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  • bd553d28aa Minor fixes jbutch 2025-12-04 19:34:17 -08:00
  • e80d9608f1 Fix installation v2 jbutch 2025-12-04 19:29:37 -08:00
  • a9196592ca Fix installation jbutch 2025-12-04 19:25:17 -08:00
  • fd24d7268b Merge pull request #54 from RosettaCommons/fix/readmes Jasper Butcher 2025-12-04 18:57:40 -08:00
  • 76f28cfdc4 Fix: linting check jbutch 2025-12-04 18:56:19 -08:00
  • 22c2a63241 Update models/rfd3/docs/input.md Jasper Butcher 2025-12-04 18:53:54 -08:00
  • 4ac2a9b7de Update models/rfd3/README.md Jasper Butcher 2025-12-04 18:53:42 -08:00
  • c4a8dffed0 Update models/rfd3/README.md Jasper Butcher 2025-12-04 18:53:33 -08:00
  • 8c36d6f78d Update models/rfd3/README.md Jasper Butcher 2025-12-04 18:53:23 -08:00
  • f0379581b4 Update models/rfd3/docs/input.md Jasper Butcher 2025-12-04 18:52:34 -08:00
  • a14f763a6e Fix: linting check jbutch 2025-12-04 18:51:06 -08:00
  • a5ff3fa976 Minor changes jbutch 2025-12-04 18:45:50 -08:00
  • 45e8a47a06 Add fles jbutch 2025-12-04 18:40:01 -08:00
  • dfdf28b102 Add files, update input.md jbutch 2025-12-04 18:31:47 -08:00
  • f8fe01e96c Turn off prevalidation by default jbutch 2025-12-04 17:45:19 -08:00
  • e0d502e0d9 Merge pull request #53 from RosettaCommons/format/make-format Jasper Butcher 2025-12-04 17:34:32 -08:00
  • 12942c2098 Make format jbutch 2025-12-04 17:33:55 -08:00
  • 05807eb849 Make format jbutch 2025-12-04 17:18:23 -08:00
  • 0d72b922d6 Merge pull request #52 from RosettaCommons/fix/alignment Jasper Butcher 2025-12-04 17:12:25 -08:00
  • 38b03fae00 Update .env Jasper Butcher 2025-12-04 17:12:15 -08:00
  • f783862501 Update src/foundry/utils/alignment.py Jasper Butcher 2025-12-04 17:12:08 -08:00
  • 5c60a1f9ae Minor fixes jbutch 2025-12-04 17:10:03 -08:00
  • 8919e1d703 Merge pull request #51 from RosettaCommons/fix/update_filename_for_training_rfd3 Jasper Butcher 2025-12-04 16:59:23 -08:00
  • c8e1b3dd32 Merge pull request #48 from RosettaCommons/fix/typo_in_pdb_name Jasper Butcher 2025-12-04 16:58:47 -08:00
  • b72ada05ff Fix: task logging, no ckpt path at cli, make format jbutch 2025-12-04 16:53:09 -08:00
  • f39fa7d726 Update parquet file name for training rfd3 Hope Woods 2025-12-04 16:37:44 -05:00
  • 0c1fb38d97 Merge pull request #42 from RosettaCommons/rfd3-sym-hotfix Aiko 2025-12-04 13:12:19 -08:00
  • d34ea4d266 Merge pull request #39 from RosettaCommons/rfd3-sym-readme Aiko 2025-12-04 13:12:03 -08:00
  • 5be99fc7d6 Fix typo in hbplus installation instructions Rachel Clune 2025-12-04 12:14:36 -08:00
  • b376933dd7 Changed input_pdb filename from 4zxb_croppped.pdb to 4zxb_cropped.pdb Hope Woods 2025-12-04 10:57:52 -05:00
  • 24f2fb17bc Merge pull request #38 from RosettaCommons/rac_docs Jasper Butcher 2025-12-03 20:38:58 -08:00
  • 5233cadb89 Merge branch 'production' into rac_docs Jasper Butcher 2025-12-03 20:38:08 -08:00
  • ffb0bcf2a7 fix: some bugs in legacy parsing and symmetry Aiko Muraishi 2025-12-03 19:14:52 -08:00
  • d9334d7075 symmetry.md updated Aiko Muraishi 2025-12-03 17:38:43 -08:00
