Pull version 1 of Mobi Victor - Luca Demo

.gitignore

@@ -1,4 +1,5 @@
 .gitignore_bkp
+.settings/
 nbproject/
 html/
 latex/
@@ -38,6 +39,12 @@ Lobo/Sources/*.o
 Lobo/Sources/*.a
 Lobo/Tests/*.a
 Lobo/Tests/*.o
+Mobi/Sources/*.o
+Mobi/Sources/*.a
+Mobi/Tests/*.a
+Mobi/Tests/*.o
+Mobi/Tests/data/*.tmp*
 tools/*.o
 tools/*.a
-tools/Depend
+tools/Depend
+/Mobi.doxyfile

Biopool/Sources/Spacer.cc

@@ -1665,6 +1665,11 @@ void Spacer::setDSSP(bool verbose) {
                 if (it != ss[i].end()) { // found a n-turn
                     char pos_s = *it;
                     int pos = atoi(&(pos_s));
+                    // ******************* PATCH FOR OUT OF BOUND SEG FAULT ******************
+                    //LUCA DEMO - MOBI
+                    // ***********************************************************************
+                    if ((i + pos - 1) >= ss.size())
+                    	break;
                     set<char> ::iterator it1 = ss[i + pos - 1].find(turns[l]);
                     if (it1 != ss[i + pos - 1].end()) { // found the same n-turn after n-1 positions
                         bool helixBreak = false;

Makefile

@@ -7,7 +7,7 @@
 # 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	Mobi/Sources	Mobi/APPS
 
 #
 # Libraries and paths (which are not defined globally).
@@ -27,8 +27,8 @@ BINPATH = bin
 
 SOURCES =
 OBJECTS =
-EXECS =
-TARGET  =
+EXECS	=
+TARGET 	=
 LIBRARY =
 
 #

Makefile.global

@@ -77,7 +77,7 @@ ifeq ($(verbose), 3)
   USERFLAGS += -DVERBOSE=3
 endif
 
-CFLAGS = $(USERFLAGS) 
+CFLAGS = $(USERFLAGS)
 
 #
 # Tools 
@@ -106,11 +106,13 @@ 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
+### MODIFIED BY MOBI - ***LUCA DEMO***
+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$(UPDIR)/Mobi/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS  -I$(UPDIR)/Lobo/APPS  -I$(UPDIR)/Mobi/APPS
 
+### MODIFIED BY MOBI - ***LUCA DEMO***
 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)/Mobi/Tests
+  SUBDIRS =  Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests Mobi/Tests
 endif
 
 ####### Implicit rules
@@ -175,6 +177,8 @@ subclean:
 	$(RM) -fr ./Energy/data
 	$(RM) -fr ./Lobo/data
 	$(RM) -fr ./Biopool/data
+	$(RM) -fr ./Mobi/data
+	$(RM) -fr ./Mobi/data/*
 
 
 

Mobi/APPS/Makefile

@@ -0,0 +1,54 @@
+#--*- makefile -*--------------------------------------------------------------
+#
+#   Standard makefile
+#
+#------------------------------------------------------------------------------
+
+# Path to project directory.
+UPDIR = ../..
+# Path to subdirectories.
+SUBDIR=
+# Path to directory for binaries:
+BINPATH = ../../bin
+
+
+#
+# Libraries and paths (which are not defined globally).
+#
+
+LIBS = -lMobi -lBiopool -ltools 
+
+LIB_PATH = -L.
+
+INC_PATH = -I. -I../../tools/ -I../../Biopool/Sources -I../../Mobi/Sources
+
+#
+# Objects and headers
+#
+
+SOURCES =   Mobi.cc
+
+OBJECTS =   Mobi.o
+
+TARGETS = Mobi
+
+EXECS = Mobi
+
+LIBRARY = APPSlibMobi.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

