
+        return nodes;
+    }
+
+
+
+    vector<Node *>
+    UnrootedTree::getLeaves() const {
+        vector<Node *> leaves;
+
+        for (auto entry : nodes) {
+            Node *node = entry.second;
+            if (node->isLeaf()) {
+                leaves.push_back(node);
+            }
+        }
+
+        return leaves;
+    }
+
+
+
+    DistanceMatrix &
+    UnrootedTree::getDistanceMatrix() const {
+        vector<Node *> leaves = getLeaves();
+        DistanceMatrix *d = new DistanceMatrix();
+
+        for (auto i : leaves) {
+            d->addOTU(i->getLabel());
+            for (auto j : leaves) {
+                if (i == j) {
+                    continue;
+                }
+                (*d)(i->getLabel(), j->getLabel(), i->getDistance(*j));
+            }
+        }
+
+        return *d;
+    }
+
+
+
+    UnrootedTree &
+    UnrootedTree::addNode(Node &node) {
+        nodes[node.getIdentifier()] = &node;
+        return *this;
+    }
+
+
+
+    RootedTree &
+    UnrootedTree::midpointRoot() const {
+        map<string, Node *> node_pool;
+
+        UnrootedTree tree = *this;
+        DistanceMatrix d  = tree.getDistanceMatrix();
+
+        // Initializes node pool
+        for (auto node : tree.getLeaves()) {
+            node_pool[node->getLabel()] = node;
+        }
+
+        // Finds most distant nodes A and B
+        pair<string, string> max = d.getMaximumPosition();
+        Node *A = node_pool[max.first],
+             *B = node_pool[max.second];
+        double max_distance = d(max.first, max.second);
+
+        // Finds adjacent nodes between which new root will be placed
+        Node *current  = A,
+             *previous = B;
+        double path_distance = max_distance;
+
+        while (path_distance >= max_distance / 2.0 && !current->isNeighbor(*B)) {
+            Node *avoid   = previous;
+            previous      = current;
+            current       = &current->getNeighborClosestTo(*B, avoid);
+            path_distance = current->getDistance(*B);
+        }
+
+        // Adds new root node between current and previous
+        Node *root = new Node();
+        tree.addNode(*root);
+        current->addBetween(*previous, *root, max_distance / 2.0 - path_distance);
+
+        return tree.asRootedTree(*root);
+    }
+
+
+
+    RootedTree &
+    UnrootedTree::asRootedTree() const {
+        return midpointRoot();
+    }
+
+
+
+    RootedTree &
+    UnrootedTree::asRootedTree(const size_t root) const {
+        return asRootedTree(getNode(root));
+    }
+
+
+
+    RootedTree &
+    UnrootedTree::asRootedTree(Node &root, const Node *parent) const {
+        RootedTree *root_node = new RootedTree(root.getLabel());
+
+        // Sets distance from parent, if parent is not null
+        if (nullptr != parent) {
+            root_node->setDistance(root.getDistance(*parent));
+        }
+
+        // Recursively adds children
+        for (auto &entry : root.neighbors) {
+            Node *neighbor = entry.second.first;
+            if (neighbor != parent) {
+                root_node->addChild(asRootedTree(*neighbor, &root));
+            }
+        }
+
+        return *root_node;
+    }
+
+
+
+    UnrootedTree &
+    UnrootedTree::asUnrootedTree() const {
+        return *(const_cast<UnrootedTree *>(this));
+    }
+
+
+
+    UnrootedTree &
+    UnrootedTree::parseNewick(const string &input) {
+        RootedTree tree;
+
+        tree.parseNewick(input);
+
+        *this = tree.asUnrootedTree();
+
+        return *this;
+    }
+
+
+
+    string
+    UnrootedTree::asNewick() const {
+        return asRootedTree().asNewick();
+    }
+
+
+
+    UnrootedTree &
+    UnrootedTree::accept(Visitor &visitor) {
+        visitor.visit(*this);
+        return *this;
+    }
+}  // namespace Phylo
+}  // namespace Victor
\ No newline at end of file
diff --git a/Phylo/Sources/UnrootedTree.h b/Phylo/Sources/UnrootedTree.h
new file mode 100644
index 0000000..c54fd57
--- /dev/null
+++ b/Phylo/Sources/UnrootedTree.h
@@ -0,0 +1,473 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_UNROOTEDTREE_H_
+#define _VICTOR_PHYLO_UNROOTEDTREE_H_
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <map>
+#include <utility>
+#include <PhylogeneticTree.h>
+
+using std::string;
+using std::vector;
+using std::map;
+using std::pair;
+using std::make_pair;
+
+namespace Victor {
+namespace Phylo {
+
+/** @brief Implements an unrooted tree.
+ *
+ * An unrooted tree is a phylogenetic tree where every node may have a
+ * label, arcs have a length and nodes may have neighbors.
+ *
+ * This class follows the Visitor Design Pattern and uses Method
+ * Cascading (through Method Chaining).
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class UnrootedTree: public PhylogeneticTree {
+ public:
+    /** @brief Implements a node in an unrooted tree. */
+    class Node {
+        friend class UnrootedTree;
+     public:
+        /** @brief Builds a node and inserts it into a tree.
+         * @param[in, out] tree      Tree this node belongs to
+         * @param[in]      label     Label of this node
+         */
+        explicit Node(UnrootedTree *tree, const string &label = "");
+
+        /** @brief Default constructor.
+         * @param[in]      label     Label of this node
+         */
+        Node(const string &label = "");
+
+
+
+        /** @brief Tells whether two nodes are equal.
+         *
+         * Two nodes are equal when they have the same identifier.
+         * @param[in]      other     Other node
+         * @retval true    Nodes are equal
+         * @retval false   Nodes are not equal
+         */
+        bool operator==(const Node &other) const;
+
+        /** @brief Tells whether two nodes are not equal.
+         *
+         * Two nodes are equal when they have the same identifier.
+         * @param[in]      other     Other node
+         * @retval true    Nodes are not equal
+         * @retval false   Nodes are equal
+         */
+        bool operator!=(const Node &other) const;
+
+
+
+        /** @brief Tells whether this node is a leaf.
+         * @retval true    This node is a leaf
+         * @retval false   This node has at least two neighbors
+         */
+        bool isLeaf() const;
+
+        /** @brief Tells whether this node has neighbors.
+         * @retval true    This node has at least one neighbor
+         * @retval false   This node does not have any neighbors
+         */
+        bool hasNeighbors() const;
+
+        /** @brief Tells whether this node is a neighbor of given node.
+         * @param[in]      identifier Identifier of given node
+         * @retval true    This node is a neighbor of giiven node
+         * @retval false   This node is not a neighbor of given node
+         */
+        bool isNeighbor(const size_t identifier) const;
+
+        /** @brief Tells whether this node is a neighbor of given node.
+         * @param[in]      node      Given node
+         * @retval true    This node is a neighbor of given node
+         * @retval false   This node is not a neighbor of given node
+         */
+        bool isNeighbor(const Node &node) const;
+
+        /** @brief Tells whether a path exists from this node to given node.
+         * @param[in]      identifier Identifier of given node
+         * @param[in]      previous  Previously visited node
+         * @retval true    A path between this node and given one exists
+         * @retval false   A path between this node and given one does not exist
+         */
+        bool hasPath(const size_t identifier, const Node *previous = nullptr) const;
+
+        /** @brief Tells whether a path exists from this node to given node.
+         * @param[in]      node      Given node
+         * @retval true    A path between this node and given one exists
+         * @retval false   A path between this node and given one does not exist
+         */
+        bool hasPath(const Node &node) const;
+
+        /** @brief Tells whether this node belongs to given tree
+         * @param[in]      tree      Given tree
+         * @retval true    This node belongs to given tree
+         * @retval false   This node does not belong to given tree
+         */
+        bool belongsTo(const UnrootedTree &tree) const;
+
+
+
+        /** @brief Returns identifier of this node.
+         * @return Identifier of this node
+         */
+        size_t getIdentifier() const;
+
+        /** @brief Returns identifier of this node.
+         * @return Identifier of this node
+         */
+        size_t getID() const;
+
+        /** @brief Returns number of neighbors of this node.
+         * @return Number of neighbors of this node
+         */
+        size_t getSize() const;
+
+        /** @brief Returns number of neighbors of this node.
+         * @return Number of neighbors of this node
+         */
+        size_t getNeighborsNumber() const;
+
+        /** @brief Returns neighbor at given index.
+         *
+         * If node is not a neighbor, returns an empty node.
+         * @param[in]      identifier Identifier of the neighbor
+         * @return Child node
+         */
+        Node &getNeighbor(const size_t identifier) const;
+
+        /** @brief Returns neighbor closest to this node.
+         * 
+         * If more than one neighbor share minimal distance, choses one
+         * in non-deterministic way.
+         *
+         * If this node has no neighbors, returns this node itself.
+         * @return Closest neighbor
+         */
+        Node &getClosestNeighbor() const;
+
+        /** @brief Returns neighbor closest to target node.
+         *
+         * If more than one neighbor share minimal distance, choses one
+         * in non-deterministic way.
+         *
+         * If this node has no neighbors, or target node is not reachable,
+         * returns this node.
+         * @param[in]   target    Target node
+         * @param[in]   avoid     Node to be avoided 
+         * @return Neighbor closest to target
+         */
+        Node &getNeighborClosestTo(const Node &target, const Node *avoid = nullptr) const;
+
+        /** @brief Returns neighbors of this node.
+         * @return Neighbors as a vector
+         */
+        vector<Node *> getNeighbors() const;
+
+        /** @brief Returns distance from this node to given one.
+         * @param[in]      identifier Identifier of the node
+         * @param[in]      previous   Neighbor which has been already visited
+         * @return Distance from this node to given one.
+         */
+        double getDistance(const size_t identifier, const Node *previous = nullptr) const;
+
+        /** @brief Returns distance from this node to given one.
+         * @param[in]      node      Node
+         * @return Distance from this node to given one.
+         */
+        double getDistance(const Node &node) const;
+
+        /** @brief Returns unrooted tree this node belongs to.
+         * @return Unrooted tree this node belongs to
+         */
+        UnrootedTree &getTree() const;
+
+        /** @brief Returns label of this node.
+         * @return Label of this node
+         */
+        string getLabel() const;
+
+
+
+        /** @brief Sets label of this node.
+         * @param[in]      label     New label of this node
+         * @return This node
+         */
+        Node &setLabel(const string &label = "");
+
+        /** @brief Sets distance between this node and given one.
+         *
+         * If given node is not a neighbor of this node, nothing happens.
+         * @param[in, out] identifier Identifier of given node
+         * @param[in]      distance  New distance
+         * @return This node
+         */
+        Node &setDistance(const size_t identifier, const double distance = NA);
+
+        /** @brief Sets distance between this node and given one.
+         *
+         * If given node is not a neighbor of this node, nothing happens.
+         * @param[in, out] node      Given node
+         * @param[in]      distance  New distance
+         * @return This node
+         */
+        Node &setDistance(Node &node, const double distance = NA);
+
+
+
+        /** @brief Adds a neighbor to this node.
+         *
+         * Neighbor node must belong to the same tree. If it does not
+         * belong to the same tree, nothing happens.
+         * @param[in, out] node      New neighbor
+         * @param[in]      distance  Distance of new neighbor
+         * @return This node
+         */
+        Node &addNeighbor(Node &node, const double distance = NA);
+
+        /** @brief Adds a node between this node and one neighbor of its.
+         *
+         * If new node does not belong to the tree, or given node is
+         * not a neighbor, nothing happens.
+         * @param[in]      neighbor  Old neighbor
+         * @param[in]      node      New neighbor
+         * @param[in]      distance  Distance from this node
+         * @return This node itself
+         */
+        Node &addBetween(Node &neighbor, Node &node, const double distance);
+
+        /** @brief Removes a neighbor from this node.
+         *
+         * If node is not a neighbor of this node, nothing happens.
+         * @param[in, out] node      Neighbor to remove
+         * @return This node
+         */
+        Node &removeNeighbor(Node &node);
+
+
+        /** @brief Returns a rooted tree rooted in this node.
+         * @return A rooted tree version of the tree this node belongs to
+         */
+        RootedTree &asRootedTree() const;
+
+
+
+     private:
+        static Node emptyNode;    ///< Empty node
+        static size_t next_ID;    ///< Next available identifier for a node
+        static const double NA;   ///< Distance Not Available
+
+        size_t ID;                ///< Identifier of this node
+        string label;             ///< Label of this node
+        map<size_t, pair<Node *, double>> neighbors;  ///< Neighbors of this node
+        UnrootedTree *tree;       ///< Unrooted tree this node belongs to
+
+
+        /** Returns next available identifier for a node.
