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openforcefield/openforcefield: 0.4.1 Bugfix Release

David L. Mobley; Jeff Wagner; John Chodera; Caitlin Bannan; Andrea Rizzi; Camila; Christopher Bayly; SimonBoothroyd; Nathan M. Lim; Victoria Lim; Yutong Zhao; Lee-Ping

0.4.1

This update fixes several toolkit bugs that have been reported by the community. Details of these bugfixes are provided below.

It also refactors how ParameterType and ParameterHandler store their attributes, by introducing ParameterAttribute and IndexedParameterAttribute. These new attribute-handling classes provide a consistent backend which should simplify manipulation of parameters and implementation of new handlers.

A richer version of these release notes with live links to API documentation is available on our ReadTheDocs page

See our installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

Bug fixes
  • PR #329: Fixed a bug where the two BondType parameter attributes k and length were treated as indexed attributes. (per the SMIRNOFF spec, k and length values that correspond to specific bond orders will be indexed under k_bondorder1, k_bondorder2, etc when implemented in the future)
  • PR #329: Fixed a bug that allowed setting indexed attributes to single values instead of strictly lists.
  • PR #370: Fixed a bug in the API where BondHandler, ProperTorsionHandler, and ImproperTorsionHandler exposed non-functional indexed parameters.
  • PR #351: Fixes Issue #344, in which the main FrozenMolecule constructor and several other Molecule-construction functions ignored or did not expose the allow_undefined_stereo keyword argument.
  • PR #351: Fixes a bug where a molecule which previously generated a SMILES using one cheminformatics toolkit returns the same SMILES, even though a different toolkit (which would generate a different SMILES for the molecule) is explicitly called.
  • PR #354: Fixes the error message that is printed if an unexpected parameter attribute is found while loading data into a ForceField (now instructs users to specify allow_cosmetic_attributes instead of permit_cosmetic_attributes)
  • PR #364: Fixes Issue #362 by modifying OpenEyeToolkitWrapper.from_smiles and RDKitToolkitWrapper.from_smiles to make implicit hydrogens explicit before molecule creation. These functions also now raise an error if the optional keyword hydrogens_are_explicit=True but the SMILES are interpreted by the backend cheminformatics toolkit as having implicit hydrogens.
  • PR #371: Fixes error when reading early SMIRNOFF 0.1 spec files enclosed by a top-level SMIRFF tag.
    • Note: The enclosing SMIRFF tag is present only in legacy files. Since developing a formal specification, the only acceptable top-level tag value in a SMIRNOFF data structure is SMIRNOFF.
Code enhancements
  • PR #329: ParameterType was refactored to improve its extensibility. It is now possible to create new parameter types by using the new descriptors ParameterAttribute and IndexedParameterAttribute.
  • PR #357: Addresses Issue #356 by raising an informative error message if a user attempts to load an OpenMM topology which is probably missing connectivity information.
Force fields added
  • PR #368: Temporarily adds test_forcefields/smirnoff99frosst_experimental.offxml to address hierarchy problems, redundancies, SMIRKS pattern typos etc., as documented in issue #367. Will ultimately be propagated to an updated forcefield in the openforcefield/smirnoff99frosst repo.
  • PR #371: Adds test_forcefields/smirff99Frosst_reference_0_1_spec.offxml, a SMIRNOFF 0.1 spec file enclosed by the legacy SMIRFF tag. This file is used in backwards-compatibility testing.

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