Mobi/APPS/Mobi.cc

@@ -0,0 +1,243 @@
+/*  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/>.
+
+    This file is part of Mobi extension created by
+ 	Luca Demo  -  University of Padova, department of Science
+ */
+/**
+ */
+
+#include <Protein.h>
+#include <PdbLoader.h>
+#include <PdbSaver.h>
+#include <IoTools.h>
+#include <GetArg.h>
+#include <MobiProtein.h>
+#include <TMScoreBin.h>
+#include <MobiMethods.h>
+#include <MobiUtils.h>
+
+#include <String2Number.h>
+#include <unistd.h>
+
+using namespace Victor;
+using namespace Victor::Biopool;
+using namespace Victor::Mobi;
+
+void sShowHelp() {
+	cout << "Victor - Mobi NMR Mobility: 1.0\n"
+		<< "Mobility defined accordingly with http://protein.bio.unipd.it/mobi/"
+		<< "Options: \n"
+		<< "\t-i <filename> \t Input PDB file (mandatory)\n"
+		<< "\t-o <filename> \t Output mobility tracks to FASTA file (default stdout)\n"
+		<< "\t-p <filename> \t Output ordered models in PDB file (default is no output)\n"
+		<< "\t-s <filename> \t Output residue mobility \"score\" (default is no output)\n"
+		<< "\t-c <id>       \t Chain identifier to read (default is first chain)\n"
+		<< "\t-m <number>   \t NMR models numbers to read, comma separated list (default is all models)\n"
+		<< "\t-t	\t TMscore binary path (default is ./TMscore)\n"
+		<< "\t--d0 <number> \t d0 scaling factor for scaled distance. Default = 4\n"
+		<< "\t--sd <number>  \t threshold for Avg Scaled Distance track. Default = 0.85\n"
+		<< "\t--sdd <number> \t threshold for Scaled Distance Deviation track. Default = 0.09\n"
+		<< "\t--phi <number> \t threshold for phi angles track. Default = 20\n"
+		<< "\t--psi <number> \t threshold for psi angles track. Default = 20\n"
+		<< "\t-v	\t verbose output\n"
+		<< "\t-d	\t even more verbose output (lot of details)\n"
+		<< "\t-h	\t shows this message\n";
+}
+
+int main(int argc, char* argv[]) {
+	cout << "Victor Mobi Mobility Calculator" << endl;
+	cout << "v. 0.1" << endl << endl;
+
+	//If -h specified, show help message
+    if (getArg("h", argc, argv)) {
+        sShowHelp();
+        return 1;
+    }
+
+    string inputFile, outputFile, outputPdb, outputScore, tmbin, chainID, modelList;
+    string d0_s,sd_s,sdd_s,phi_s,psi_s;
+    bool verbose, debug;
+    vector<unsigned int> models;
+
+
+    getArg("i", inputFile, argc, argv, "!");
+    getArg("o", outputFile, argc, argv, "!");
+    getArg("p", outputPdb, argc, argv, "!");
+    getArg("s", outputScore, argc, argv, "!");
+    getArg("t", tmbin, argc, argv, "!");
+    getArg("c", chainID, argc, argv, "!");
+    getArg("m", modelList, argc, argv, "!");
+    getArg("-d0", d0_s, argc, argv, "!");
+    getArg("-sd", sd_s, argc, argv, "!");
+    getArg("-sdd", sdd_s, argc, argv, "!");
+    getArg("-psi", psi_s, argc, argv, "!");
+    getArg("-phi", phi_s, argc, argv, "!");
+    verbose = getArg("v", argc, argv);
+    debug = getArg("d", argc, argv);
+
+    if (debug)
+    	verbose = true;
+
+    // Check input file
+    if (inputFile == "!") {
+        cout << "Missing input file specification. Aborting. (-h for help)" << endl;
+        return -1;
+    }
+    ifstream inFile(inputFile.c_str());
+    if (!inFile){
+        ERROR("Input file not found.", exception);
+    }else{
+		if (verbose)
+			cout << "Using PDB input file: " << inputFile << endl;
+    }
+    // check TM
+    if (tmbin == "!") {
+    	tmbin = "./TMscore";
+    }
+    if(access(tmbin.c_str(), X_OK) != 0){
+    	ERROR("TM binary (" + tmbin + ") does not exist or not executable.", exception);
+    }else{
+    	if (verbose)
+    		cout << "Using TMscore binary: " << tmbin << endl;