+         * @return Next available identifier
+         */
+        static size_t getNextIdentifier();
+    };
+
+
+
+    /** @brief Default constructor.
+     *
+     * Produces an empty unrooted tree.
+     */
+    UnrootedTree();
+
+    /** @brief Destructor. */
+    virtual ~UnrootedTree();
+
+
+
+    /** @brief Equality test for unrooted trees.
+     *
+     * Two unrooted trees are equal if (they point to the same
+     * memory area, or) they have the same nodes.
+     * @param[in]       other     Other tree
+     * @retval true     Trees are equal
+     * @retval false    Trees are not equal
+     */
+    bool operator==(const UnrootedTree &other) const;
+
+    /** @brief Inequality test for unrooted trees.
+     *
+     * Two unrooted trees are equal if (they point to the same
+     * memory area, or) they have the same nodes.
+     * @param[in]       other     Other tree
+     * @retval true     Trees are not equal
+     * @retval false    Trees are equal
+     */
+    bool operator!=(const UnrootedTree &other) const;
+
+    /** @brief Adds a node to this tree.
+     * @param[in, out]  node      Node to be added
+     * @return This tree itself
+     */
+    UnrootedTree &operator+(Node &node);
+
+    /** @brief Returns node with given identifier.
+     *
+     * If indentifier is invalid, returns an empty node.
+     * @param[in]       identifier Index of the node
+     * @return Node with given identifier
+     */
+    Node &operator[](const size_t identifier) const;
+
+
+
+    /** @brief Tells whether this tree is empty.
+     * @retval true     This tree is empty
+     * @retval false    There is at least one node in this tree
+     */
+    bool isEmpty() const;
+
+    /** @brief Tells whether a node belongs to this tree.
+     * @param[in]       ID        Identifier of given node
+     * @retval true     Node belongs to this tree
+     * @retval false    Node does not belong to this tree
+     */
+    bool hasNode(const size_t ID) const;
+
+    /** @brief Tells whether a node belongs to this tree.
+     * @param[in]       node      Given node
+     * @retval true     Node belongs to this tree
+     * @retval false    Node does not belong to this tree
+     */
+    bool hasNode(const Node &node) const;
+
+
+
+    /** @brief Returns number of nodes in this unrooted tree
+     * @return Number of nodes in this tree
+     */
+    size_t getSize() const;
+
+    /** @brief Returns node with given identifier.
+     *
+     * If identifier is invalid, returns an empty node.
+     * @param[in]       identifier Identifier of the node
+     * @return Node with given identifier
+     */
+    Node &getNode(const size_t identifier) const;
+
+    /** @brief Returns every node in this tree.
+     * @return Nodes as a vector
+     */
+    vector<Node *> getNodes() const;
+
+    /** @brief Returns leaves in this tree.
+     * @return Leaves as a vector
+     */
+    vector<Node *> getLeaves() const;
+
+    /** @brief Returns matrix of distances among leaves.
+     * @return Distance matrix
+     */
+    virtual DistanceMatrix &getDistanceMatrix() const;
+
+
+
+    /** @brief Adds a node into this tree.
+     * @param[in]      node      Node to insert
+     * @return This tree itself
+     */
+    UnrootedTree &addNode(Node &node);
+
+
+
+    /** @brief Returns a rooted version of this tree.
+     * 
+     * Root node is chosen using the midpoint rooting strategy.
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &midpointRoot() const;
+
+    /** @brief Returns a rooted version of this tree.
+     *
+     * Root node is chosen with a midpoint strategy.
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &asRootedTree() const;
+
+    /** @brief Returns a rooted version of this tree.
+     *
+     * Tree is rooted in one node of its.
+     * @param[in]       root      Identifier of the root node
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &asRootedTree(const size_t root) const;
+
+    /** @brief Returns a rooted version of this tree.
+     *
+     * Tree is rooted in one node of its.
+     * @param[in]       root      Node that will become root
+     * @param[in]       parent    Pointer to parent node
+     * @return A rooted version of this tree
+     */
+    virtual RootedTree &asRootedTree(Node &root, const Node *parent = nullptr) const;
+
+    /** @brief Returns an unrooted version of this tree.
+     * @return An unrooted version of this tree
+     */
+    virtual UnrootedTree &asUnrootedTree() const;
+
+    /** @brief Parses a string in Newick format.
+     * @param[in]       input     String in Newick format
+     * @return This tree itself
+     */
+    virtual UnrootedTree &parseNewick(const string &input);
+
+    /** @brief Returns a Newick version of this tree.
+     * @return String representing this tree in Newick format
+     */
+    virtual string asNewick() const;
+
+
+
+    /** @brief Accepts a visitor.
+     * @param[in, out]  visitor   Visitor to accept
+     * @return This tree itself
+     */
+    virtual UnrootedTree &accept(Visitor &visitor);
+
+
+
+ private:
+    /** Empty tree. */
+    static UnrootedTree emptyTree;
+
+    /** Nodes in this tree. */
+    map<const size_t, Node *> nodes;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_UNROOTEDTREE_H_
\ No newline at end of file
diff --git a/Phylo/Sources/Visitor.h b/Phylo/Sources/Visitor.h
new file mode 100644
index 0000000..80bb3fe
--- /dev/null
+++ b/Phylo/Sources/Visitor.h
@@ -0,0 +1,63 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_VISITOR_H_
+#define _VICTOR_PHYLO_VISITOR_H_
+
+namespace Victor {
+namespace Phylo {
+
+// Forward class declaration
+class PhylogeneticTree;
+class RootedTree;
+class UnrootedTree;
+
+/** @brief A visitor for the phylogenetic tree hierarchy.
+ * 
+ * This class defines the interface of a visitor for the phylogenetic
+ * tree hierarchy: PhylogeneticTree, RootedTree and UnrootedTree.
+ *
+ * This class follows the Visitor Design Pattern.
+ *
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class Visitor {
+ public:
+    /** @brief Destructor. */
+    virtual ~Visitor() = 0;
+
+
+
+    /** @brief Visits a phylogenetic tree.
+     * @param[in, out]  tree      Phylogenetic tree to visit
+     */
+    virtual void visit(PhylogeneticTree &tree) = 0;
+
+    /** @brief Visits a rooted tree.
+     * @param[in, out]  tree      Rooted tree to visit
+     */
+    virtual void visit(RootedTree &tree) = 0;
+
+    /** @brief Visits an unrooted tree.
+     * @param[in, out]  tree      Unrooted tree to visit
+     */
+    virtual void visit(UnrootedTree &tree) = 0;
+};
+
+}  // namespace Phylo
+}  // namespace Victor
+
+#endif  // _VICTOR_PHYLO_VISITOR_H_
\ No newline at end of file
diff --git a/Phylo/Sources/phylo.h b/Phylo/Sources/phylo.h
new file mode 100644
index 0000000..c0dde03
--- /dev/null
+++ b/Phylo/Sources/phylo.h
@@ -0,0 +1,58 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef _VICTOR_PHYLO_PHYLO_
+#define _VICTOR_PHYLO_PHYLO_
+
+
+namespace Victor {
+/** @brief Molecular PHYLOgenenesys package.
+ * 
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+namespace Phylo {}
+}
+
+#include <AminoAcid.h>
+#include <Sequence.h>
+#include <SubstitutionMatrix.h>
+
+#include <DistanceMatrix.h>
+#include <DistanceMatrixBuilder.h>
+#include <IdentityPercentage.h>
+#include <LevenshteinDistance.h>
+#include <FengDoolittleDistance.h>
+
+#include <PhylogeneticTree.h>
+#include <RootedTree.h>
+#include <UnrootedTree.h>
+#include <NewickParser.h>
+
+#include <PhylogeneticAlgorithm.h>
+#include <ClusteringAlgorithm.h>
+#include <UPGMA.h>
+#include <FitchMargoliash.h>
+#include <NJ.h>
+
+#include <MultipleAlignment.h>
+
+#include <MultipleAlignmentAlgorithm.h>
+#include <FengDoolittle.h>
+#include <ClustalW.h>
+
+#include <Visitor.h>
+
+#endif  // _VICTOR_PHYLO_PHYLO_
\ No newline at end of file
diff --git a/Phylo/Sources/precalculated_matrices.h b/Phylo/Sources/precalculated_matrices.h
new file mode 100644
index 0000000..ef10b5f
--- /dev/null
+++ b/Phylo/Sources/precalculated_matrices.h
@@ -0,0 +1,864 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+/* These matrices are extracted form the official ClustalW implementation.
+ * Credits go to Mark Larkin, Copyright (c) 2007 Des Higgins, Julie Thompson
+ * and Toby Gibson.  
