Foyer Versions Save

Maintenance

• Update Github CI by @daico007 in https://github.com/mosdef-hub/foyer/pull/539
• Do not use deprecated OpenFF Toolkit iterator by @mattwthompson in https://github.com/mosdef-hub/foyer/pull/541
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #542, #544 - #548, #552 - #554
• Fix failing CI tests on main by @daico007 in https://github.com/mosdef-hub/foyer/pull/551

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.12.0...0.12.1

Features

• Update nbfix to use parmed structure.copy by @jaclark5 in https://github.com/mosdef-hub/foyer/pull/530
• Add note explaining the origin of the name "foyer" by @ctk3b in https://github.com/mosdef-hub/foyer/pull/532
• change default of use_residue_map to be False by @daico007 in https://github.com/mosdef-hub/foyer/pull/535

Bug Fixes

• Update how xml_writer derive scaling factors by @daico007 in https://github.com/mosdef-hub/foyer/pull/518

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #519, #521, #524, #525, #526, #527, #528, #534
• chore: fix typos by @e-kwsm in https://github.com/mosdef-hub/foyer/pull/522
• Add CodeQL workflow for GitHub code scanning by @lgtm-com in https://github.com/mosdef-hub/foyer/pull/520
• Turn off fail-fast by @daico007 in https://github.com/mosdef-hub/foyer/pull/523
• Attempting to fix failing CI by @daico007 in https://github.com/mosdef-hub/foyer/pull/533
• Remove obsolete requirement files by @daico007 in https://github.com/mosdef-hub/foyer/pull/537
• Add testing for py3.10 by @daico007 in https://github.com/mosdef-hub/foyer/pull/536

New Contributors

• @lgtm-com made their first contribution in https://github.com/mosdef-hub/foyer/pull/520
• @jaclark5 made their first contribution in https://github.com/mosdef-hub/foyer/pull/530

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.11.3...0.12

Breaking change

• Stop testing and supporting Python 3.7 by @mattwthompson in https://github.com/mosdef-hub/foyer/pull/513

Feature

• Update TopologyGraph.from_openff_topology for new API by @mattwthompson in https://github.com/mosdef-hub/foyer/pull/469

Bug fix

• Bugfix for atomtyper by @daico007 in https://github.com/mosdef-hub/foyer/pull/514

Maintenance

• Update docs environment to use Python 3.8+ by @mattwthompson in https://github.com/mosdef-hub/foyer/pull/517
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/foyer/pull/515

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.11.2...0.11.3

Breaking change

• drop general forcefield by @daico007 in https://github.com/mosdef-hub/foyer/pull/512

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #507, #508

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.11.1...0.11.2

Features

• Add CITATION.cff file for easier repo citation by @justinGilmer in https://github.com/mosdef-hub/foyer/pull/498

Bugfixes

• Modify opls_validation ".top" impropers by @CalCraven in https://github.com/mosdef-hub/foyer/pull/506

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #499, #502
• Use github actions for CI by @umesh-timalsina in https://github.com/mosdef-hub/foyer/pull/503

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.11.0...0.11.1

Breaking Changes

• Officially stop testing on Python 3.6 and add testing for Python 3.9 in https://github.com/mosdef-hub/foyer/pull/480

Features

• Report missing bonds' types when using verbose flag by @jennyfothergill in https://github.com/mosdef-hub/foyer/pull/486
• Modify XML parsing order of general forcefield by @daico007 in https://github.com/mosdef-hub/foyer/pull/488
• Remove untyped connections by @chrisiacovella in https://github.com/mosdef-hub/foyer/pull/493
• Storing meta data in typed parmed structure by @daico007 in https://github.com/mosdef-hub/foyer/pull/496

Bug fixes

• Fix scaling factors and mixing rule bug when atomtyping with general_forcefield by @daico007 in https://github.com/mosdef-hub/foyer/pull/489

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #478, #481, #492, #494
• Update links in README by @daico007 in https://github.com/mosdef-hub/foyer/pull/484
• Fix typo in issue template by @jennyfothergill in https://github.com/mosdef-hub/foyer/pull/487

Full Changelog: https://github.com/mosdef-hub/foyer/compare/0.10.0...0.11.0

Features

• Decouple forcefield from atomtyping step (#467)

Bug Fixes

• Return periodic torsion parameters, regardless of k value (#471)

Maintenance

• pre-commit ci autoupdate (#462, #473, #475)
• Update docker image and re-add anaconda user (#463)
• Miscellaneous updates related to executable files, accidently tracked files, PEP8 E722 and F523 (#465). Thanks @e-kwsm
• Use codecov uploader in favor of bash uploader for coverage reports (#468)

This is a patch release for making foyer compatible with latest API changes in openmm version 7.6.

Maintenance

• Update import syntax in foyer to work with OpenMM v7.6 (#455, #457)
• Pre-commit autoupdate (#456)

Features

• Add combining rule to TRAPPE-UA XML (#452)
• Integrate ele to the atomtyping step (#428)
• Update SMARTS string for opls_154 (#450)

Bug Fix

• Collapsing combining_rule of forcefield when loading multiple forcefield files (#442)

Maintenance

• Fix typo in pre-commit yml (#439)
• Add Foyer graphic to README.md (#443)
• Update Foyer documentation (#415)
• Pre-commit autoupdate (#444, #445, #449)
• Migrate azure pipeline environment creation use mamba (#447)
• Update docker building routine (#451)

Bug fixes

• This is a patch release for the issue related to the combining rule used to calculate 1-4 nonbonded interactions (#435)
  • Currently, the 1-4 nonbonded calculations are calculated using the Lorentz Berthelot combining rule (https://en.wikipedia.org/wiki/Combining_rules#Lorentz-Berthelot_rules), and the parameters are not updated when forcefield.combining_rule is updated. This release adds a patch to recalculate sigma when forcefield.combining_rule is updated to “geometric” (#433)
  • NOTE - This applies to all instances of parametrizing with foyer, all mixing rules were calculated using Lorentz-Berthelot, even when geometric was specified

Features

• Include combination_rule as top-level metadata in forcefield XMLs (#433)
• Update references and SMARTS strings for ester groups in oplsaa.xml, refer to CHANGELOG for list of affected atomtypes (#429)

Maintenance

• Explicitly list default cloud-based pre-commit options in .pre-commit-config.yaml (#425)
• Include detailed tests for forcefield metadata (#435)
• Increase performance for unit testing gmso integration (#437)