Highlights
- Scores are now in line with other community efforts, 1.0 representing full agreement, 0.0 representing complete disagreement.
- the
gathercommand now performs a MLE to yield absolute binding free energies, there are also options for other breakdowns - includes many documentation improvements
What's Changed
- fixes implementation of transmuting_methyl_into_ring_score by @richardjgowers in #526
- Assert hybrid PDB contents by @IAlibay in #530
- Add optional path to sys probe by @mikemhenry in #519
- Remove softcore electrostatics entry by @IAlibay in #521
- Adds MLE estimates on gather command by @richardjgowers in #495
- Allow extra attributes in AlchemicalSettings by @richardjgowers in #535
- ci: print duration of 10 slowest tests by @richardjgowers in #534
- Use 1.0 for good AtomMapping scores, 0.0 for bad AtomMapping scores by @richardjgowers in #529
- annotate dry run many molecules test as slow by @richardjgowers in #533
- add flaky marker to test_dry_run_user_charges by @richardjgowers in #537
- Cookbook flowchart by @Yoshanuikabundi in #520
- remove LigandNetwork by @richardjgowers in #536
- rework handle_trajectories to use replicas by @richardjgowers in #539
- support pydantic v1 and v2 by @mikemhenry in #540
- Rejuvenate API refs by @Yoshanuikabundi in #527
- network_from_indices raises warning on disconnected network by @richardjgowers in #514
- docs: fixup typo in tutorial links by @richardjgowers in #542
Full Changelog: v0.12.0...v0.12.1