João Morado 939e0af545 Reader of Tinker files (#4769) ...

* Add basic version of TinkerFiles

* Refactor TinkerFiles

* Update docstring, type hints, and fix bug when setting box vectors

* Small fixes

* Add unit tests for the TinkerFiles class

* Fixes and updates to TinkerFiles

* Add simuteTinker example

* Update Modeller to work with AMOEBA force fields

* Small fixes

* Relax type hinting

* Fix indices in modeller

* Fix modeller indices

* Fix type hints and usage of Quantity

* Remove numpy protector

* Add reader of .seq files

* Add topology parsing of some protein residues, waters, ions, and generic molecules.

* Miscellaneous improvements

* Update amino acids and nucleotides list

* Various fixes to XML writing, and separate XML writing into a new class

* Comments/warnings

* Add nucleic topological definitions

* Improved handling of peptide residues

* Fix for CYX (disulfide bonds)

* Refactor the topology creation methods

* General improvements, and add support for nucleic-like residues

* No need to handle MP, DP, TP

* Minor improvements

* General refactoring, add automatic determination of topology

* Add TinkerAtomType dataclass, and remove references to biotypes as they are not needed

* Re-add missing parsing of forces and scalars

* Updates to createSystem()

* Add AMOEBA forces

* Add angle-related forces to createSystem

* Add placeholders for missing forces

* Beginning of support for AmoebaMultipoleForce

* Finished support for AmoebaMultipoleForce

* Support for AmoebaVdwForce

* TinkerFiles supports vdw

* Misc updates, and add AmoebaTorsionTorsion, AmoebaWcaDispersion, and AmoebaGeneralizedKirkwood

* Remove XML writer

* Fixes

* Fix wrong indentation in _findBitorsions

* Remove pdb debugging

* Documentation and fixes

* Remove files

* Revert checks in AmoebaVdwForceBuilder and ## @private  markers

* Remove duplicated static methods _getChiralAtomIndex

* Fix GK force

* Fix WcaDispersion force

* Fix WcaDisp

* Fixes and updates

* Cleanup and removing duplicated code

* Bug fixes

* A few more unit conversions

* Minor cleanup

* Misc fixes and updates

* Fix Add AmoebaStretchBendForce

* Simplify force builders

* Update ForceField

* Fix AmoebaPiTorsionForce

* Only add AmoebaWcaDispersionForce if using implicitSolvent

* Simplify amoebaforces

* Stretch torsion and angle torsion

* Misc. fixes

* Improve tests

* Fix cap group identification

* Add/improve tests

* Remove whitespaces from residue names

* Improve tests

* Consistent use of atomClasses list

* Fix match condition in AmoebaOutOfPlaneBendForceBuilder

* Fix AmoebaStretchBendForce

* Final fix for AmoebaStretchBendForce

* Fix AmoebaAngleForce

* Small fixes and improvements

* Update assertion tolerances

* Simplify torsion-torsion force creation

* Small fixes in the tests

* Review comments, type hints, docs for tinkerfiles.py

* Only use standard PDB for AA

* Type hint and docs for amoebaforces

* Reduce tolerances for failing tests

* Fixed error with ZOnly axis type when x particle is not specified

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Co-authored-by: peastman <peastman@stanford.edu>

2025-09-18 18:00:59 -07:00

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