+ */
+
+#ifndef _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_
+#define _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_
+
+#include <string>
+
+using std::string;
+
+namespace Victor {
+namespace Phylo {
+
+/** Sorted residues used in precalculated matrices. */
+const string _residues = "ABCDEFGHIKLMNPQRSTVWXYZ";
+
+
+
+////////////////////////////////////////////////////////////////////////
+// BLOSUM family
+int _blosum30[] = {
+    4,
+    0,  5,
+   -3, -2, 17,
+    0,  5, -3,  9,
+    0,  0,  1,  1,  6,
+   -2, -3, -3, -5, -4, 10,
+    0,  0, -4, -1, -2, -3,  8,
+   -2, -2, -5, -2,  0, -3, -3, 14,
+    0, -2, -2, -4, -3,  0, -1, -2,  6,
+    0,  0, -3,  0,  2, -1, -1, -2, -2,  4,
+   -1, -1,  0, -1, -1,  2, -2, -1,  2, -2,  4,
+    1, -2, -2, -3, -1, -2, -2,  2,  1,  2,  2,  6,
+    0,  4, -1,  1, -1, -1,  0, -1,  0,  0, -2,  0,  8,
+   -1, -2, -3, -1,  1, -4, -1,  1, -3,  1, -3, -4, -3, 11,
+    1, -1, -2, -1,  2, -3, -2,  0, -2,  0, -2, -1, -1,  0,  8,
+   -1, -2, -2, -1, -1, -1, -2, -1, -3,  1, -2,  0, -2, -1,  3,  8,
+    1,  0, -2,  0,  0, -1,  0, -1, -1,  0, -2, -2,  0, -1, -1, -1,  4,
+    1,  0, -2, -1, -2, -2, -2, -2,  0, -1,  0,  0,  1,  0,  0, -3,  2,  5,
+    1, -2, -2, -2, -3,  1, -3, -3,  4, -2,  1,  0, -2, -4, -3, -1, -1,  1,  5,
+   -5, -5, -2, -4, -1,  1,  1, -5, -3, -2, -2, -3, -7, -3, -1,  0, -3, -5, -3, 20,
+    0, -1, -2, -1, -1, -1, -1, -1,  0,  0,  0,  0,  0, -1,  0, -1,  0,  0,  0, -2, -1,
+   -4, -3, -6, -1, -2,  3, -3,  0, -1, -1,  3, -1, -4, -2, -1,  0, -2, -1,  1,  5, -1,  9,
+    0,  0,  0,  0,  5, -4, -2,  0, -3,  1, -1, -1, -1,  0,  4,  0, -1, -1, -3, -1,  0, -2,  4
+};
+
+int _blosum35[] = {
+    5,
+   -1,  5,
+   -2, -2, 15,
+   -1,  5, -3,  8,
+   -1,  0, -1,  2,  6,
+   -2, -2, -4, -3, -3,  8,
+    0,  0, -3, -2, -2, -3,  7,
+   -2,  0, -4,  0, -1, -3, -2, 12,
+   -1, -2, -4, -3, -3,  1, -3, -3,  5,
+    0,  0, -2, -1,  1, -1, -1, -2, -2,  5,
+   -2, -2, -2, -2, -1,  2, -3, -2,  2, -2,  5,
+    0, -2, -4, -3, -2,  0, -1,  1,  1,  0,  3,  6,
+   -1,  4, -1,  1, -1, -1,  1,  1, -1,  0, -2, -1,  7,
+   -2, -1, -4, -1,  0, -4, -2, -1, -1,  0, -3, -3, -2, 10,
+    0,  0, -3, -1,  2, -4, -2, -1, -2,  0, -2, -1,  1,  0,  7,
+   -1, -1, -3, -1, -1, -1, -2, -1, -3,  2, -2,  0, -1, -2,  2,  8,
+    1,  0, -3, -1,  0, -1,  1, -1, -2,  0, -2, -1,  0, -2,  0, -1,  4,
+    0, -1, -1, -1, -1, -1, -2, -2, -1,  0,  0,  0,  0,  0,  0, -2,  2,  5,
+    0, -2, -2, -2, -2,  1, -3, -4,  4, -2,  2,  1, -2, -3, -3, -1, -1,  1,  5,
+   -2, -3, -5, -3, -1,  1, -1, -4, -1,  0,  0,  1, -2, -4, -1,  0, -2, -2, -2, 16,
+    0, -1, -2, -1, -1, -1, -1, -1,  0,  0,  0,  0,  0, -1, -1, -1,  0,  0,  0, -1, -1,
+   -1, -2, -5, -2, -1,  3, -2,  0,  0, -1,  0,  0, -2, -3,  0,  0, -1, -2,  0,  3, -1,  8,
+   -1,  0, -2,  1,  5, -3, -2, -1, -3,  1, -2, -2,  0,  0,  4,  0,  0, -1, -2, -1,  0, -1,  4
+};
+
+int _blosum40[] = {
+    5,
+   -1,  5,
+   -2, -2, 16,
+   -1,  6, -2,  9,
+   -1,  1, -2,  2,  7,
+   -3, -3, -2, -4, -3,  9,
+    1, -1, -3, -2, -3, -3,  8,
+   -2,  0, -4,  0,  0, -2, -2, 13,
+   -1, -3, -4, -4, -4,  1, -4, -3,  6,
+   -1,  0, -3,  0,  1, -3, -2, -1, -3,  6,
+   -2, -3, -2, -3, -2,  2, -4, -2,  2, -2,  6,
+   -1, -3, -3, -3, -2,  0, -2,  1,  1, -1,  3,  7,
+   -1,  4, -2,  2, -1, -3,  0,  1, -2,  0, -3, -2,  8,
+   -2, -2, -5, -2,  0, -4, -1, -2, -2, -1, -4, -2, -2, 11,
+    0,  0, -4, -1,  2, -4, -2,  0, -3,  1, -2, -1,  1, -2,  8,
+   -2, -1, -3, -1, -1, -2, -3,  0, -3,  3, -2, -1,  0, -3,  2,  9,
+    1,  0, -1,  0,  0, -2,  0, -1, -2,  0, -3, -2,  1, -1,  1, -1,  5,
+    0,  0, -1, -1, -1, -1, -2, -2, -1,  0, -1, -1,  0,  0, -1, -2,  2,  6,
+    0, -3, -2, -3, -3,  0, -4, -4,  4, -2,  2,  1, -3, -3, -3, -2, -1,  1,  5,
+   -3, -4, -6, -5, -2,  1, -2, -5, -3, -2, -1, -2, -4, -4, -1, -2, -5, -4, -3, 19,
+    0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1,  0, -1, -2, -1, -1,  0,  0, -1, -2, -1,
+   -2, -3, -4, -3, -2,  4, -3,  2,  0, -1,  0,  1, -2, -3, -1, -1, -2, -1, -1,  3, -1,  9,
+   -1,  2, -3,  1,  5, -4, -2,  0, -4,  1, -2, -2,  0, -1,  4,  0,  0, -1, -3, -2, -1, -2,  5
+};
+
+int _blosum45[] = {
+    5,
+   -1,  4,
+   -1, -2, 12,
+   -2,  5, -3,  7,
+   -1,  1, -3,  2,  6,
+   -2, -3, -2, -4, -3,  8,
+    0, -1, -3, -1, -2, -3,  7,
+   -2,  0, -3,  0,  0, -2, -2, 10,
+   -1, -3, -3, -4, -3,  0, -4, -3,  5,
+   -1,  0, -3,  0,  1, -3, -2, -1, -3,  5,
+   -1, -3, -2, -3, -2,  1, -3, -2,  2, -3,  5,
+   -1, -2, -2, -3, -2,  0, -2,  0,  2, -1,  2,  6,
+   -1,  4, -2,  2,  0, -2,  0,  1, -2,  0, -3, -2,  6,
+   -1, -2, -4, -1,  0, -3, -2, -2, -2, -1, -3, -2, -2,  9,
+   -1,  0, -3,  0,  2, -4, -2,  1, -2,  1, -2,  0,  0, -1,  6,
+   -2, -1, -3, -1,  0, -2, -2,  0, -3,  3, -2, -1,  0, -2,  1,  7,
+    1,  0, -1,  0,  0, -2,  0, -1, -2, -1, -3, -2,  1, -1,  0, -1,  4,
+    0,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1,  0, -1, -1, -1,  2,  5,
+    0, -3, -1, -3, -3,  0, -3, -3,  3, -2,  1,  1, -3, -3, -3, -2, -1,  0,  5,
+   -2, -4, -5, -4, -3,  1, -2, -3, -2, -2, -2, -2, -4, -3, -2, -2, -4, -3, -3, 15,
+    0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0,  0, -1, -2, -1,
+   -2, -2, -3, -2, -2,  3, -3,  2,  0, -1,  0,  0, -2, -3, -1, -1, -2, -1, -1,  3, -1,  8,
+   -1,  2, -3,  1,  4, -3, -2,  0, -3,  1, -2, -1,  0, -1,  4,  0,  0, -1, -3, -2, -1, -2,  4
+};
+
+int _blosum50[] = {
+    5,
+   -2,  5,
+   -1, -3, 13,
+   -2,  5, -4,  8,
+   -1,  1, -3,  2,  6,
+   -3, -4, -2, -5, -3,  8,
+    0, -1, -3, -1, -3, -4,  8,
+   -2,  0, -3, -1,  0, -1, -2, 10,
+   -1, -4, -2, -4, -4,  0, -4, -4,  5,
+   -1,  0, -3, -1,  1, -4, -2,  0, -3,  6,
+   -2, -4, -2, -4, -3,  1, -4, -3,  2, -3,  5,
+   -1, -3, -2, -4, -2,  0, -3, -1,  2, -2,  3,  7,
+   -1,  4, -2,  2,  0, -4,  0,  1, -3,  0, -4, -2,  7,
+   -1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10,
+   -1,  0, -3,  0,  2, -4, -2,  1, -3,  2, -2,  0,  0, -1,  7,
+   -2, -1, -4, -2,  0, -3, -3,  0, -4,  3, -3, -2, -1, -3,  1,  7,
+    1,  0, -1,  0, -1, -3,  0, -1, -3,  0, -3, -2,  1, -1,  0, -1,  5,
+    0,  0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1,  0, -1, -1, -1,  2,  5,
+    0, -4, -1, -4, -3, -1, -4, -4,  4, -3,  1,  1, -3, -3, -3, -3, -2,  0,  5,
+   -3, -5, -5, -5, -3,  1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15,
+   -1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1,  0, -1, -3, -1,
+   -2, -3, -3, -3, -2,  4, -3,  2, -1, -2, -1,  0, -2, -3, -1, -1, -2, -2, -1,  2, -1,  8,
+   -1,  2, -3,  1,  5, -4, -2,  0, -3,  1, -3, -1,  0, -1,  4,  0,  0, -1, -3, -2, -1, -2,  5
+};
+
+int _blosum55[] = {
+    5,
+   -2,  5,
+    0, -4, 13,
+   -2,  5, -4,  8,
+   -1,  1, -4,  2,  7,
+   -3, -5, -3, -5, -4,  9,
+    0, -1, -3, -2, -3, -4,  8,
+   -2,  0, -4, -1, -1, -1, -2, 11,
+   -2, -4, -2, -4, -4,  0, -5, -4,  6,
+   -1,  0, -4, -1,  1, -4, -2,  0, -4,  6,
+   -2, -4, -2, -5, -4,  1, -5, -3,  2, -3,  6,
+   -1, -3, -2, -4, -3,  0, -3, -2,  2, -2,  3,  8,
+   -2,  4, -3,  2,  0, -4,  0,  1, -4,  0, -4, -3,  8,
+   -1, -2, -3, -2, -1, -5, -3, -3, -3, -1, -4, -3, -2, 10,
+   -1,  0, -4,  0,  2, -4, -2,  1, -4,  2, -3,  0,  0, -1,  7,
+   -2, -1, -4, -2,  0, -3, -3,  0, -4,  3, -3, -2, -1, -3,  1,  8,
+    2,  0, -1,  0,  0, -3,  0, -1, -3,  0, -3, -2,  1, -1,  0, -1,  5,
+    0, -1, -1, -1, -1, -3, -2, -2, -1, -1, -2, -1,  0, -1, -1, -1,  2,  6,
+    0, -4, -1, -4, -3, -1, -4, -4,  4, -3,  1,  1, -4, -3, -3, -3, -2,  0,  5,
+   -4, -5, -4, -5, -3,  2, -3, -3, -3, -4, -3, -2, -5, -5, -2, -3, -4, -3, -4, 15,
+   -1, -1, -2, -2, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1,
+   -2, -3, -3, -3, -2,  4, -4,  2, -1, -2, -1, -1, -2, -4, -1, -2, -2, -2, -2,  3, -1,  9,
+   -1,  2, -4,  1,  5, -4, -3,  0, -4,  1, -3, -2,  0, -1,  4,  0,  0, -1, -3, -3, -1, -2,  5
+};
+
+int _blosum62[] = {
+    4,
+   -2,  4,
+    0, -3,  9,
+   -2,  4, -3,  6,
+   -1,  1, -4,  2,  5,
+   -2, -3, -2, -3, -3,  6,
+    0, -1, -3, -1, -2, -3,  6,
+   -2,  0, -3, -1,  0, -1, -2,  8,
+   -1, -3, -1, -3, -3,  0, -4, -3,  4,
+   -1,  0, -3, -1,  1, -3, -2, -1, -3,  5,