+    }
+
+    //Check mobi parameters
+    double d0 = DEF_D0;
+    if (d0_s != "!")
+    	d0 = stodDEF(d0_s);
+    double sd_th = DEF_SD_TH;
+    if (sd_s != "!")
+    	sd_th = stodDEF(sd_s);
+    double sdsd_th = DEF_SDSD_TH;
+    if (sdd_s != "!")
+    	sdsd_th = stodDEF(sdd_s);
+    double phi_th = DEF_PHI_TH;
+    if (phi_s != "!")
+    	phi_th = stodDEF(phi_s);
+    double psi_th = DEF_PSI_TH;
+	if (psi_s != "!")
+		psi_th = stodDEF(psi_s);
+
+    //MOBI
+    PdbLoader pl(inFile);
+    // Set PdbLoader variables
+    if (!debug) {
+        pl.setNoVerbose();
+    }else{
+    	pl.setVerbose();
+    }
+
+    // User selected chain
+    if (chainID != "!") {
+        if (chainID.size() > 1)
+            ERROR("You can choose only 1 chain", error);
+        pl.setChain(chainID[0]);
+        pl.checkAndSetChain();
+        if (verbose)
+        	cout << "Selected chain: " << chainID[0] << endl;
+    }// First chain
+    else {
+        if (pl.getAllChains().size() > 0){
+			pl.setChain(pl.getAllChains()[0]);
+			if (verbose)
+				cout << "Selected chain: " << pl.getAllChains()[0] << endl;
+			chainID = pl.getAllChains()[0];
+        }else
+        	if (verbose)
+        		ERROR("No chains found. Quit...", exception);
+
+    }
+
+    // User selected models
+    if (modelList != "!"){
+    	models = sToVectorOfUIntDEF(translate(modelList,',',' '));
+    		for (unsigned int i = 0; i < models.size(); i++)
+    			if (models[i] > pl.getMaxModels() || models[i] < 1)
+    				ERROR("You specified out of bound model number(s). Max for this input pdb is " + pl.getMaxModels(), exception);
+    }else{
+    	for (unsigned int i = 1; i <= pl.getMaxModels(); i++)
+    		models.push_back(i);
+    }
+    if (verbose){
+    	cout << "Selected models: ";
+    	for (unsigned int i = 0; i < models.size(); i++)
+    		cout << models[i] << " ";
+    	cout << endl;
+    }
+
+    // Load the protein object
+    MobiProtein* prot = new MobiProtein();
+    if (debug)
+    	prot->setVerbose(true);
+    else
+    	prot->setVerbose(false);
+    if (verbose)
+    	cout << "Loading models..." << endl;
+    prot->load(pl,models);
+    cout << endl;
+
+    // TMscore: here we use the external binary
+    TMScoreBin* tm = new TMScoreBin(tmbin,".");
+    // Set MobiMethods Thresholds
+    MobiMethods mm(d0, CA, sd_th, sdsd_th, psi_th, phi_th);
+    if (verbose)
+    	mm.verbosity(1);	//Outputs tracks on cout
+    if (debug)
+    	mm.verbosity(2);	//Output tracks and other calculation details
+
+    //Mobility
+    cout << "Mobility calculation..." << endl;
+	vector<int> mobility = mm.mobiMobility(prot,tm);
+
+	if (verbose){	//cout output
+		MobiUtils::printFastaFile(mm);
+		cout << endl;
+	}
+	if (outputFile != "!"){	//save fasta
+		ofstream fastaOut(outputFile.c_str());
+		MobiUtils::printFastaFile(mm,fastaOut);
+		fastaOut.close();
+		if (verbose)
+			cout << "Tracks saved in FASTA file: " << outputFile << endl;
+	}
+
+	if (outputPdb != "!"){	//save Pdb
+		ofstream pdbOut(outputPdb.c_str());
+		MobiUtils::saveMobiPdb(prot,MobiUtils::sortModels(mm.getDistances()),mm.getSDMeans(), mm.getSDDevs(),pdbOut);
+		pdbOut.close();
+		if (verbose)
+			cout << "Models saved in Pdb file: " << outputPdb << endl;
+	}
+
+	if (outputScore != "!"){	//Save Score
+		ofstream scoreOut(outputScore.c_str());
+		MobiUtils::saveScore(mm,chainID[0],scoreOut);
+		scoreOut.close();
+		if (verbose)
+			cout << "Score saved in file: " << outputScore << endl;
+	}
+
+
+
+	//Close
+	tm->cleanup();
+	delete prot;
+	delete tm;
+
+	//Goodbye
+	cout << endl << "Done." << endl;
+    return 0;
+}