  • 7f6656ebf4 Merge pull request #37 from RosettaCommons/readme-fixes Jasper Butcher 2025-12-03 17:13:05 -08:00
  • 3aa634158d Minor updates to readme jbutch 2025-12-03 17:12:19 -08:00
  • 27126f0f17 Add new file jbutch 2025-12-03 16:39:58 -08:00
  • 536af6eff4 Update README.md Jasper Butcher 2025-12-03 15:39:54 -08:00
  • 20e8105a79 Add example input files and update documentation for RFD3 Rachel Clune 2025-12-03 15:19:17 -08:00
  • 5582c7d248 Fix checkpoint directory flag in installation command Rachel Clune 2025-12-03 14:50:04 -08:00
  • ab6b438137 Update README jbutch 2025-12-03 14:16:41 -08:00
  • 6d18903e43 Merge pull request #36 from RosettaCommons/feat/collab Rohith Krishna 2025-12-03 10:52:24 -08:00
  • 70c6b2c4e2 Fix command option for checkpoint directory Rachel Clune 2025-12-03 10:00:38 -08:00
  • 04cb7f2ca6 feat: collab notebook feat/collab ncorley 2025-12-03 09:31:41 -08:00
  • 395737750a Merge pull request #32 from RosettaCommons/fix/readmes Rohith Krishna 2025-12-03 02:45:31 -08:00
  • 48d7d565c4 Merge pull request #34 from RosettaCommons/inference-runner Nathaniel Corley 2025-12-03 02:42:36 -08:00
  • 51c6228072 Merge pull request #35 from RosettaCommons/fix/notebook Rohith Krishna 2025-12-03 02:39:49 -08:00
  • 97a803d1c4 fix: notebook ncorley 2025-12-03 02:37:54 -08:00
  • bae631b9b4 force include yamls for inference v0.1.6 inference-runner Rohith Krishna 2025-12-03 02:35:36 -08:00
  • 3106504ae1 fix: notebook ncorley 2025-12-03 02:25:06 -08:00
  • 86137ef3ed fix: remove rootutils from inference.py v0.1.5 Rohith Krishna 2025-12-03 02:17:30 -08:00
  • 2da0087880 Add file Ubiquinone-dot 2025-12-03 01:52:12 -08:00
  • 7c8a29437b Add assets, cleanup READMEs, remove old files Ubiquinone-dot 2025-12-03 01:50:50 -08:00
  • eb4f8ab83e Merge pull request #33 from RosettaCommons/fix/checkpoints Rohith Krishna 2025-12-03 01:50:44 -08:00
  • 1bf46afa21 chore: ruff, fix checkpoint code ncorley 2025-12-03 01:48:46 -08:00
  • d14203b264 Merge pull request #31 from RosettaCommons/fix/rootutils Rohith Krishna 2025-12-03 01:17:01 -08:00
  • 7668d03d04 use .foundry as default for checkpoint dir v0.1.3 v0.1.2 Rohith Krishna 2025-12-03 01:15:23 -08:00
  • c859ce4fc0 remove use of rootutils to allow for pypi Rohith Krishna 2025-12-03 01:12:14 -08:00
  • 5ae1567d3a Merge pull request #30 from timkartar/patch-1 Rohith Krishna 2025-12-03 00:53:02 -08:00
  • fc9aea95a2 Merge branch 'RosettaCommons:production' into patch-1 Raktim Mitra 2025-12-03 00:51:40 -08:00
  • 30231f1457 Update README.md Raktim Mitra 2025-12-03 00:50:53 -08:00
  • 31cedb1d0a Merge pull request #29 from timkartar/patch-1 Rohith Krishna 2025-12-03 00:50:35 -08:00
  • 46eeaa45f0 Update README.md fix trajectory.png link Raktim Mitra 2025-12-03 00:47:49 -08:00
  • e79dcb71ab Merge pull request #28 from RosettaCommons/stage_for_production Rohith Krishna 2025-12-03 00:35:28 -08:00
  • dfe5402a5d add in weights docs and help string fix (#727) AndrewKubaney 2025-12-03 00:09:46 -08:00
  • 98b12108c7 Added details and fixed typos in NA binder design examples (#721) Rachel Clune 2025-12-03 00:07:34 -08:00
  • d72e49aa96 docs: dataset readme (#726) Nathaniel Corley 2025-12-03 00:07:21 -08:00
