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0.3.0 API Improvements

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@j-wags j-wags released this 17 May 22:25
0.3.0
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0.3.0

DOI

This release makes several improvements and changes to public API.

User feedback indicated a need for a Topology.to_openmm() function, which has been created.

We have also added infrastructure to load forcefields using a plugin-like infrastructure from other packages in the environment. In the near future, an independent smirnoff99Frosst package will be available that provides the validated, revision-controlled forcefield series.

Some functionality that was inadvertently exposed in the 0.2.0 release has been removed (for example, the ForceField.to_smirnoff_data method is now private). Other convenience functions have been added, such as ForceField.to_string, as a close substitute for the functionality removed.

Several bugs were fixed and more informative error messages were added. Details of these changes are below.

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.

New features

  • PR #292 : Implement Topology.to_openmm and remove ToolkitRegistry.toolkit_is_available
  • PR #322: Install directories for the lookup of OFFXML files through the entry point group openforcefield.smirnoff_forcefield_directory. The ForceField class doesn't search in the data/forcefield/ folder anymore (now renamed data/test_forcefields/), but only in data/.

API-breaking Changes

  • PR #278: Standardize variable/method names
  • PR #291: Remove ForceField.load/to_smirnoff_data, add ForceField.to_file/string and ParameterHandler.add_parameters. Change behavior of ForceField.register_X_handler functions.

Bugfixes and Optimizations

  • PR #327: Fix units in tip3p.offxml (note that this file is not loadable by current toolkit)
  • PR #325: Fix solvent box for provided test system to resolve periodic clashes.
  • PR #325: Add informative message containing Hill chemical formula when a molecule can't be matched in Topology.from_openmm.
  • PR #325: Provide warning or error message as appropriate when a molecule is missing stereochemistry.
  • PR #316: Fix formatting issues in GBSA section of SMIRNOFF spec
  • PR #308: Cache molecule SMILES to improve system creation speed
  • PR #306: Allow single-atom molecules with all zero coordinates to be converted to OE/RDK mols
  • PR #313: Fix issue where constraints are applied twice to constrained bonds
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