+   -1, -4, -1, -4, -3,  0, -4, -3,  2, -2,  4,
+   -1, -3, -1, -3, -2,  0, -3, -2,  1, -1,  2,  5,
+   -2,  3, -3,  1,  0, -3,  0,  1, -3,  0, -3, -2,  6,
+   -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2,  7,
+   -1,  0, -3,  0,  2, -3, -2,  0, -3,  1, -2,  0,  0, -1,  5,
+   -1, -1, -3, -2,  0, -3, -2,  0, -3,  2, -2, -1,  0, -2,  1,  5,
+    1,  0, -1,  0,  0, -2,  0, -1, -2,  0, -2, -1,  1, -1,  0, -1,  4,
+    0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1,  0, -1, -1, -1,  1,  5,
+    0, -3, -1, -3, -2, -1, -3, -3,  3, -2,  1,  1, -3, -2, -2, -3, -2,  0,  4,
+   -3, -4, -2, -4, -3,  1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11,
+    0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1,  0,  0, -1, -2, -1,
+   -2, -3, -2, -3, -2,  3, -3,  2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1,  2, -1,  7,
+   -1,  1, -3,  1,  4, -3, -2,  0, -3,  1, -3, -1,  0, -1,  3,  0,  0, -1, -2, -3, -1, -2,  4
+};
+
+int _blosum65[] = {
+    4,
+   -2,  4,
+    0, -3,  9,
+   -2,  4, -4,  6,
+   -1,  1, -4,  2,  5,
+   -2, -3, -2, -4, -3,  6,
+    0, -1, -3, -1, -2, -3,  6,
+   -2,  0, -3, -1,  0, -1, -2,  8,
+   -1, -3, -1, -3, -3,  0, -4, -3,  4,
+   -1,  0, -3, -1,  1, -3, -2, -1, -3,  5,
+   -2, -4, -1, -4, -3,  0, -4, -3,  2, -3,  4,
+   -1, -3, -2, -3, -2,  0, -3, -2,  1, -2,  2,  6,
+   -2,  3, -3,  1,  0, -3, -1,  1, -3,  0, -4, -2,  6,
+   -1, -2, -3, -2, -1, -4, -2, -2, -3, -1, -3, -3, -2,  8,
+   -1,  0, -3,  0,  2, -3, -2,  1, -3,  1, -2,  0,  0, -1,  6,
+   -1, -1, -4, -2,  0, -3, -2,  0, -3,  2, -2, -2,  0, -2,  1,  6,
+    1,  0, -1,  0,  0, -2,  0, -1, -2,  0, -3, -2,  1, -1,  0, -1,  4,
+    0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1,  0, -1, -1, -1,  1,  5,
+    0, -3, -1, -3, -3, -1, -3, -3,  3, -2,  1,  1, -3, -2, -2, -3, -2,  0,  4,
+   -3, -4, -2, -5, -3,  1, -3, -2, -2, -3, -2, -2, -4, -4, -2, -3, -3, -3, -3, 10,
+   -1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -2, -1,
+   -2, -3, -2, -3, -2,  3, -3,  2, -1, -2, -1, -1, -2, -3, -2, -2, -2, -2, -1,  2, -1,  7,
+   -1,  1, -4,  1,  4, -3, -2,  0, -3,  1, -3, -2,  0, -1,  3,  0,  0, -1, -2, -3, -1, -2,  4
+};
+
+int _blosum70[] = {
+    4,
+   -2,  4,
+   -1, -4,  9,
+   -2,  4, -4,  6,
+   -1,  1, -4,  1,  5,
+   -2, -4, -2, -4, -4,  6,
+    0, -1, -3, -2, -2, -4,  6,
+   -2, -1, -4, -1,  0, -1, -2,  8,
+   -2, -4, -1, -4, -4,  0, -4, -4,  4,
+   -1, -1, -4, -1,  1, -3, -2, -1, -3,  5,
+   -2, -4, -2, -4, -3,  0, -4, -3,  2, -3,  4,
+   -1, -3, -2, -3, -2,  0, -3, -2,  1, -2,  2,  6,
+   -2,  3, -3,  1,  0, -3, -1,  0, -4,  0, -4, -2,  6,
+   -1, -2, -3, -2, -1, -4, -3, -2, -3, -1, -3, -3, -2,  8,
+   -1,  0, -3, -1,  2, -3, -2,  1, -3,  1, -2,  0,  0, -2,  6,
+   -2, -1, -4, -2,  0, -3, -3,  0, -3,  2, -3, -2, -1, -2,  1,  6,
+    1,  0, -1,  0,  0, -3, -1, -1, -3,  0, -3, -2,  0, -1,  0, -1,  4,
+    0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -2, -1,  0, -1, -1, -1,  1,  5,
+    0, -3, -1, -4, -3, -1, -4, -3,  3, -3,  1,  1, -3, -3, -2, -3, -2,  0,  4,
+   -3, -4, -3, -5, -4,  1, -3, -2, -3, -3, -2, -2, -4, -4, -2, -3, -3, -3, -3, 11,
+   -1, -1, -2, -2, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1,
+   -2, -3, -3, -4, -3,  3, -4,  2, -1, -2, -1, -1, -2, -3, -2, -2, -2, -2, -2,  2, -2,  7,
+   -1,  0, -4,  1,  4, -4, -2,  0, -3,  1, -3, -2,  0, -1,  3,  0,  0, -1, -3, -3, -1, -2,  4
+};
+
+int _blosum75[] = {
+    4,
+   -2,  4,
+   -1, -4,  9,
+   -2,  4, -4,  6,
+   -1,  1, -5,  1,  5,
+   -3, -4, -2, -4, -4,  6,
+    0, -1, -3, -2, -3, -4,  6,
+   -2, -1, -4, -1,  0, -2, -2,  8,
+   -2, -4, -1, -4, -4,  0, -5, -4,  4,
+   -1, -1, -4, -1,  1, -4, -2, -1, -3,  5,
+   -2, -4, -2, -4, -4,  0, -4, -3,  1, -3,  4,
+   -1, -3, -2, -4, -2,  0, -3, -2,  1, -2,  2,  6,
+   -2,  3, -3,  1, -1, -4, -1,  0, -4,  0, -4, -3,  6,
+   -1, -2, -4, -2, -1, -4, -3, -2, -3, -1, -3, -3, -3,  8,
+   -1,  0, -3, -1,  2, -4, -2,  1, -3,  1, -3,  0,  0, -2,  6,
+   -2, -1, -4, -2,  0, -3, -3,  0, -3,  2, -3, -2, -1, -2,  1,  6,
+    1,  0, -1, -1,  0, -3, -1, -1, -3,  0, -3, -2,  0, -1,  0, -1,  5,
+    0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -2, -1,  0, -1, -1, -1,  1,  5,
+    0, -4, -1, -4, -3, -1, -4, -4,  3, -3,  1,  1, -3, -3, -2, -3, -2,  0,  4,
+   -3, -5, -3, -5, -4,  1, -3, -2, -3, -4, -2, -2, -4, -5, -2, -3, -3, -3, -3, 11,
+   -1, -2, -2, -2, -1, -2, -2, -1, -2, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1,
+   -2, -3, -3, -4, -3,  3, -4,  2, -2, -2, -1, -2, -3, -4, -2, -2, -2, -2, -2,  2, -2,  7,
+   -1,  0, -4,  1,  4, -4, -2,  0, -4,  1, -3, -2,  0, -2,  3,  0,  0, -1, -3, -3, -1, -3,  4
+};
+
+int _blosum80[] = {
+    7,
+   -3,  6,
+   -1, -6, 13,
+   -3,  6, -7, 10,
+   -2,  1, -7,  2,  8,
+   -4, -6, -4, -6, -6, 10,
+    0, -2, -6, -3, -4, -6,  9,
+   -3, -1, -7, -2,  0, -2, -4, 12,
+   -3, -6, -2, -7, -6, -1, -7, -6,  7,
+   -1, -1, -6, -2,  1, -5, -3, -1, -5,  8,
+   -3, -7, -3, -7, -6,  0, -7, -5,  2, -4,  6,
+   -2, -5, -3, -6, -4,  0, -5, -4,  2, -3,  3,  9,
+   -3,  5, -5,  2, -1, -6, -1,  1, -6,  0, -6, -4,  9,
+   -1, -4, -6, -3, -2, -6, -5, -4, -5, -2, -5, -4, -4, 12,
+   -2, -1, -5, -1,  3, -5, -4,  1, -5,  2, -4, -1,  0, -3,  9,
+   -3, -2, -6, -3, -1, -5, -4,  0, -5,  3, -4, -3, -1, -3,  1,  9,
+    2,  0, -2, -1, -1, -4, -1, -2, -4, -1, -4, -3,  1, -2, -1, -2,  7,
+    0, -1, -2, -2, -2, -4, -3, -3, -2, -1, -3, -1,  0, -3, -1, -2,  2,  8,
+   -1, -6, -2, -6, -4, -2, -6, -5,  4, -4,  1,  1, -5, -4, -4, -4, -3,  0,  7,
+   -5, -8, -5, -8, -6,  0, -6, -4, -5, -6, -4, -3, -7, -7, -4, -5, -6, -5, -5, 16,
+   -1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2,
+   -4, -5, -5, -6, -5,  4, -6,  3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3,  3, -3, 11,
+   -2,  0, -7,  1,  6, -6, -4,  0, -6,  1, -5, -3, -1, -2,  5,  0, -1, -2, -4, -5, -1, -4,  6
+};
+
+int _blosum85[] = {
+    5,
+   -2,  4,
+   -1, -4,  9,
+   -2,  4, -5,  7,
+   -1,  0, -5,  1,  6,
+   -3, -4, -3, -4, -4,  7,
+    0, -1, -4, -2, -3, -4,  6,
+   -2, -1, -5, -2, -1, -2, -3,  8,
+   -2, -5, -2, -5, -4, -1, -5, -4,  5,
+   -1, -1, -4, -1,  0, -4, -2, -1, -3,  6,
+   -2, -5, -2, -5, -4,  0, -5, -3,  1, -3,  4,
+   -2, -4, -2, -4, -3, -1, -4, -3,  1, -2,  2,  7,
+   -2,  4, -4,  1, -1, -4, -1,  0, -4,  0, -4, -3,  7,
+   -1, -3, -4, -2, -2, -4, -3, -3, -4, -2, -4, -3, -3,  8,
+   -1, -1, -4, -1,  2, -4, -3,  1, -4,  1, -3,  0,  0, -2,  6,
+   -2, -2, -4, -2, -1, -4, -3,  0, -4,  2, -3, -2, -1, -2,  1,  6,
+    1,  0, -2, -1, -1, -3, -1, -1, -3, -1, -3, -2,  0, -1, -1, -1,  5,
+    0, -1, -2, -2, -1, -3, -2, -2, -1, -1, -2, -1,  0, -2, -1, -2,  1,  5,
+   -1, -4, -1, -4, -3, -1, -4, -4,  3, -3,  0,  0, -4, -3, -3, -3, -2,  0,  5,
+   -3, -5, -4, -6, -4,  0, -4, -3, -3, -5, -3, -2, -5, -5, -3, -4, -4, -4, -3, 11,
+   -1, -2, -3, -2, -1, -2, -2, -2, -2, -1, -2, -1, -2, -2, -1, -2, -1, -1, -1, -3, -2,
+   -3, -4, -3, -4, -4,  3, -5,  2, -2, -3, -2, -2, -3, -4, -2, -3, -2, -2, -2,  2, -2,  7,
+   -1,  0, -5,  1,  4, -4, -3,  0, -4,  1, -4, -2, -1, -2,  4,  0, -1, -1, -3, -4, -1, -3,  4
+};
+
+int _blosum90[] = {
+    5,
+   -2,  4,
+   -1, -4,  9,
+   -3,  4, -5,  7,
+   -1,  0, -6,  1,  6,
+   -3, -4, -3, -5, -5,  7,
+    0, -2, -4, -2, -3, -5,  6,
+   -2, -1, -5, -2, -1, -2, -3,  8,
+   -2, -5, -2, -5, -4, -1, -5, -4,  5,
+   -1, -1, -4, -1,  0, -4, -2, -1, -4,  6,
+   -2, -5, -2, -5, -4,  0, -5, -4,  1, -3,  5,
+   -2, -4, -2, -4, -3, -1, -4, -3,  1, -2,  2,  7,
+   -2,  4, -4,  1, -1, -4, -1,  0, -4,  0, -4, -3,  7,
+   -1, -3, -4, -3, -2, -4, -3, -3, -4, -2, -4, -3, -3,  8,
+   -1, -1, -4, -1,  2, -4, -3,  1, -4,  1, -3,  0,  0, -2,  7,
+   -2, -2, -5, -3, -1, -4, -3,  0, -4,  2, -3, -2, -1, -3,  1,  6,
+    1,  0, -2, -1, -1, -3, -1, -2, -3, -1, -3, -2,  0, -2, -1, -1,  5,
+    0, -1, -2, -2, -1, -3, -3, -2, -1, -1, -2, -1,  0, -2, -1, -2,  1,  6,
+   -1, -4, -2, -5, -3, -2, -5, -4,  3, -3,  0,  0, -4, -3, -3, -3, -2, -1,  5,
+   -4, -6, -4, -6, -5,  0, -4, -3, -4, -5, -3, -2, -5, -5, -3, -4, -4, -4, -3, 11,
+   -1, -2, -3, -2, -2, -2, -2, -2, -2, -1, -2, -1, -2, -2, -1, -2, -1, -1, -2, -3, -2,
