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 #155
• Docs: Fix bug in fix network description by @hannahbaumann in #188
• Support local force fields when planning a network by @jthorton in #189
• Update docs for the extract_results script by @hannahbaumann in #196
• Move FAQ by @jthorton in #198
• Fudge fix for the zero error case by @IAlibay in #200
• Data gathering script by @hannahbaumann in #156
• Store numpy data in text files by @jthorton in #205
• Add docs for the gathering of results by @hannahbaumann in #197
• Experimental CSV instructions by @jthorton in #210
• Rename exp data script by @jthorton in #211
• Info form for private datasets by @hannahbaumann in #213
• Update readme and docs for current phase of benchmarking by @jthorton in #215
• Adding docs for how to submit results by @hannahbaumann in #214
• Updating the docs for submitting results by @hannahbaumann in #227
• Analysis script Part 1 gathering edge data by @jthorton in #230
• Use subsampling and calculate DG for each nanosecond of production simulation by @jthorton in #232
• Analysis metadata table by @jthorton in #234
• Update upload steps by @mikemhenry in #235
• ziped -> zipped by @mikemhenry in #236
• Add pymbar4 analysis script by @jthorton in #233
• Remove wait for instructions placeholder text by @mikemhenry in #237
• Don't fail if not all units are ProtocolResultFailures by @IAlibay in #238
• Upload public datasets so far by @jthorton in #240
• Add results from FEP+ paper by @hannahbaumann in #254
• Update public datasets by @jthorton in #255
• Update the public datasets v2 by @jthorton in #258
• Private datasets v1 by @jthorton in #259
• Add input systems for Merck PFKFB3 by @IAlibay in #256
• Update merck shp2 ligand names by @hannahbaumann in #260
• update private datatsets by @jthorton in #277
• update the public datasets by @jthorton in #278
• Update the private dataset names by @jthorton in #280
• Add fragment sets hsp90 and p38 by @jthorton in #282
• Update ligand names pfkfb3 by @hannahbaumann in #279
• Add genentech private by @jthorton in #286
• Add pfkfb3 rerun edges by @jthorton in #287
• add final public sets by @jthorton in #288
• final private datasets by @jthorton in #289
• Remove public macrocycle dataset as not applicable by @jthorton in #302
• Add a script that calculates statistics for datasets by @hannahbaumann in #303
• Small fix in get_statistics script by @hannahbaumann in #306
• remove claimed systems from docs by @atravitz in #317
• Add MMGBSA data and move pfkfb3 new to overall csv files by @hannahbaumann in #327
• Add notebook for convergence analysis by @hannahbaumann in #321
• Add notebook for overall DG analysis by @hannahbaumann in #315
• add draft analysis notebooks by @jthorton in #313

New Contributors

• @mikemhenry made their first contribution in #77
• @vgapsys made their first contribution in #93
• @steinbt2 made their first contribution in #95
• @BillSwope made their first contribution in #101
• @tlhr made their first contribution in #100
• @sergioperezconesa made their first contribution in #98
• @MCompChem made their first contribution in #82
• @RiesBen made their first contribution in #85
• @ChayaSt made their first contribution in #105
• @jbluck made their first contribution in #90
• @MarcoKlahn made their first contribution in #118
• @nupurbansal made their first contribution in #115
• @benefrg made their first contribution in #129
• @alexanderhwilliams made their first contribution in #97
• @levtsid made their first contribution in #133
• @Lili-Cao made their first contribution in #106
• @atravitz made their first contribution in #317

Full Changelog: https://github.com/OpenFreeEnergy/IndustryBenchmarks2024/commits/v1.0.0