openforcefield/openforcefield: 0.7.1 OETK2020 Compatibility and Minor Update

0.7.1

This is the first of our patch releases on our new planned monthly release schedule.

Detailed release notes are below, but the major new features of this release are updates for compatibility with the new 2020 OpenEye Toolkits release, the get_available_force_fields function, and the disregarding of pyrimidal nitrogen stereochemistry in molecule isomorphism checks.

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.

• PR #646: Checking for Molecule equality using the == operator now disregards all pyrimidal nitrogen stereochemistry by default. To re-enable, use Molecule.{is|are}_isomorphic with the strip_pyrimidal_n_atom_stereo=False keyword argument.
• PR #646: Adds an optional toolkit_registry keyword argument to Molecule.are_isomorphic, which identifies the toolkit that should be used to search for pyrimidal nitrogens.

• PR #647: Updates OpenEyeToolkitWrapper for 2020.0.4 OpenEye Toolkit behavior/API changes.
• PR #646: Fixes a bug where Molecule.chemical_environment_matches was not able to accept a ChemicalEnvironment object as a query.
• PR #634: Fixes a bug in which calling RDKitToolkitWrapper.from_file directly would not load files correctly if passed lowercase file_format. Note that this bug did not occur when calling Molecule.from_file.
• PR #631: Fixes a bug in which calling unit_to_string returned None when the unit is dimensionless. Now "dimensionless" is returned.
• PR #630: Closes issue #629 in which the wrong exception is raised when attempting to instantiate a ForceField from an unparsable string.

• PR #632: Adds ForceField.registered_parameter_handlers
• PR #614: Adds ToolkitRegistry.deregister_toolkit to de-register registered toolkits, which can include toolkit wrappers loaded into GLOBAL_TOOLKIT_REGISTRY by default.
• PR #656: Adds a new allowed am1elf10 option to the OpenEye implementation of assign_partial_charges which calculates the average partial charges at the AM1 level of theory using conformers selected using the ELF10 method.
• PR #643: Adds openforcefield.typing.engines.smirnoff.forcefield.get_available_force_fields, which returns paths to the files of force fields available through entry point plugins.