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peleffy 1.1.0 - Improvements in parameterization API, OBC template for OPLS2005 and Molecule initializators

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@martimunicoy martimunicoy released this 01 Dec 21:47
· 298 commits to master since this release
1.1.0
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This minor release introduces improvements to the parameterization API of peleffy. It also integrates the parameterization of OBC radii and scale factors required by the OPLS2005 implementation of PELE. It also improves the initialization of the Molecule class with a PDB checking and fixer and taking RDKit and OpenFF molecular representations as input. It also adds support for the new openff-1.3.0. Besides, it fixes a serious bug in the atom ordering of the Impact template that affected PELE's side chain prediction algorithm.

New features

  • PR #86: New method to check the input PDB prior building the molecule.
  • PR #88: New method to retrieve atom degrees with RDKit.
  • PR #90: Add support for openff-1.3.0.
  • PR #92: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
  • PR #94: New method for the OPLS OBC parameters.
  • PR #100: New writer for the OPLS OBC parameters.
  • PR #106: New method to initialize a Molecule object directly from an RDKit and OpenFF molecular representations.
  • PR #112: New method to fix an input PDB file with no atomic element identifiers.

Bugfixes

  • PR #107: A bad ordering of the atoms in the Impact template generated by peleffy is now fixed.

API-breaking changes

  • PR #94: Methods to write to a file are given a unique standard name, to_file(), to simplify the API.
  • PR #97: The parameterization API changes and a new Topology class is used as a container for all the topological elements.
  • PR #103: The OpenFF output of PELE changes from DataLocal/Templates/OFF/Parsley/HeteroAtoms/ to DataLocal/Templates/OpenFF/Parsley/.

Tests added

  • PR #88: Adds tests to validate the atom degrees getter.
  • PR #86: Adds tests to validate the PDB check up.
  • PR #90: General validation of supported force fields.
  • PR #92: New test to check the behaviour of the allow_undefined_stereo parameter.
  • PR #94: Adds tests to validate the OPLS OBC parameters generator.
  • PR #97: Includes tests for the new Topology container class.
  • PR #100: Adds tests to validate the solvent template writers.
  • PR #106: Adds tests to check the RDKit and OpenFF molecular initializers.
  • PR #112: Adds one test to check the new PDB fixer method.
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