v1.0.0

Summary

This v1.0.0 marks a stable state of this repo that is prepped for submission of the corresponding OpenFE benchmarking manuscript.

All PRs included in this release

• Get RTD build going by @IAlibay in #13
• Test the RTD build with some truth by @IAlibay in #14
• Input preparation and contribution instructions by @hannahbaumann in #15
• Add input validation MD script by @IAlibay in #16
• Phase 1-4 instructions by @hannahbaumann in #19
• Add claimed systems by @hannahbaumann in #18
• Add PR template by @IAlibay in #20
• Contributing inputs section by @hannahbaumann in #17
• Reorganize things by @IAlibay in #24
• Update utility script instructions to point to the full python script. by @IAlibay in #30
• Add dir for missing datasets by @hannahbaumann in #38
• Update README by @hannahbaumann in #37
• Change instructions to create fork first by @hannahbaumann in #25
• Add test for input validation of a protein with PTM by @hannahbaumann in #39
• Add run instructions by @hannahbaumann in #42
• Cleanup script for trajectories by @hannahbaumann in #45
• Do we need to keep 21 instead of 20 frames? by @IAlibay in #59
• Add installation instructions by @hannahbaumann in #66
• Script to plan RBFE alchemical networks by @hannahbaumann in #31
• Adding ligand prep instructions by @hannahbaumann in #41
• Fix TOC tree by @hannahbaumann in #69
• Update .yml file name in run instructions based on James feedback by @hannahbaumann in #71
• Change run instructions to run each input json three times by @hannahbaumann in #65
• Update front page [WIP] by @hannahbaumann in #67
• Clean up a few things by @IAlibay in #73
• Updated installation instructions by @mikemhenry in #77
• Quick fix of a typo by @mikemhenry in #79
• fix up run script to match quickrun better by @IAlibay in #76
• Improve various docs things by @IAlibay in #80
• update validation script link in docs by @IAlibay in #81
• fix conda-lock install typo by @mikemhenry in #84
• Add micromamba instructions to loc file install docs by @mikemhenry in #86
• Add protonation state instructions to PR template by @hannahbaumann in #92
• Add maestro instructions by @hannahbaumann in #89
• Prepared input files for t4l and mcl1 by @vgapsys in #93
• Prepared input files for mup1, liga, bace, p38 by @steinbt2 in #95
• Protein check script by @IAlibay in #94
• Prepare systems tyk2 by @BillSwope in #101
• Prepared input files for DLK by @tlhr in #100
• Add a small script to check for ligand duplicates by @IAlibay in #102
• charge anhilation set Lilly (Sergio Perez and Howard Broughton) by @sergioperezconesa in #98
• Prepared inputs for cmet and hif2a merck datasets by @MCompChem in #82
• Add a reviewers guide by @IAlibay in #103
• Phase I: Preperation for JNK1, PTP1b, EGFR and Factor Xa by @RiesBen in #85
• added galectin prepped files by @ChayaSt in #105
• Add prepared systems by JB by @jbluck in #90
• Add JACS CKD2 inputs by @IAlibay in #107
• prepared chk1 and hsp90_kung in waterset by @vgapsys in #108
• [WIP] Script to extract DDG results by @hannahbaumann in #109
• Add plotting script by @IAlibay in #112
• Fix file paths and runtype assignment by @hannahbaumann in #116
• print traceback if simulation has errors by @mikemhenry in #117
• AZ Input files for EG5 - Merck by @MarcoKlahn in #118
• Prepare inputs for 3 systems: FAAH(misc), BACE prospective (janssen), BACE p3 Arg368in (Janssen) by @nupurbansal in #115
• Prepare systems: btk by @BillSwope in #120
• Draft cleanup results script by @mikemhenry in #83
• Fix #122 by @IAlibay in #123
• Prepared input files for jacs_set/thrombin by @BillSwope in #121
• Fix URL in cleanup script by @mikemhenry in #125
• Prepared input files for fragments/jak2_set1 system by @BillSwope in #126
• Prepared input files for fragments/jak2_set2 system by @BillSwope in #127
• Fix cleanup and results extraction script by @mikemhenry in #130
• Prepare cdk8 koehler by @BillSwope in #131
• Prepare cdk8 5cei by @BillSwope in #132
• Add documentation for handling failed simulations by @hannahbaumann in #135
• Skip correlation statistics if bootstrapping fails by @hannahbaumann in #143
• inputs for taf12 and thrombin in waterset by @vgapsys in #138
• AZ Input files for ephx2 ptp1b - charge_annihilation by @benefrg in #129
• MCL1, SHP2, Renin, HNE sets added. by @alexanderhwilliams in #97
• Hsp90 woodhead urokinase scyt dehyd by @vgapsys in #145
• add double quote to prevent globbing and word splitting by @mikemhenry in #147
• Prepared syk hsp and p38 by @levtsid in #133
• Fix hne mcl1 inputs by @IAlibay in #146
• Prepared input files for system tnks2 by @Lili-Cao in #106
• Saving DG values to file and plotting OpenFE against FEP+ by @hannahbaumann in #136
• Add check for missing result .json files by @hannahbaumann in #150
• Dont fail on missing edges by @IAlibay in #152
• Private phase 1 (and some 2) instructions by @IAlibay in #151
• fix typos and explain more how to find failed edges by @mikemhenry in #153
• Asap bace by @mikemhenry in #154
• Fix networks by @IAlibay in ...