v0.15.0

Highlights

• The ability to do charge correction through alchemical waters has been added to the RBFE protocol.
• Structural analysis (using openfe_analysis) of the RBFE simulations is now provided as part of the results.
• Addition of Kartograf bindings to openfe.

What's Changed

• Fix checkpoint name by @IAlibay in #594
• Create CONTRIBUTING.md by @richardjgowers in #597
• [skip ci] Update README.md by @richardjgowers in #599
• Add duecredit by @IAlibay in #601
• Charge correction via alchemical waters by @IAlibay in #569
• Add neutralize to system_creation's addSolvent by @IAlibay in #613
• use Lomap package's bindings by @richardjgowers in #478
• Remove replica states from results dictionary by @IAlibay in #603
• remove obsolete test data file by @richardjgowers in #621
• cli: gather raw option by @richardjgowers in #620
• Yaml format for CLI input by @richardjgowers in #583
• Kartograf integration by @RiesBen in #249
• Structural analysis by @richardjgowers in #571
• Fix docker image building + CI improvements by @mikemhenry in #641
• Allow Manual Running of Slow Tests by @mikemhenry in #649
• Change get_simsteps function to handle NVT equilibration in plain MD protocol by @hannahbaumann in #647
• emove duecredit.p file by @IAlibay in #655
• Use uuid for unit repeat ids for HFE protocol by @IAlibay in #650
• update to use openfe_analysis 0.2.0+ by @richardjgowers in #656
• Issue 335 float quantity in settings by @richardjgowers in #657

New Contributors

• @hannahbaumann made their first contribution in #647

Full Changelog: v0.14.0...v0.15.0

v0.14.0

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_network for more robust ligand networks
• Allows gather CLI 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

v0.13.0

Highlights

• Scores are now in line with other community efforts, 1.0 representing full agreement, 0.0 representing complete disagreement.
• the gather command 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

v0.12.0

Highlights

• Adds ability to read FEP+ / Orion NES ligand network files using openfe.setup.ligand_network_planning.load_fepplus_network and openfe.setup.ligand_network_planning.load_orion_network
• Adds openfe.setup.ligand_network_planning.generate_network_from_names and openfe.setup.ligand_network_planning.generate_network_from_indices to create arbitrary networks
• OpenMM RBFE Protocol pdb output now labels A and B state using BFactor column
• network layouts from cli tool now much easier to understand

What's Changed

• Make super slow tests integration tests by @IAlibay in #484
• Added DCO by @mikemhenry in #475
• fix issue with new notebook version by @mikemhenry in #498
• Tell users to install the latest version of openfe by @mikemhenry in #497
• Unpin libnetcdf by @dwhswenson in #500
• add ps to the docker image (interline needed this) by @mikemhenry in #501
• Network planner functions from indices/names by @richardjgowers in #482
• remove version name and upload files by @mikemhenry in #503
• API docs updates by @Yoshanuikabundi in #493
• Update openfecli/tests/data/rbfe_results.tar.gz by @mikemhenry in #496
• Logging improvements in quickrun by @dwhswenson in #504
• see if py311 works okay by @mikemhenry in #508
• Migrate common settings to omm_utils by @IAlibay in #512
• Read network from external files by @IAlibay in #511
• Add system probe by @mikemhenry in #505
• pin pydantic and autodoc_pydantic by @IAlibay in #517
• rfe protocol: Adds bfactor labels to output topology by @richardjgowers in #499
• update network layout to use graphviz by @richardjgowers in #523
• Check the ability to pass user charges by @IAlibay in #524

New Contributors

• @Yoshanuikabundi made their first contribution in #493

Full Changelog: v0.11.1...v0.12.0

v0.11.1 - Lomap performance patch

What's Changed

• Use common core option when using the Lomap Atom Mapper by @richardjgowers in #485

Full Changelog: v0.11.0...v0.11.1

v0.11.0 - Cofactor CLI support

What's Changed

• Update installer and container images to python 310 by @mikemhenry in #465
• Pin units - same thing as in gufe by @IAlibay in #466
• Actually actually fix silence_root_logging by @dwhswenson in #467
• CodeCov only on PR by @dwhswenson in #469
• cofactors from CLI by @richardjgowers in #456
• Fix minor typo by @slochower in #471
• Sort while running gather by @dwhswenson in #472
• Reconfigure stdout to be line-buffered in quickrun by @dwhswenson in #468
• Add PDB serialization in RFE protocol by @IAlibay in #450
• Code of Conduct by @mikemhenry in #474
• end to end integration tests for tyk2 tutorial by @richardjgowers in #476
• allow gathering of legacy results by @richardjgowers in #477
• Force no oechem by @richardjgowers in #479
• fixup manifest for new test files by @richardjgowers in #481

New Contributors

• @slochower made their first contribution in #471

Full Changelog: v0.10.1...v0.11.0

v0.10.1 - Hotfix

Fixes some test failures that weren't actually harmful.

What's Changed

• Install GUFE after we restore cache to alwasys get a fresh version by @mikemhenry in #452
• Update to support the newest version of openmmtools by @mikemhenry in #451
• allow single AtomMapper to be passed to network planners by @richardjgowers in #454
• Fix silence_root_logging by @dwhswenson in #453
• explain how to use nvidia-smi to figure out cudatoolkit version by @mikemhenry in #455
• need to update slow tests following execute_DAG update by @richardjgowers in #459
• Run slow tests on push & release by @IAlibay in #460

Full Changelog: v0.10.0...v0.10.1

v0.10.0

What's Changed

• Cautiously allow core element changes by @IAlibay in #438
• Fix handling of ThreeParticleAverageSite virtual sites by @IAlibay in #395
• Pin PyMBAR to sub v4 by @IAlibay in #444
• Add to_openff() intermediary for to_openeye() calls by @IAlibay in #446
• rename water molecules so addSolvent doesn't replace with ion by @richardjgowers in #441
• quickrun command now retries simulations by @richardjgowers in #447
• add fetchables for showcase notebook inputs by @mikemhenry in #437
• remove rate_of_convergence by @richardjgowers in #433
• Update gather.py - protocol failure robustness by @RiesBen in #381

Full Changelog: v0.9.1...v0.10.0

v0.9.1

By default, now not water is the selection used to write out particle coordinates instead of all.
This setting is controlled by the output_indices setting in SimulationSettings for the RFE Settings object.

What's Changed

• Don't build docker image on tags by @mikemhenry in #435
• all to not water for writing by @IAlibay in #431

Full Changelog: v0.9.0...v0.9.1

v0.9.0

Improvements to the OpenMM RBFE Protocol. see #387

What's Changed

• Switch rbfe tutorial fetch to point to main; not master by @dwhswenson in #430
• [RFE protocol] Allow multiple small molecules + allow running with non-OpenFF force fields by @IAlibay in #387

Full Changelog: v0.8.1...v0.9.0