+   -3, -4, -4, -4, -4,  3, -5,  1, -2, -3, -2, -2, -3, -4, -3, -3, -3, -2, -3,  2, -2,  8,
+   -1,  0, -5,  0,  4, -4, -3,  0, -4,  1, -4, -2, -1, -2,  4,  0, -1, -1, -3, -4, -1, -3,  4
+};
+
+
+
+////////////////////////////////////////////////////////////////////////
+// PAM family
+int _pam20[] = {
+    6,
+   -5,  6,
+   -8,-14, 10,
+   -4,  6,-16,  8,
+   -3,  0,-16,  2,  8,
+   -9,-12,-15,-17,-16,  9,
+   -3, -4,-11, -4, -5,-10,  7,
+   -8, -2, -8, -5, -6, -7,-10,  9,
+   -6, -7, -7, -9, -6, -3,-13,-11,  9,
+   -8, -3,-16, -6, -5,-16, -8, -8, -7,  7,
+   -7,-10,-17,-15,-10, -4,-12, -7, -2, -9,  7,
+   -6,-12,-16,-13, -8, -5,-10,-13, -2, -3,  0, 11,
+   -5,  6,-13,  1, -3,-10, -4, -1, -6, -2, -8,-11,  8,
+   -2, -8, -9, -9, -7,-11, -7, -5,-10, -8, -8, -9, -7,  8,
+   -5, -4,-16, -4,  0,-15, -8,  0, -9, -4, -6, -5, -5, -4,  9,
+   -8, -9, -9,-12,-11,-10,-11, -3, -6, -1,-10, -5, -7, -5, -2,  9,
+   -1, -2, -4, -5, -5, -7, -3, -7, -8, -5, -9, -6, -1, -3, -6, -4,  7,
+   -1, -4, -9, -6, -7,-10, -7, -8, -3, -4, -8, -5, -3, -5, -7, -8,  0,  7,
+   -3, -9, -7, -9, -8, -9, -7, -7,  1,-10, -3, -2, -9, -7, -8, -9, -8, -4,  7,
+  -16,-11,-18,-17,-19, -6,-17, -8,-16,-14, -7,-15, -9,-16,-15, -3, -6,-15,-18, 13,
+   -4, -6,-11, -7, -6, -9, -6, -6, -6, -6, -7, -6, -4, -6, -6, -7, -4, -5, -6,-13, -6,
+   -9, -7, -5,-13, -9,  1,-16, -4, -7,-10, -8,-13, -5,-16,-14,-11, -8, -7, -8, -6, -9, 10,
+   -4, -1,-16,  0,  6,-16, -6, -2, -7, -5, -8, -6, -4, -5,  7, -5, -6, -7, -8,-17, -6,-11,  6
+};
+
+int _pam60[] = {
+    5,
+   -2,  5,
+   -5, -9,  9,
+   -2,  5,-10,  7,
+   -1,  2,-10,  3,  7,
+   -6, -8, -9,-11,-10,  8,
+    0, -2, -7, -2, -2, -7,  6,
+   -5,  0, -6, -2, -3, -4, -6,  8,
+   -3, -4, -4, -5, -4, -1, -7, -6,  7,
+   -5, -1,-10, -2, -3,-10, -5, -4, -4,  6,
+   -4, -7,-11, -9, -7, -1, -8, -4,  0, -6,  6,
+   -3, -6,-10, -7, -5, -2, -6, -7,  1,  0,  2, 10,
+   -2,  5, -7,  2,  0, -6, -1,  1, -4,  0, -5, -6,  6,
+    0, -4, -6, -5, -3, -7, -4, -2, -6, -4, -5, -6, -4,  7,
+   -3, -1,-10, -1,  2, -9, -5,  2, -5, -1, -3, -2, -2, -1,  7,
+   -5, -5, -6, -6, -6, -7, -7,  0, -4,  2, -6, -2, -3, -2,  0,  8,
+    1,  0, -1, -2, -2, -5,  0, -4, -4, -2, -6, -4,  1,  0, -3, -2,  5,
+    1, -2, -5, -3, -4, -6, -3, -5, -1, -2, -5, -2, -1, -2, -4, -4,  1,  6,
+   -1, -5, -4, -6, -4, -5, -4, -5,  3, -6, -1,  0, -5, -4, -5, -5, -4, -1,  6,
+  -10, -8,-12,-11,-12, -3,-11, -5,-10, -8, -4, -9, -6,-10, -9,  0, -4, -9,-11, 13,
+   -2, -3, -6, -3, -3, -5, -3, -3, -3, -3, -4, -3, -2, -3, -3, -4, -2, -2, -3, -8, -3,
+   -6, -5, -2, -8, -7,  3,-10, -2, -4, -7, -5, -7, -3,-10, -8, -8, -5, -5, -5, -3, -5,  9,
+   -2,  1,-10,  2,  5,-10, -3,  0, -4, -2, -5, -4, -1, -2,  6, -2, -3, -4, -5,-11, -3, -7,  5
+};
+
+int _pam120[] = {
+    3,
+    0,  4,
+   -3, -6,  9,
+    0,  4, -7,  5,
+    0,  3, -7,  3,  5,
+   -4, -5, -6, -7, -7,  8,
+    1,  0, -4,  0, -1, -5,  5,
+   -3,  1, -4,  0, -1, -3, -4,  7,
+   -1, -3, -3, -3, -3,  0, -4, -4,  6,
+   -2,  0, -7, -1, -1, -7, -3, -2, -3,  5,
+   -3, -4, -7, -5, -4,  0, -5, -3,  1, -4,  5,
+   -2, -4, -6, -4, -3, -1, -4, -4,  1,  0,  3,  8,
+   -1,  3, -5,  2,  1, -4,  0,  2, -2,  1, -4, -3,  4,
+    1, -2, -4, -3, -2, -5, -2, -1, -3, -2, -3, -3, -2,  6,
+   -1,  0, -7,  1,  2, -6, -3,  3, -3,  0, -2, -1,  0,  0,  6,
+   -3, -2, -4, -3, -3, -5, -4,  1, -2,  2, -4, -1, -1, -1,  1,  6,
+    1,  0,  0,  0, -1, -3,  1, -2, -2, -1, -4, -2,  1,  1, -2, -1,  3,
+    1,  0, -3, -1, -2, -4, -1, -3,  0, -1, -3, -1,  0, -1, -2, -2,  2,  4,
+    0, -3, -3, -3, -3, -3, -2, -3,  3, -4,  1,  1, -3, -2, -3, -3, -2,  0,  5,
+   -7, -6, -8, -8, -8, -1, -8, -3, -6, -5, -3, -6, -4, -7, -6,  1, -2, -6, -8, 12,
+   -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -1, -2, -1, -2, -1, -1, -1, -5, -2,
+   -4, -3, -1, -5, -5,  4, -6, -1, -2, -5, -2, -4, -2, -6, -5, -5, -3, -3, -3, -2, -3,  8,
+   -1,  2, -7,  3,  4, -6, -2,  1, -3, -1, -3, -2,  0, -1,  4, -1, -1, -2, -3, -7, -1, -5,  4
+};
+
+int _pam160[] = {
+    2,
+    0,  3,
+   -2, -4,  9,
+    0,  3, -5,  4,
+    0,  2, -5,  3,  4,
+   -3, -4, -5, -6, -5,  7,
+    1,  0, -3,  0,  0, -4,  4,
+   -2,  1, -3,  0,  0, -2, -3,  6,
+   -1, -2, -2, -3, -2,  0, -3, -3,  5,
+   -2,  0, -5,  0, -1, -5, -2, -1, -2,  4,
+   -2, -4, -6, -4, -3,  1, -4, -2,  2, -3,  5,
+   -1, -3, -5, -3, -2,  0, -3, -3,  2,  0,  3,  7,
+    0,  2, -4,  2,  1, -3,  0,  2, -2,  1, -3, -2,  3,
+    1, -1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -2, -1,  5,
+   -1,  1, -5,  1,  2, -5, -2,  2, -2,  0, -2, -1,  0,  0,  5,
+   -2, -1, -3, -2, -2, -4, -3,  1, -2,  3, -3, -1, -1, -1,  1,  6,
+    1,  0,  0,  0,  0, -3,  1, -1, -2, -1, -3, -2,  1,  1, -1, -1,  2,
+    1,  0, -2, -1, -1, -3, -1, -2,  0,  0, -2, -1,  0,  0, -1, -1,  1,  3,
+    0, -2, -2, -3, -2, -2, -2, -2,  3, -3,  1,  1, -2, -2, -2, -3, -1,  0,  4,
+   -5, -5, -7, -6, -7, -1, -7, -3, -5, -4, -2, -4, -4, -5, -5,  1, -2, -5, -6, 12,
+    0, -1, -3, -1, -1, -3, -1, -1, -1, -1, -2, -1,  0, -1, -1, -1,  0,  0, -1, -4, -1,
+   -3, -3,  0, -4, -4,  5, -5,  0, -2, -4, -2, -3, -2, -5, -4, -4, -3, -3, -3, -1, -3,  8,
+    0,  2, -5,  2,  3, -5, -1,  1, -2,  0, -3, -2,  1, -1,  3,  0, -1, -1, -2, -6, -1, -4,  3
+};
+
+int _pam250[] = {
+    2,
+    0,  3,
+   -2, -4, 12,
+    0,  3, -5,  4,
+    0,  3, -5,  3,  4,
+   -3, -4, -4, -6, -5,  9,
+    1,  0, -3,  1,  0, -5,  5,
+   -1,  1, -3,  1,  1, -2, -2,  6,
+   -1, -2, -2, -2, -2,  1, -3, -2,  5,
+   -1,  1, -5,  0,  0, -5, -2,  0, -2,  5,
+   -2, -3, -6, -4, -3,  2, -4, -2,  2, -3,  6,
+   -1, -2, -5, -3, -2,  0, -3, -2,  2,  0,  4,  6,
+    0,  2, -4,  2,  1, -3,  0,  2, -2,  1, -3, -2,  2,
+    1, -1, -3, -1, -1, -5,  0,  0, -2, -1, -3, -2,  0,  6,
+    0,  1, -5,  2,  2, -5, -1,  3, -2,  1, -2, -1,  1,  0,  4,
+   -2, -1, -4, -1, -1, -4, -3,  2, -2,  3, -3,  0,  0,  0,  1,  6,
+    1,  0,  0,  0,  0, -3,  1, -1, -1,  0, -3, -2,  1,  1, -1,  0,  2,
+    1,  0, -2,  0,  0, -3,  0, -1,  0,  0, -2, -1,  0,  0, -1, -1,  1,  3,
+    0, -2, -2, -2, -2, -1, -1, -2,  4, -2,  2,  2, -2, -1, -2, -2, -1,  0,  4,
+   -6, -5, -8, -7, -7,  0, -7, -3, -5, -3, -2, -4, -4, -6, -5,  2, -2, -5, -6, 17,
+    0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1,  0,  0, -1, -4, -1,
+   -3, -3,  0, -4, -4,  7, -5,  0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2,  0, -2, 10,
+    0,  2, -5,  3,  3, -5,  0,  2, -2,  0, -3, -2,  1,  0,  3,  0,  0, -1, -2, -6, -1, -4,  3
+};
+
+int _pam350[] = {
+    2,
+    1,  3,
+   -2, -5, 18,
+    1,  3, -6,  4,
+    1,  3, -6,  4,  4,
+   -4, -5, -5, -6, -6, 13,
+    2,  1, -4,  1,  1, -6,  5,
+   -1,  1, -4,  1,  1, -2, -2,  7,
+    0, -2, -3, -2, -2,  2, -2, -2,  5,
+   -1,  1, -6,  1,  0, -6, -1,  1, -2,  5,
+   -2, -4, -7, -4, -4,  3, -4, -2,  4, -3,  8,
+   -1, -2, -6, -3, -2,  1, -3, -2,  3,  0,  5,  6,
+    0,  2, -4,  2,  2, -4,  1,  2, -2,  1, -3, -2,  2,
+    1,  0, -3,  0,  0, -5,  0,  0, -2, -1, -3, -2,  0,  6,
+    0,  2, -6,  2,  3, -5, -1,  3, -2,  1, -2, -1,  1,  1,  4,
+   -1,  0, -4, -1,  0, -5, -2,  2, -2,  4, -3,  0,  1,  0,  2,  7,
+    1,  1,  0,  1,  0, -4,  1, -1, -1,  0, -3, -2,  1,  1,  0,  0,  1,
+    1,  0, -2,  0,  0, -3,  1, -1,  0,  0, -2, -1,  1,  1,  0, -1,  1,  2,
+    0, -2, -2, -2, -2, -1, -1, -2,  4, -2,  3,  2, -2, -1, -2, -3, -1,  0,  5,
+   -7, -6,-10, -8, -8,  1, -8, -3, -6, -4, -2, -5, -5, -7, -5,  4, -3, -6, -7, 27,
+    0,  0, -3, -1,  0, -2, -1,  0,  0, -1, -1,  0,  0,  0,  0, -1,  0,  0,  0, -5, -1,
+   -4, -4,  1, -5, -5, 11, -6,  0,  0, -5,  0, -2, -3, -6, -5, -5, -3, -3, -2,  1, -2, 14,
+    0,  2, -6,  3,  3, -6,  0,  2, -2,  1, -3, -2,  2,  0,  3,  1,  0,  0, -2, -7,  0, -5,  3
+};
+
+
+
+////////////////////////////////////////////////////////////////////////
+// MD family
+int _md40[] = {
+    9,
+    0,  0,
+   -7,  0, 16,
+   -6,  0,-13, 11,
+   -5,  0,-15,  3, 11,
+  -11,  0, -5,-15,-16, 13,
+   -3,  0, -7, -4, -4,-15, 10,
+   -9,  0, -6, -4, -8, -7,-10, 14,
+   -6,  0,-11,-12,-12, -5,-13,-11, 11,
+   -8,  0,-12, -8, -3,-16, -9, -6,-11, 11,
+   -9,  0,-10,-14,-13, -1,-14, -7, -1,-12,  9,
+   -6,  0, -9,-12,-11, -7,-12, -9,  1, -7,  1, 14,
