openforcefield/openff-toolkit: 0.10.5 Bugfix release

0.10.5 Bugfix release

This release includes a significant refactor of the code handling virtual sites.

• PR #1252: Refactors virtual site support, resolving Issue #1235, Issue #1233, Issue #1222, Issue #1221, and Issue #1206.
  • Attempts to make virtual site handler more resilient through code simplification.
  • Virtual sites are now associated with a particular 'parent' atom, rather than with a set of atoms. In particular, when checking if a v-site has been assigned we now only check the main 'parent' atom associated with the v-site, rather than all additional orientation atoms. As an example, if a force field contained a bond-charge v-site that matches [O:1]=[C:2] and a monovalent lone pair that matches [O:1]=[C:2]-[*:3] in that order, then only the monovalent lone pair will be assigned to formaldehyde as the oxygen is the main atom that would be associated with both v-sites, and the monovalent lone pair appears later in the hierarchy. This constitutes a behaviour change over previous versions.
  • All v-site exclusion policies have been removed except for 'parents' which has been updated to match OFF-EP 0006.
  • checks have been added to enforce that the 'match' keyword complies with the SMIRNOFF spec.
  • Molecule virtual site classes no longer store FF data such as epsilon and sigma.
  • Sanity checks have been added when matching chemical environments for v-sites that ensure the environment looks like one of our expected test cases.
  • Fixes di- and trivalent lone pairs mixing the :1 and :2 indices.
  • Fixes trivalent v-site positioning.
  • Correctly splits TopologyVirtualSite and TopologyVirtualParticle so that virtual particles no longer have attributes such as particles, and ensure that indexing methods now work correctly.

For the complete release notes, please see our documentation

For help getting the OpenFF Toolkit running, 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.