0.10.5 Bugfix release

0.10.5 Bugfix release

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

Critical bugfixes

• 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.

0.10.4 Bugfix release

0.10.4 Bugfix release

Critical bugfixes

• PR #1242: Fixess Issue #837. If OpenEye Toolkits are available ToolkitAM1BCCHandler will use the ELF10 method to select conformers for AM1-BCC charge assignment.
• PR #1184: Fixes Issue #1181 and Issue #1190, where in rare cases double bond stereochemistry would cause Molecule.to_rdkit to raise an error. The transfer of double bond stereochemistry from OpenFF's E/Z representation to RDKit's local representation is now handled as a constraint satisfaction problem.

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.

0.10.3 Major Bugfix release

0.10.3 Major bugfix release

This release fixes a bug where using Sage to parameterize a topology containing water would assign AM1BCC charges instead of TIP3P library charges. This bug was present in OpenFF Toolkit versions 0.10.1 and 0.10.2, and therefore did not affect the Sage fitting.

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.

0.10.2 Bugfix release

0.10.2 Bugfix release

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.

0.10.1 Minor feature and bugfix release

0.10.1 Minor feature and bugfix release

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.

0.10.0 Improvements for force field fitting

0.10.0 Improvements for force field fitting

For the complete release notes, please see our documentation

This release does not have a single major new feature, but instead encompasses several small new methods and behavior changes. These changes should be clear improvements, but they will modify the formats of some outputs (like removing the header line when RDKitToolkitWrapper writes to a SMILES file) and will slightly change some numerical values (by, for example, correcting for partial charge rounding errors). Please read the release notes for a full summary of these.

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.

0.9.2 Minor feature and bugfix release

0.9.2 Minor feature and bugfix release

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.

0.9.1 Minor feature and bugfix release

0.9.1 Minor feature and bugfix release

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.

0.8.4 Minor feature and bugfix release

0.8.4 Minor feature and bugfix release

For the complete release notes, please see our documentation

This release is intended to be functionally identical to 0.9.1. The only difference is that it uses the "openforcefield" namespace.

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.

0.9.0 Namespace Migration

0.9.0 Namespace Migration

For the complete release notes, please see our documentation

This minor release marks the transition from the old openforcefield branding over to its new identity as openff-toolkit. This change has been made to better represent the role of the toolkit, and highlight its place in the larger Open Force Field (OpenFF) ecosystem.

From version 0.9.0 onwards the toolkit will need to be imported as import openff.toolkit.XXX and from openff.toolkit import XXX.

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.