  • 94bb987998 Refactor/checkpoint defaults (#723) Jasper Butcher 2025-12-02 23:43:51 -08:00
  • d07d003ae2 remove notebook outputs Rohith Krishna 2025-12-02 23:36:10 -08:00
  • 2cd401665b initial progress on documentation cleanup (#722) Rohith Krishna 2025-12-02 23:23:02 -08:00
  • 5ec34da7c1 chore: fix regression tests for rf3 (#725) Nathaniel Corley 2025-12-02 23:21:25 -08:00
  • adb11204c8 remove more instances of foundry (#724) Rohith Krishna 2025-12-02 23:15:45 -08:00
  • 3414c0e833 Refactor/sm binder cleanup (#720) Raktim Mitra 2025-12-02 22:07:52 -08:00
  • 264bb79ee4 hbplus_instruction (#719) Raktim Mitra 2025-12-02 21:10:39 -08:00
  • 1d12ccdf7d add in weights docs and help string fix (#727) v0.1.1 AndrewKubaney 2025-12-03 00:09:46 -08:00
  • a74480a499 Added details and fixed typos in NA binder design examples (#721) Rachel Clune 2025-12-03 00:07:34 -08:00
  • 3d5a227444 docs: dataset readme (#726) Nathaniel Corley 2025-12-03 00:07:21 -08:00
  • 9604dd57ec Refactor/checkpoint defaults (#723) Jasper Butcher 2025-12-02 23:43:51 -08:00
  • 94e03b1763 remove notebook outputs Rohith Krishna 2025-12-02 23:36:10 -08:00
  • 0ff792f718 initial progress on documentation cleanup (#722) Rohith Krishna 2025-12-02 23:23:02 -08:00
  • ed796ec622 chore: fix regression tests for rf3 (#725) Nathaniel Corley 2025-12-02 23:21:25 -08:00
  • 6bdd755fd6 remove more instances of foundry (#724) Rohith Krishna 2025-12-02 23:15:45 -08:00
  • a6a3826a51 Refactor/sm binder cleanup (#720) Raktim Mitra 2025-12-02 22:07:52 -08:00
  • 8ccaebc14f hbplus_instruction (#719) Raktim Mitra 2025-12-02 21:10:39 -08:00
  • faa2935417 remove ipd specific files Rohith Krishna 2025-12-02 20:56:06 -08:00
  • bf8b44a83f feat: enable installing checkpoints from command line Rohith Krishna 2025-12-02 20:29:09 -08:00
  • db7cbf37d1 fix: fix path in paths for pdb parsing (#715) Rohith Krishna 2025-12-02 17:55:02 -08:00
  • 62cbbe28e5 Finalizing READMEs (#711) Jasper Butcher 2025-12-02 16:46:33 -08:00
  • 76e61e0c2d docs: update RFD3 README (#714) Rachel Clune 2025-12-02 16:42:04 -08:00
  • 050390fd67 Feat/notebook and rf3 confidence refactor (#713) Nathaniel Corley 2025-12-02 16:26:38 -08:00
  • a8bcaa0ffa move parquet paths into default paths config: (#712) Rohith Krishna 2025-12-02 14:50:19 -08:00
  • 9a9d4c40d8 Remove old code for reference frame jbutch 2025-12-02 02:24:01 -08:00
  • a9ced98137 Fixes to training jbutch 2025-12-02 02:32:40 -08:00
  • d6d113f3d6 Minor config changes, fixes to training jbutch 2025-12-02 01:22:10 -08:00
  • 33cbd92b44 Less verbose logging jbutch 2025-12-02 00:16:43 -08:00
  • 152a0911f1 DRAFT: docs for release, soft code hbplus (#699) Raktim Mitra 2025-12-01 18:23:02 -08:00
  • f3c01c2a2d refactor: rf3 and rfd3 lab training (#709) Nathaniel Corley 2025-12-01 18:14:07 -08:00
  • a5532404f5 Refactor/rf3 rfd3 training (#705) Jasper Butcher 2025-11-30 00:35:07 -08:00
  • d603dee7c4 Make format mpnn & with unsafe fixes jbutch 2025-11-29 22:46:41 -08:00
  • 87264c2cb3 feat: add mpnn to refactor/rf3-lab (#704) AndrewKubaney 2025-11-29 22:34:05 -08:00