+   -6,  0, -8,  1, -5,-12, -5,  0, -8, -1,-12, -9, 12,
+   -2,  0,-11,-11,-11,-11, -9, -4,-11,-10, -5,-10, -9, 12,
+   -7,  0,-12, -6,  0,-14, -9,  2,-12, -1, -6, -8, -5, -3, 12,
+   -7,  0, -5,-10, -8,-15, -4,  0,-10,  3, -9, -8, -6, -6,  0, 11,
+    0,  0, -2, -6, -8, -6, -2, -6, -8, -7, -7, -8,  1, -1, -7, -5,  9,
+    1,  0, -7, -8, -8,-11, -7, -7, -2, -5, -9, -2, -2, -4, -7, -6,  1, 10,
+   -1,  0, -7, -9, -8, -6, -8,-12,  4,-12, -2,  0,-10, -9,-11,-11, -7, -4, 10,
+  -14,  0, -4,-15,-15, -7, -7,-13,-13,-13, -8,-11,-14,-14,-11, -4, -9,-12,-10, 18,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+  -13,  0, -2, -8,-14,  2,-13,  2, -9,-13, -9,-11, -6,-13, -9,-10, -7,-10,-11, -6,  0, 14,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+};
+
+int _md120[] = {
+    6,
+    0,  0,
+   -3,  0, 14,
+   -2,  0, -7,  8,
+   -2,  0, -8,  5,  8,
+   -6,  0, -2, -9,-10, 11,
+    0,  0, -3,  0, -1, -9,  8,
+   -4,  0, -2, -1, -3, -2, -4, 11,
+   -1,  0, -5, -7, -7, -1, -6, -6,  7,
+   -4,  0, -6, -2,  0, -9, -4, -1, -6,  8,
+   -4,  0, -5, -8, -8,  2, -8, -4,  2, -6,  7,
+   -2,  0, -5, -7, -6, -2, -6, -5,  3, -4,  3, 10,
+   -1,  0, -3,  3, -1, -6, -1,  2, -4,  1, -6, -5,  8,
+    0,  0, -5, -5, -5, -5, -4, -1, -5, -4, -2, -5, -3,  9,
+   -3,  0, -6, -1,  2, -7, -4,  4, -6,  2, -3, -4, -1,  0,  9,
+   -3,  0, -2, -4, -3, -8, -1,  2, -6,  4, -5, -4, -2, -2,  2,  8,
+    2,  0,  0, -2, -3, -3,  0, -2, -3, -3, -3, -3,  2,  1, -3, -2,  5,
+    2,  0, -3, -3, -4, -6, -2, -3,  0, -2, -4,  0,  1,  0, -3, -3,  2,  6,
+    1,  0, -3, -5, -5, -2, -4, -6,  5, -6,  1,  2, -5, -4, -6, -6, -3,  0,  7,
+   -8,  0,  0, -9, -9, -3, -3, -6, -7, -6, -4, -6, -8, -8, -6, -1, -5, -7, -6, 17,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+   -7,  0,  2, -4, -7,  5, -8,  4, -5, -7, -4, -6, -2, -7, -4, -5, -3, -6, -6, -2,  0, 12,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+};
+
+int _md250[] = {
+    2,
+    0,  0,
+   -1,  0, 11,
+   -1,  0, -3,  5,
+   -1,  0, -4,  4,  5,
+   -3,  0,  0, -5, -5,  8,
+    1,  0, -1,  1,  1, -5,  5,
+   -2,  0,  0,  0,  0,  0, -2,  6,
+    0,  0, -2, -3, -3,  0, -3, -3,  4,
+   -1,  0, -3,  0,  1, -5, -1,  1, -3,  5,
+   -1,  0, -2, -4, -4,  2, -4, -2,  2, -3,  5,
+    0,  0, -2, -3, -3,  0, -3, -2,  3, -2,  3,  6,
+    0,  0, -1,  2,  1, -3,  0,  1, -2,  1, -3, -2,  3,
+    1,  0, -2, -2, -2, -2, -1,  0, -2, -1,  0, -2, -1,  6,
+   -1,  0, -3,  0,  2, -4, -1,  3, -3,  2, -2, -2,  0,  0,  5,
+   -1,  0, -1, -1,  0, -4,  0,  2, -3,  4, -3, -2,  0, -1,  2,  5,
+    1,  0,  1,  0, -1, -2,  1, -1, -1, -1, -2, -1,  1,  1, -1, -1,  2,
+    2,  0, -1, -1, -1, -2,  0, -1,  1, -1, -1,  0,  1,  1, -1, -1,  1,  2,
+    1,  0, -2, -3, -2,  0, -2, -3,  4, -3,  2,  2, -2, -1, -3, -3, -1,  0,  4,
+   -4,  0,  1, -5, -5, -1, -1, -3, -4, -3, -2, -3, -4, -4, -3,  0, -3, -4, -3, 15,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+   -3,  0,  2, -2, -4,  5, -4,  4, -2, -3, -1, -3, -1, -3, -2, -2, -1, -3, -3,  0,  0,  9,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+};
+
+int _md350[] = {
+    1,
+    0,  0,
+    0,  0,  9,
+    0,  0, -2,  3,
+    0,  0, -2,  3,  3,
+   -2,  0,  1, -3, -4,  6,
+    1,  0,  0,  1,  1, -3,  4,
+   -1,  0,  0,  0,  0,  0, -1,  3,
+    0,  0, -1, -2, -2,  1, -2, -2,  3,
+   -1,  0, -1,  0,  1, -3,  0,  1, -2,  3,
+   -1,  0, -1, -3, -3,  2, -2, -1,  2, -2,  3,
+    0,  0, -1, -2, -2,  1, -2, -1,  2, -2,  2,  3,
+    0,  0, -1,  1,  1, -2,  0,  1, -1,  1, -2, -1,  2,
+    1,  0, -1, -1, -1, -2, -1,  0, -1, -1,  0, -1,  0,  4,
+   -1,  0, -2,  1,  1, -2,  0,  2, -2,  2, -1, -1,  0,  0,  3,
+   -1,  0,  0,  0,  0, -3,  0,  1, -2,  3, -2, -1,  0,  0,  2,  3,
+    1,  0,  0,  0,  0, -1,  1,  0, -1,  0, -1, -1,  1,  1,  0,  0,  1,
+    1,  0,  0,  0, -1, -1,  0, -1,  0,  0, -1,  0,  0,  1, -1,  0,  1,  1,
+    0,  0, -1, -2, -2,  0, -1, -2,  2, -2,  1,  2, -1, -1, -2, -2,  0,  0,  2,
+   -3,  0,  1, -4, -3,  0, -1, -2, -3, -2, -1, -2, -3, -3, -2,  0, -2, -3, -2, 14,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+   -2,  0,  2, -2, -2,  5, -3,  3, -1, -2,  0, -1, -1, -2, -1, -1, -1, -2, -2,  0,  0,  7,
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+};
+
+
+
+////////////////////////////////////////////////////////////////////////
+// Identity matrix
+int _idmat[] = {
+ 1,
+ 0, 1,
+ 0, 0, 1,
+ 0, 0, 0, 1,
+ 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1
+};
+
+
+
+////////////////////////////////////////////////////////////////////////
+// GON family
+int _gon40[] = {
+    92,
+     0,   0,
+   -31,   0, 163,
+   -56,   0,-135, 111,
+   -37,   0,-140,  16, 105,
+   -92,   0, -64,-152,-143, 126,
+   -32,   0, -91, -51, -76,-152, 105,
+   -65,   0, -67, -41, -40, -50, -81, 145,
+   -76,   0, -87,-150,-106, -39,-158, -94, 104,
+   -54,   0,-132, -47, -13,-127, -79, -34, -86, 103,
+   -68,   0, -85,-155,-108, -13,-141, -85,   5, -85,  89,
+   -45,   0, -63,-130, -80, -16,-114, -60,  10, -57,  16, 140,
+   -62,   0, -83,   6, -38,-104, -40,  -7, -99, -20,-112, -91, 115,
+   -37,   0,-137, -69, -60,-128, -87, -71,-108, -62, -83,-119, -78, 124,
+   -43,   0,-113, -32,  10,-100, -71,   0, -91,   2, -60, -35, -25, -46, 118,
+   -61,   0, -86, -77, -50,-130, -69, -31,-103,  19, -84, -81, -47, -73,  -6, 112,
+     0,   0, -35, -36, -41,-111, -37, -48, -95, -43, -95, -64, -11, -35, -35, -51,  99,
+   -25,   0, -59, -47, -52, -90, -85, -46, -51, -34, -78, -44, -27, -42, -39, -52,  13, 100,
+   -22,   0, -43,-133, -74, -58,-122, -98,  28, -82, -18, -22,-103, -86, -79, -88, -74, -25,  97,
+  -120,   0, -68,-171,-131,  -6,-108, -70, -93,-127, -71, -72,-119,-149, -87, -63, -98,-120,-115, 181,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -95,   0, -56, -98,-107,  31,-129,   5, -76, -88, -64, -66, -62,-106, -81, -75, -69, -87, -73,   1,   0, 135,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+ };
+
+int _gon80[] = {
+    75,
+     0,   0,
+   -10,   0, 154,
+   -31,   0, -93,  96,
+   -17,   0, -94,  31,  88,
+   -64,   0, -39,-111,-102, 114,
+   -11,   0, -61, -26, -47,-115,  97,
+   -39,   0, -43, -17, -17, -26, -53, 127,
+   -43,   0, -54,-106, -73, -15,-114, -64,  86,
+   -30,   0, -88, -21,   4, -89, -50, -12, -59,  85,
+   -43,   0, -55,-109, -75,   7,-104, -57,  22, -58,  77,
+   -26,   0, -39, -88, -53,   3, -83, -38,  25, -37,  31, 117,
+   -34,   0, -55,  21, -13, -75, -18,   9, -71,  -2, -79, -62,  97,
+   -16,   0, -93, -42, -35, -93, -58, -45, -75, -37, -58, -78, -48, 114,
+   -22,   0, -76,  -9,  23, -70, -44,  14, -60,  17, -39, -19,  -6, -24,  95,
+   -36,   0, -60, -44, -23, -90, -43, -10, -71,  33, -58, -53, -22, -45,  11,  97,
+    14,   0, -15, -14, -19, -77, -16, -25, -62, -20, -64, -41,   5, -14, -15, -27,  78,
+    -5,   0, -34, -24, -27, -62, -52, -24, -28, -15, -49, -25,  -7, -20, -18, -27,  25,  81,
+    -6,   0, -21, -89, -51, -31, -86, -65,  41, -54,   3,   1, -69, -57, -51, -60, -43,  -9,  80,
+   -87,   0, -43,-124, -98,  16, -81, -43, -63, -89, -44, -45, -86,-112, -62, -41, -72, -87, -80, 173,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -65,   0, -32, -69, -74,  49, -94,  21, -47, -60, -35, -37, -39, -76, -53, -50, -46, -58, -47,  23,   0, 123,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+ };
+
+int _gon120[] = {
+    59,
+     0,   0,
+    -1,   0, 144,
+   -18,   0, -69,  82,
+    -9,   0, -68,  35,  72,
+   -48,   0, -26, -87, -78, 102,
+    -3,   0, -45, -14, -31, -92,  90,
+   -26,   0, -31,  -7,  -6, -14, -37, 110,
+   -27,   0, -36, -80, -55,  -3, -87, -48,  72,
+   -19,   0, -64,  -8,  11, -67, -34,  -2, -44,  69,
+   -30,   0, -39, -82, -57,  15, -82, -42,  28, -44,  66,
+   -17,   0, -26, -64, -40,  11, -65, -28,  29, -27,  34,  95,
+   -20,   0, -41,  26,  -1, -58,  -7,  14, -55,   5, -61, -46,  80,
+    -6,   0, -68, -28, -22, -72, -41, -31, -56, -24, -44, -56, -32, 105,
+   -12,   0, -56,   1,  25, -53, -30,  17, -43,  20, -30, -14,   1, -14,  74,
+   -23,   0, -45, -27, -10, -68, -30,  -1, -53,  36, -44, -38, -10, -30,  16,  83,
+    16,   0,  -7,  -5,  -9, -58,  -6, -14, -44, -10, -47, -29,  10,  -5,  -7, -15,  60,
