* Correct AmoebaAngleTorsion in test_Amoeba18Nucleic of TestForceField
* Update processTinkerForceField to handle latest .prm Tinker files
* Update amoeba2018 XML files
* Update amoeba2013 XML files
* Update amoeba2009 XML files
* Adapt addTorTor to new format in the .prm files
* Fix TorsionTorsion
* Also update the total energy in test_Amoeba18Nucleic
* Update amoebabio18.prm
* Fix nucleic acid test energies
* Correct AmoebaAngleTorsionForce params
* Add new addTorTor to TinkerFiles
* Revert unit fix
* Change to .pdb file which Tinker likes
* Update test_Amoeba18BPTI
* Remove trailing zeros from XML files
* Leave trailing zeros only on 2018 ff
* New element names in 2018
* More digits for surfaceAreaFactor
* More digits for surfaceAreaFactor
* More digits
* Remove debugging print
* Add support to 2009 and 2013 AMOEBA ffs to processTinkerForceField.py
* Add FF specific residues XML files
* Delete old residuesFinal.xml
* Update AMOEBA XML ffs
* Update FFs
* Fix some formatting issues
* Fix "." in scientific notation
* Remove old assertions
* Fresh branch refactoring the new AMOEBA code
* Finish cleaning up AmoebaAngleForce and AmoebaInPlaneAngleForce
* Cleanup AmoebaTorsionTorsionForce
* Cleanup AmoebaOutOfPlaneBend
* Cleanup AmoebaMultipoleForce
* Remove unnecessary gkForce
* Simplify usage of atomClasses in ForceField
* Formatting
* Fix type of class on WCA
* Simplify angle forces
* Add parsing of units to PiTorsion and StretchBond, and misc. formatting adjustments
* Update code per review feedback
* Clearly defined API for TorsionTorsion, and correct matching for UB,
* Unindent break statements
* Raise ValueError if classes and types are mixed in a Urey-Bradley term definition
* 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>
