The Open Free Energy library

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-7-0

What's Changed

• Update citation file with new ordering. by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1452
• use isolated folder for conda cron ci by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1453
• Evaluate host idxs atoms in DSSP filters after distance evaluation [Issue #1418] by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1440
• Fix minimum distance in host finding [Issue #1422] by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1442
• Always use atoms in both helices and beta sheets in the DSSP filter by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1462
• Update restraint settings (force constant and min/max distance) by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1463
• Implement single residue boresch host finding by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1470
• add pyproject toml formatting by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1475
• Change bonded host strategy to use lowest variance restraint by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1477
• Changes in Boresch restraint default settings by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1486
• don't run CI for rtd changes by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1490
• Bump number of retires when fetching data with pooch by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1487
• Move ligand utils to gufe by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1479
• SepTop Protocol by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1057
• temporary pin to pre-pydantic v2 gufe commit by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1533
• SepTop: Addressing issues raised in review by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1532
• Ensure PEP-639 Support by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1546
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/openfe/pull/1552
• add comment to explain gufe pin in env yamls by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1553
• Add clear error for constraint KeyError by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1529
• Release prep v1.6.1 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1544
• Change the default atom mapping in the CLI to Kartograf by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1530
• add espaloma tests by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1450
• Add SepTop to gen serialized results by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1560
• Disable user supplied host & guest atoms in restraint settings by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1557
• Fix test to check if we are printing --allow-partial when a user uses --allow-partial by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1564
• migrate to pydantic v2 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1535
• fix nb link by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1574
• General HTF improvments and speed ups! by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1566
• Fix validation in AHFE Protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1572
• add dark mode to docs by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1565
• Expose geometry objects as the BoreschRestraintGeometry objects by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1578
• Add RBFE equilibration method details by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1581
• rename gufe.settings.types -> gufe.settings.typing by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1583
• Remove duplicate available_platforms fixture from septop slow tests by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1586
• Fix inline comment in slow septop test by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1587
• Add the standard correction to the error estimate in SepTop by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1588
• Remove thermostat when getting restrained system in SepTop by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1584
• Update DOI badge link in README.md by @hmacdope in https://github.com/OpenFreeEnergy/openfe/pull/1593
• Fix sampler setup for dry runs by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1590
• Make CUDA the default compute platform by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1576
• Fast/ adaptive settings by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1523
• Fix docs and validations for the lambda schedules by @hannahbaumann in https://github.com/OpenFreeEnergy/openfe/pull/1597
• deprecate openfe utils 3dviz in favor of gufe method by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1592
• Update expected atom count in SepTop solvent slow test by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1598
• ABFE protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1045
• Prepare for release v1.7 by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1601

New Contributors

• @ijpulidos made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/1539
• @hmacdope made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/1593

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.6.1...v1.7.0