+     2,   0, -21, -13, -15, -47, -35, -14, -17,  -6, -34, -16,   0, -10,  -9, -16,  26,  64,
+     0,   0, -11, -65, -38, -17, -65, -47,  42, -39,  13,  10, -50, -42, -36, -44, -28,  -3,  65,
+   -68,   0, -29, -96, -78,  27, -66, -28, -46, -68, -29, -31, -68, -89, -49, -30, -57, -67, -59, 166,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -48,   0, -20, -53, -56,  55, -74,  26, -31, -44, -20, -22, -28, -59, -38, -37, -35, -42, -33,  33,   0, 111,
+    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+};
+
+int _gon160[] = {
+    46,
+     0,   0,
+     3,   0, 135,
+   -11,   0, -53,  70,
+    -4,   0, -52,  34,  59,
+   -38,   0, -18, -70, -62,  91,
+     2,   0, -34,  -7, -21, -76,  82,
+   -18,   0, -23,  -1,  -1,  -7, -27,  93,
+   -18,   0, -25, -62, -43,   3, -70, -37,  59,
+   -12,   0, -48,  -1,  13, -53, -24,   2, -35,  55,
+   -22,   0, -29, -65, -45,  19, -67, -32,  30, -34,  57,
+   -12,   0, -19, -50, -31,  14, -52, -21,  29, -21,  34,  76,
+   -12,   0, -31,  26,   5, -47,  -2,  15, -44,   8, -48, -36,  65,
+    -1,   0, -52, -19, -14, -58, -30, -22, -43, -16, -35, -42, -22,  96,
+    -7,   0, -42,   6,  23, -41, -21,  17, -32,  20, -24, -12,   5,  -8,  56,
+   -16,   0, -35, -16,  -3, -53, -21,   3, -41,  35, -35, -29,  -4, -21,  17,  71,
+    16,   0,  -2,   0,  -3, -45,  -1,  -8, -33,  -4, -36, -23,  11,   0,  -2,  -9,  44,
+     5,   0, -14,  -6,  -8, -36, -24,  -8, -12,  -2, -24, -11,   3,  -4,  -4,  -9,  23,  50,
+     1,   0,  -6, -49, -30,  -8, -52, -35,  40, -30,  17,  14, -38, -32, -27, -34, -20,   0,  53,
+   -55,   0, -21, -78, -64,  32, -55, -19, -34, -54, -20, -22, -55, -74, -40, -24, -47, -54, -45, 158,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -37,   0, -13, -42, -44,  56, -60,  27, -20, -35, -11, -13, -22, -48, -29, -29, -28, -32, -24,  38,   0, 100,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+ };
+
+int _gon250[] = {
+    24,
+     0,   0,
+     5,   0, 115,
+    -3,   0, -32,  47,
+     0,   0, -30,  27,  36,
+   -23,   0,  -8, -45, -39,  70,
+     5,   0, -20,   1,  -8, -52,  66,
+    -8,   0, -13,   4,   4,  -1, -14,  60,
+    -8,   0, -11, -38, -27,  10, -45, -22,  40,
+    -4,   0, -28,   5,  12, -33, -11,   6, -21,  32,
+   -12,   0, -15, -40, -28,  20, -44, -19,  28, -21,  40,
+    -7,   0,  -9, -30, -20,  16, -35, -13,  25, -14,  28,  43,
+    -3,   0, -18,  22,   9, -31,   4,  12, -28,   8, -30, -22,  38,
+     3,   0, -31,  -7,  -5, -38, -16, -11, -26,  -6, -23, -24,  -9,  76,
+    -2,   0, -24,   9,  17, -26, -10,  12, -19,  15, -16, -10,   7,  -2,  27,
+    -6,   0, -22,  -3,   4, -32, -10,   6, -24,  27, -22, -17,   3,  -9,  15,  47,
+    11,   0,   1,   5,   2, -28,   4,  -2, -18,   1, -21, -14,   9,   4,   2,  -2,  22,
+     6,   0,  -5,   0,  -1, -22, -11,  -3,  -6,   1, -13,  -6,   5,   1,   0,  -2,  15,  25,
+     1,   0,   0, -29, -19,   1, -33, -20,  31, -17,  18,  16, -22, -18, -15, -20, -10,   0,  34,
+   -36,   0, -10, -52, -43,  36, -40,  -8, -18, -35,  -7, -10, -36, -50, -27, -16, -33, -35, -26, 142,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -22,   0,  -5, -28, -27,  51, -40,  22,  -7, -21,   0,  -2, -14, -31, -17, -18, -19, -19, -11,  41,   0,  78,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+};
+
+int _gon300[] = {
+    16,
+     0,   0,
+     5,   0, 104,
+    -1,   0, -24,  37,
+     1,   0, -23,  23,  27,
+   -18,   0,  -5, -37, -31,  60,
+     5,   0, -15,   3,  -4, -42,  58,
+    -6,   0, -10,   5,   4,   0, -10,  45,
+    -6,   0,  -7, -30, -21,  11, -36, -16,  33,
+    -2,   0, -21,   6,  11, -26,  -7,   5, -17,  24,
+    -9,   0, -10, -32, -22,  19, -36, -14,  25, -17,  33,
+    -5,   0,  -6, -24, -16,  15, -28, -10,  22, -11,  24,  31,
+    -1,   0, -14,  18,   9, -25,   5,  10, -22,   8, -24, -17,  27,
+     3,   0, -23,  -4,  -2, -30, -11,  -8, -20,  -3, -18, -19,  -6,  66,
+    -1,   0, -18,   9,  14, -20,  -6,   9, -15,  13, -13,  -8,   7,  -1,  18,
+    -4,   0, -17,   0,   5, -25,  -6,   6, -19,  22, -18, -13,   4,  -6,  13,  37,
+     8,   0,   1,   5,   3, -22,   4,  -1, -14,   2, -17, -11,   7,   4,   2,   0,  15,
+     5,   0,  -3,   1,   1, -17,  -7,  -1,  -4,   2,  -9,  -5,   4,   2,   1,  -1,  11,  17,
+     0,   0,   1, -23, -15,   4, -26, -15,  26, -13,  17,  15, -17, -14, -12, -15,  -8,   0,  26,
+   -29,   0,  -7, -42, -36,  36, -34,  -5, -13, -28,  -4,  -6, -30, -41, -23, -14, -27, -28, -19, 132,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -17,   0,  -3, -22, -22,  46, -33,  18,  -3, -17,   3,   1, -12, -25, -14, -14, -15, -15,  -7,  40,   0,  67,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+};
+
+int _gon350[] = {
+    10,
+     0,   0,
+     4,   0,  93,
+     0,   0, -19,  29,
+     1,   0, -17,  19,  20,
+   -14,   0,  -3, -30, -25,  51,
+     5,   0, -12,   4,  -2, -35,  51,
+    -4,   0,  -8,   5,   4,   1,  -7,  33,
+    -4,   0,  -5, -24, -17,  11, -29, -13,  27,
+    -1,   0, -16,   6,   9, -21,  -4,   5, -13,  18,
+    -7,   0,  -7, -25, -18,  18, -30, -11,  22, -14,  28,
+    -4,   0,  -4, -19, -13,  14, -23,  -8,  19,  -9,  21,  23,
+     0,   0, -11,  15,   9, -20,   5,   8, -18,   7, -19, -14,  20,
+     3,   0, -18,  -2,   0, -25,  -7,  -5, -16,  -2, -15, -14,  -3,  56,
+     0,   0, -14,   8,  11, -16,  -4,   7, -11,  10, -11,  -7,   6,   0,  12,
+    -2,   0, -13,   2,   6, -20,  -4,   6, -15,  18, -14, -11,   4,  -4,  10,  28,
+     6,   0,   1,   5,   3, -18,   5,   0, -11,   2, -13,  -9,   6,   4,   2,   1,  10,
+     4,   0,  -2,   2,   1, -13,  -5,  -1,  -3,   2,  -7,  -4,   4,   2,   1,   0,   8,  11,
+     0,   0,   2, -18, -12,   5, -21, -11,  22, -10,  16,  14, -13, -11,  -9, -12,  -6,   0,  21,
+   -24,   0,  -4, -35, -29,  35, -30,  -3,  -9, -23,  -1,  -3, -24, -34, -19, -12, -22, -23, -14, 124,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
+   -14,   0,  -1, -18, -17,  42, -27,  15,  -1, -14,   5,   2, -10, -20, -11, -12, -12, -12,  -4,  39,   0,  57,
+     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0
+};
+
+}  // namespace Victor
+}  // namespace Phylo
+
+#endif  // _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_
\ No newline at end of file
diff --git a/Phylo/Tests/Makefile b/Phylo/Tests/Makefile
new file mode 100644
index 0000000..3a380f5
--- /dev/null
+++ b/Phylo/Tests/Makefile
@@ -0,0 +1,59 @@
+#--*- makefile -*--------------------------------------------------------------
+#
+#   Standard makefile
+#
+#------------------------------------------------------------------------------
+
+# Path to project directory
+PROJECT_ROOT = ../..
+BINPATH      = $(PROJECT_ROOT)/bin/
+LIBPATH      = $(PROJECT_ROOT)/lib/
+UPDIR        = $(PROJECT_ROOT)
+SUBDIR       = 
+
+
+
+#
+# Libraries and paths (which are not defined globally).
+#
+
+LIBS     = -lPhylo -lAlign2 -ltools -L/usr/lib/ -lm -ldl -lcppunit
+INC_PATH = -I. -I ../../Phylo/Sources -I../../tools/ -I../../Align2/Sources
+LIB_PATH = -L.
+
+
+
+#
+# Objects and headers
+#
+
+SOURCES =  TestPhylo.cc TestTree.h TestDistanceMatrix.h TestClustering.h TestMSA.h
+OBJECTS =  $(SOURCES:.cpp=.o)
+TARGETS = TestPhylo
+EXECS   = TestPhylo
+LIBRARY = TESTlibPhylo.a
+
+
+
+#
+# Install rule
+#
+
+compile: all
+	
+all: install
+
+install: $(LIBRARY) $(TARGETS)
+	mv $(EXECS) $(UPDIR)/bin
+	mv $(LIBRARY) $(UPDIR)/lib
+
+
+	
+#
+# Call global Makefile to do the job.
+#
+
+include ../../Makefile.global
+
+# Overriding to use C++11
+STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c
\ No newline at end of file
diff --git a/Phylo/Tests/TestClustering.h b/Phylo/Tests/TestClustering.h
new file mode 100644
index 0000000..710d2e0
--- /dev/null
+++ b/Phylo/Tests/TestClustering.h
@@ -0,0 +1,142 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <iostream>
+#include <cppunit/TestFixture.h>
+#include <cppunit/TestAssert.h>
+#include <cppunit/TestCaller.h>
+#include <cppunit/TestSuite.h>
+#include <cppunit/TestCase.h>
+#include <phylo.h>
+
+using namespace std;
+using namespace Victor;
+using namespace Victor::Phylo;
+
+/** @brief Test on phylogenetic trees.
