Highlights
- Fixes errors caused by conformer generation failing
- Addresses high variance in partial charge generation through Ambertools giving high variance to estimates
- By default the OpenMM_RFE protocol produces energetic analysis of the simulations
- Adds
openfe.setup.ligand_network_planning.generate_minimal_redundant_networkfor more robust ligand networks - Allows
gatherCLI command to process partially finished/complete results
What's Changed
- test pydantic v2 by @mikemhenry in #541
- Analysing free energies by @IAlibay in #531
- fix forwards/backwards analysis for very small files by @richardjgowers in #545
- Fix Zenodo by @mikemhenry in #547
- Update CITATION.cff by @richardjgowers in #553
- ci: update to use setup-micromamba by @richardjgowers in #552
- don't include central ligand self edge in radial networks by @richardjgowers in #546
- Log system probe info by @dwhswenson in #513
- Update CITATION.cff by @richardjgowers in #554
- Add Zenodo badge to README by @richardjgowers in #555
- [WIP] Fix RTHP results serialization and test results load by @IAlibay in #550
- Fix energy results out by @richardjgowers in #556
- Added missing nc file by @mikemhenry in #562
- Tests: Test coverage for RFE ProtocolResult by @richardjgowers in #560
- Improve error message if missing one leg for ligand pair by @dwhswenson in #568
- Switch to a unified Sphinx theme by @Yoshanuikabundi in #563
- Fixup mypy matplotlib by @richardjgowers in #575
- add function to create a minimal network with redundancy for all nodes by @JenkeScheen in #559
- Combine installation guides and fix typos by @Yoshanuikabundi in #561
- Get ExampleNotebooks into docs by @Yoshanuikabundi in #538
- clear up language a bit for dg report help text by @mikemhenry in #549
- Absolute solvation free energies + base things for ABFEs by @IAlibay in #573
- rfe protocol: partial charges fix by @richardjgowers in #577
- Explicitly set navigation_keys to False to avoid warning by @IAlibay in #584
- Test AHFE user charges by @IAlibay in #586
- Enforce charges generated by input conformer by @IAlibay in #587
- Add
gather --allow-partial, improve related error message by @dwhswenson in #588
New Contributors
- @JenkeScheen made their first contribution in #559
Full Changelog: v0.13.0...v0.14.0