Fix ModXNA compatibility#1168

Merged

drroe merged 19 commits into

Amber-MD:masterfrom

drroe:fix.modxna

Mar 12, 2026

Commits on Mar 12, 2026

Start adding back the old Builder class for modXNA
Daniel R. Roe
committed
Add OldBuilder to the build and add the old BuildAtom class too
Daniel R. Roe
committed
Add missing include
Daniel R. Roe
committed
Add back old model class for modXNA
Daniel R. Roe
committed
Split BuildAtom back out
Daniel R. Roe
committed
Add old Model class to the build
Daniel R. Roe
committed
Add old routine back to Zmatrix for modXNA
Daniel R. Roe
committed
Start adding the old sequence code back for modXNA
Daniel R. Roe
committed
Add mode argument. DSL no longer needs to be passed in to the generate sequence function
Daniel R. Roe
committed
Only process the arg if it is present
Daniel R. Roe
committed
To maintain backwards compatibility with modXNA, ensure mol2 files are loaded with default bond REQ parameters
Daniel R. Roe
committed
Ensure modxna metadata is preserved after a strip, and if no title is set for mol2 files write out modxna metadata instead
Daniel R. Roe
committed
Dont do title or natom count when getting units. Report if modxna info is present
Daniel R. Roe
committed
Pass in unit arrays to the sequence functions
Daniel R. Roe
committed
If no other sequence mode specified and modxna info is present, force the old sequence mode
Daniel R. Roe
committed
Add notes to the v7 changelog about changes made specifically to maintain backwards compatbility with modXNA
Daniel R. Roe
committed
Version 7.1.0. Minor version bump since cpptraj will produce different (and backwards compatible) output for ModXNA with 7.1.0 compared to 7.00.0.
Daniel R. Roe
committed
ModXNA test
Daniel R. Roe
committed
Enable modxna test
Daniel R. Roe
committed

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Fix ModXNA compatibility#1168

Fix ModXNA compatibility#1168
drroe merged 19 commits into
Amber-MD:masterfrom
drroe:fix.modxna

Commits on Mar 12, 2026

Start adding back the old Builder class for modXNA

Add OldBuilder to the build and add the old BuildAtom class too

Add missing include

Add back old model class for modXNA

Split BuildAtom back out

Add old Model class to the build

Add old routine back to Zmatrix for modXNA

Start adding the old sequence code back for modXNA

Add mode argument. DSL no longer needs to be passed in to the generate sequence function

Only process the arg if it is present

To maintain backwards compatibility with modXNA, ensure mol2 files are loaded with default bond REQ parameters

Ensure modxna metadata is preserved after a strip, and if no title is set for mol2 files write out modxna metadata instead

Dont do title or natom count when getting units. Report if modxna info is present

Pass in unit arrays to the sequence functions

If no other sequence mode specified and modxna info is present, force the old sequence mode

Add notes to the v7 changelog about changes made specifically to maintain backwards compatbility with modXNA

Version 7.1.0. Minor version bump since cpptraj will produce different (and backwards compatible) output for ModXNA with 7.1.0 compared to 7.00.0.

ModXNA test

Enable modxna test