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class TestClustering: public CppUnit::TestFixture {
+ public:
+    TestClustering() {
+    }
+
+
+
+    /** @brief Builds a suite of tests. */
+    static CppUnit::Test *suite() {
+        CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestClustering");
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestClustering>("Test1 - UPGMA.",
+            &TestClustering::Test_A)
+        );
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestClustering>("Test2 - Nighbor joining.",
+            &TestClustering::Test_B)
+        );
+
+        return suiteOfTests;
+    }
+
+
+
+    /** @brief Setup method. */
+    void setUp() {
+    }
+
+
+
+    /** @brief Teardown method. */
+    void tearDown() {
+    }
+
+
+
+ protected:
+    /** @brief Test for UPGMA. */
+    void Test_A() {
+        DistanceMatrix D;
+        D.addOTU("Human")
+         .addOTU("Chimp")
+         .addOTU("Gorilla")
+         .addOTU("Orang");
+
+        D("Human",   "Chimp",   0.095);
+        D("Human",   "Gorilla", 0.113);
+        D("Human",   "Orang",   0.183);
+        D("Chimp",   "Gorilla", 0.118);
+        D("Chimp",   "Orang",   0.201);
+        D("Gorilla", "Orang",   0.195);
+
+        UPGMA upgma;
+        RootedTree tree = upgma(D).asRootedTree();
+        const string result = tree.asNewick();
+
+        CPPUNIT_ASSERT(result == "(((Chimp:0.0475,Human:0.0475):0.01025,Gorilla:0.05775):0.03875,Orang:0.0965)");
+    }
+
+
+
+    /** @brief Test for neighbor joining. */
+    void Test_B() {
+        DistanceMatrix D;
+        D.addOTU("A")
+         .addOTU("B")
+         .addOTU("C")
+         .addOTU("D")
+         .addOTU("E")
+         .addOTU("F")
+         .addOTU("G")
+         .addOTU("H");
+
+        D("A", "B",  7);
+        D("A", "C",  8);
+        D("A", "D", 11);
+        D("A", "E", 13);
+        D("A", "F", 16);
+        D("A", "G", 13);
+        D("A", "H", 17);
+        D("B", "C",  5);
+        D("B", "D",  8);
+        D("B", "E", 10);
+        D("B", "F", 13);
+        D("B", "G", 10);
+        D("B", "H", 14);
+        D("C", "D",  5);
+        D("C", "E",  7);
+        D("C", "F", 10);
+        D("C", "G",  7);
+        D("C", "H", 11);
+        D("D", "E",  8);
+        D("D", "F", 11);
+        D("D", "G",  8);
+        D("D", "H", 12);
+        D("E", "F",  5);
+        D("E", "G",  6);
+        D("E", "H", 10);
+        D("F", "G",  9);
+        D("F", "H", 13);
+        D("G", "H",  8);
+
+        NJ nj;
+        UnrootedTree tree = nj(D).asUnrootedTree();
+        const string result = tree.asNewick();
+
+        CPPUNIT_ASSERT(result == "(((E:1,F:4):2,(G:2,H:6):1):1.5,(D:3,(C:1,((A:5,B:2):1):1):1):0.5)");
+    }
+};
\ No newline at end of file
diff --git a/Phylo/Tests/TestDistanceMatrix.h b/Phylo/Tests/TestDistanceMatrix.h
new file mode 100644
index 0000000..936391b
--- /dev/null
+++ b/Phylo/Tests/TestDistanceMatrix.h
@@ -0,0 +1,122 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <iostream>
+#include <cppunit/TestFixture.h>
+#include <cppunit/TestAssert.h>
+#include <cppunit/TestCaller.h>
+#include <cppunit/TestSuite.h>
+#include <cppunit/TestCase.h>
+#include <phylo.h>
+
+using namespace std;
+using namespace Victor;
+using namespace Victor::Phylo;
+
+/** @brief Test on phylogenetic trees.
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class TestDistanceMatrix: public CppUnit::TestFixture {
+ public:
+    TestDistanceMatrix() {
+    }
+
+
+
+    /** @brief Builds a suite of tests. */
+    static CppUnit::Test *suite() {
+        CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestDistanceMatrix");
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestDistanceMatrix>("Test1 - Builds a matrix.",
+            &TestDistanceMatrix::Test_A)
+        );
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestDistanceMatrix>("Test2 - Get maximum value.",
+            &TestDistanceMatrix::Test_B)
+        );
+
+        return suiteOfTests;
+    }
+
+
+
+    /** @brief Setup method. */
+    void setUp() {
+    }
+
+
+
+    /** @brief Teardown method. */
+    void tearDown() {
+    }
+
+
+
+ protected:
+    /** @brief Test for creation. */
+    void Test_A() {
+        vector<string> OTUs;
+        OTUs.push_back("A");
+        OTUs.push_back("B");
+        OTUs.push_back("C");
+
+        const double ab = 0.1, ac = 9.5, bc = 0.333;
+
+        DistanceMatrix d;
+        d.addOTU(OTUs[0])
+         .addOTU(OTUs[1])
+         .addOTU(OTUs[2]);
+
+        d("A", "B", ab);
+        d("A", "C", ac);
+        d("B", "C", bc);
+
+        CPPUNIT_ASSERT(
+            d.getSize() == 3 &&
+            d("A", "B") == ab &&
+            d("B", "C") == bc &&
+            d("A", "C") == ac
+        );
+    }
+
+
+
+    /** @brief Test for get values. */
+    void Test_B() {
+        vector<string> OTUs;
+        OTUs.push_back("A");
+        OTUs.push_back("B");
+        OTUs.push_back("C");
+
+        const double ab = 0.1, ac = 9.5, bc = 0.333;
+
+        DistanceMatrix d;
+        d.addOTU(OTUs[0])
+         .addOTU(OTUs[1])
+         .addOTU(OTUs[2]);
+
+        d("A", "B", ab);
+        d("A", "C", ac);
+        d("B", "C", bc);
+
+        CPPUNIT_ASSERT(
+            d.getMaximum() == 9.5 &&
+            d.getMinimum() == 0.1
+        );
+    }
+};
\ No newline at end of file
diff --git a/Phylo/Tests/TestMSA.h b/Phylo/Tests/TestMSA.h
new file mode 100644
index 0000000..763f651
--- /dev/null
+++ b/Phylo/Tests/TestMSA.h
@@ -0,0 +1,117 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <iostream>
+#include <sstream>
+#include <cppunit/TestFixture.h>
+#include <cppunit/TestAssert.h>
+#include <cppunit/TestCaller.h>
+#include <cppunit/TestSuite.h>
+#include <cppunit/TestCase.h>
+#include <phylo.h>
+
+using namespace std;
+using namespace Victor;
+using namespace Victor::Phylo;
+
+/** @brief Test on phylogenetic trees.
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class TestMSA: public CppUnit::TestFixture {
+ public:
+    TestMSA() {
+    }
+
+
+
+    /** @brief Builds a suite of tests. */
+    static CppUnit::Test *suite() {
+        CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestMSA");
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestMSA>("Test1 - Feng-Doolittle.",
+            &TestMSA::Test_A)
+        );
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestMSA>("Test2 - ClustalW.",
+            &TestMSA::Test_B)
+        );
+
+        return suiteOfTests;
+    }
+
+
+
+    /** @brief Setup method. */
+    void setUp() {
+    }
+
+
+
+    /** @brief Teardown method. */
+    void tearDown() {
+    }
+
+
+
+protected:
+    /** @brief Test for Feng-Doolittle. */
+    void Test_A() {
+        stringstream input;
+
+        input << ">Seq1\nMAAAAATLRGAMVGPRGAGLP\n"
+              << ">Seq2\nMAAAAASLRGVVLGPRGAGL\n"
+              << ">Seq3\nMTEFKAGSAKKGATLFKTRCL\n"
+              << ">Seq4\nMAAAAASLRRTVLGPRGVGLPGASAPGLL\n"
+              << ">Seq5\nMFSQKLLANGKLLSKLAIVSGVVG\n"
+              << "\n";
+
+        Alignment alignment;
+        alignment.loadFasta(input);
+        FengDoolittle feng_doolittle;
+        MultipleAlignment MSA  = feng_doolittle(alignment);
+
+        CPPUNIT_ASSERT(MSA.getConsensus() == "MAAFKAAASLRGAVLGPRGAGLAGASAPGLG");
+    }
+
+
+
+    /** @brief Test for ClustalW. */
+    void Test_B() {
+        stringstream input;
+
+        input << ">Seq1\nMAAAAATLRGAMVGPRGAGLP\n"
+              << ">Seq2\nMAAAAASLRGVVLGPRGAGL\n"
+              << ">Seq3\nMTEFKAGSAKKGATLFKTRCL\n"
+              << ">Seq4\nMAAAAASLRRTVLGPRGVGLPGASAPGLL\n"
+              << ">Seq5\nMFSQKLLANGKLLSKLAIVSGVVG\n"
+              << "\n";
+
+        Alignment alignment;
+        alignment.loadFasta(input);
+
+        SubMatrix matrix(SubstitutionMatrix(SubstitutionMatrix::BLOSUM62).asSubMatrix());
+        AGPFunction gap_function(10.0, 0.2);
+        IdentityPercentage build_matrix(matrix, gap_function);
+        NJ build_tree;
+        ClustalW clustalw(build_matrix, build_tree, ClustalW::BLOSUM);
+
+        MultipleAlignment MSA  = clustalw(alignment);
+        
+        CPPUNIT_ASSERT(MSA.getConsensus() == "MAAAAASLRGKVLGPRGAGLPGASAGCLG");
+    }
+};
\ No newline at end of file
diff --git a/Phylo/Tests/TestPhylo.cc b/Phylo/Tests/TestPhylo.cc
new file mode 100644
index 0000000..e4603aa
--- /dev/null
+++ b/Phylo/Tests/TestPhylo.cc
@@ -0,0 +1,43 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <iostream>
+#include <cppunit/TestSuite.h>
+#include <cppunit/ui/text/TestRunner.h>
+#include <TestTree.h>
+#include <TestDistanceMatrix.h>
+#include <TestClustering.h>
+#include <TestMSA.h>
+
+using namespace::std;
+using namespace::Victor;
+
+int main(int argc, char *argv[]) {
+    CppUnit::TextUi::TestRunner runner;
+
+    cout << "Creating Test Suite:" << endl;
+    runner.addTest(TestTree::suite());
+    runner.addTest(TestDistanceMatrix::suite());
+    runner.addTest(TestClustering::suite());
+    runner.addTest(TestMSA::suite());
+    cout << "Running the unit tests:" << endl;
+    runner.run();
+
+    (void) argc;
+    (void) argv;
+
+    return 0;
+}
\ No newline at end of file
diff --git a/Phylo/Tests/TestPhylo.o b/Phylo/Tests/TestPhylo.o
new file mode 100644
index 0000000..950c22c
Binary files /dev/null and b/Phylo/Tests/TestPhylo.o differ
diff --git a/Phylo/Tests/TestTree.h b/Phylo/Tests/TestTree.h
new file mode 100644
index 0000000..39424db
--- /dev/null
+++ b/Phylo/Tests/TestTree.h
@@ -0,0 +1,109 @@
+/*  This file is part of Victor.
+    
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Victor is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <iostream>
+#include <cppunit/TestFixture.h>
+#include <cppunit/TestAssert.h>
+#include <cppunit/TestCaller.h>
+#include <cppunit/TestSuite.h>
+#include <cppunit/TestCase.h>
+#include <phylo.h>
+
+using namespace std;
+using namespace Victor;
+using namespace Victor::Phylo;
+
+/** @brief Test on phylogenetic trees.
+ * @author Marco Zanella <marco.zanella.9@studenti.unipd.it>
+ */
+class TestTree: public CppUnit::TestFixture {
+ public:
+    TestTree() {
+    }
+
+
+
+    /** @brief Builds a suite of tests. */
+    static CppUnit::Test *suite() {
+        CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestTree");
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestTree>("Test1 - Parses a Newick string.",
+            &TestTree::TestTree_A)
+        );
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestTree>("Test2 - Count leaves.",
+            &TestTree::TestTree_B)
+        );
+
+        suiteOfTests->addTest(
+            new CppUnit::TestCaller<TestTree>("Test3 - Distances.",
+            &TestTree::TestTree_C)
+        );
+
+        return suiteOfTests;
+    }
+
+
+
+    /** @brief Setup method. */
+    void setUp() {
+    }
+
+
+
+    /** @brief Teardown method. */
+    void tearDown() {
+    }
+
+
+
+ protected:
+    /** @brief Test for parse/write. */
+    void TestTree_A() {
+        RootedTree tree;
+        const string load_newick = "(A:0.5,B:0.25):0.36;";
+        tree.parseNewick(load_newick);
+        const string save_newick = tree.asNewick() + ";";
+
+        CPPUNIT_ASSERT(load_newick == save_newick);
+    }
+
+
+
+    /** @brief Test for number of leaves. */
+    void TestTree_B() {
+        RootedTree tree;
+        const string load_newick = "(A:0.5,B:0.25):0.36;";
+        tree.parseNewick(load_newick);
+        const size_t leaves = tree.getLeavesNumber();
+
+        CPPUNIT_ASSERT(leaves == 2);
+    }
+
+
+
+    /** @brief Test for distance. */
+    void TestTree_C() {
+        RootedTree tree;
+        const string load_newick = "(A:0.5,B:0.25):0.36;";
+        tree.parseNewick(load_newick);
+        const double max_distance = tree.getMaxDistance();
+
+        CPPUNIT_ASSERT(max_distance == 0.86);
+    }
+};
\ No newline at end of file