pub_soft/openfold
3
0
Fork 0
mirror of https://github.com/aqlaboratory/openfold.git synced 2026-06-04 12:44:26 +08:00
Code Issues Packages Projects Releases Wiki Activity

Commit Graph

  • be2ec1841f Merge pull request #560 from borisfom/fix-cueq-scaling main Jennifer Wei 2025-12-16 16:41:53 +07:00
  • 6839eafa81 Fixed cueq external fallback and scaling Boris Fomitchev 2025-12-16 00:54:57 -08:00
  • b7143a5bc2 Bump actions/checkout from 5 to 6 dependabot/github_actions/actions/checkout-6 dependabot[bot] 2025-11-20 20:07:53 +00:00
  • 56da08ec75 Merge pull request #553 from borisfom/nv_upstream_trt_cuequivariance Jennifer Wei 2025-11-17 19:59:34 +07:00
  • a5257447a5 Install docs added Boris Fomitchev 2025-11-16 17:04:18 -08:00
  • 4292bd6c95 Addressing code review comments: test skip, docs Boris Fomitchev 2025-11-14 16:05:10 -08:00
  • 007d854759 Merge remote-tracking branch 'gh/main' into nv_upstream_trt_cuequivariance Boris Fomitchev 2025-11-14 14:39:26 -08:00
  • 96a89c6683 Merge remote-tracking branch 'b/nv_upstream_trt_cuequivariance' into nv_upstream_trt_cuequivariance Boris Fomitchev 2025-11-07 13:38:19 -08:00
  • e2d4bb9e4e Fixed the bug for multimer case Boris Fomitchev 2025-11-07 13:37:00 -08:00
  • ad830e6d5c Fix configuration call of cuequivariance Jennifer Wei 2025-11-06 18:19:43 +07:00
  • 410267f6fe restore missing relax_protein input Jennifer Wei 2025-11-06 18:15:22 +07:00
  • a1cf318e2a CuEq->DeepSpeed Fallback Boris Fomitchev 2025-10-24 16:37:05 -07:00
  • cdf9d6927c Fixing fake bias shape Boris Fomitchev 2025-10-23 21:24:43 -07:00
  • 65a327053b Merge branch 'main' into dependabot/github_actions/actions/setup-python-6 dependabot/github_actions/actions/setup-python-6 Jennifer Wei 2025-09-15 11:10:15 +07:00
  • ce0029e119 Merge pull request #550 from aqlaboratory/dependabot/github_actions/actions/checkout-5 Jennifer Wei 2025-09-15 11:09:13 +07:00
  • 51c9069e8c Added uniform copyright strings Boris Fomitchev 2025-09-10 13:50:12 -07:00
  • b713c1bbcf TensorRT integration Boris Fomitchev 2025-09-07 16:39:02 -07:00
  • 41d1c82165 cuEquivariance integration Boris Fomitchev 2025-09-04 13:09:38 -07:00
  • 9d8dcc7d05 Bump actions/setup-python from 5 to 6 dependabot[bot] 2025-09-04 20:18:31 +00:00
  • 9361292548 Bump actions/checkout from 4 to 5 dependabot[bot] 2025-08-12 05:04:36 +00:00
  • e938c184a2 Merge pull request #534 from aqlaboratory/pl_upgrades v2.2.0 Jennifer Wei 2025-04-26 08:31:36 +07:00
  • c587b06e8a add Open In Colab banner to notebook. pl_upgrades jnwei 2025-04-25 20:07:15 -05:00
  • 50a2e756e7 Update OpenFold notebook to updated pytorch2 commit jnwei 2025-04-25 20:00:11 -05:00
  • 1ffd197489 Merge pull request #533 from jnwei/pl_upgrades Jennifer Wei 2025-04-26 05:07:47 +07:00
  • 620a54fb13 Update amber_minimize.py Jennifer Wei 2025-04-26 05:06:20 +07:00
  • a5433c3af6 Update config.py Jennifer Wei 2025-04-26 05:05:25 +07:00
  • fe10216190 update version number. Jennifer Wei 2025-04-25 21:59:55 +00:00
  • 16af434172 fix inference documentation Jennifer Wei 2025-04-25 21:50:42 +00:00
  • 0672517777 Update installation docs to build CUDA12 version Jennifer Wei 2025-04-25 20:35:25 +00:00
  • 4312aec6b2 Add link to issue for deepspeed_evo_attention test. Jennifer Wei 2025-04-25 20:31:38 +00:00
  • da37880bb7 Allow numpy>2 and support compute capability >9 Jennifer Wei 2025-04-24 22:25:20 +00:00
  • cb899a5ab4 Merge pull request #2 from aqlaboratory/pl_upgrades Jennifer Wei 2025-04-25 04:55:51 +07:00
  • 7e06ed9821 support openmm>8 and fix tolerance units in amber minimization Jennifer Wei 2025-04-24 21:33:53 +00:00
  • 9caf30ae13 Change casting for deepspeed compare model test to fp32 Jennifer Wei 2025-04-24 20:51:34 +00:00
  • 0c2d455efe fix environment to support tests Jennifer Wei 2025-04-23 23:47:26 +00:00
  • ab4a245985 Merge branch 'main' into pl_upgrades Jennifer Wei 2025-04-23 20:18:29 +00:00
  • 100a309e01 Maintainance to pl_upgrades Jennifer Wei 2025-04-23 20:13:32 +00:00
  • 815a042c69 Merge pull request #516 from nenuadrian/patch-1 Jennifer Wei 2025-02-24 10:36:56 +07:00
  • 26d1a5dacc Merge pull request #520 from etowahadams/etowahadams/update-script Jennifer Wei 2025-02-24 10:36:34 +07:00
  • e8d355874c updated script etowahadams 2025-02-23 18:52:59 -05:00
  • a364defcd2 Minor typo fix in Installation.md Adrian (Mircea) Nenu 2024-12-26 09:50:59 +00:00
  • a1192c8d3a Merge pull request #505 from etowahadams/update-install Jennifer Wei 2024-12-04 15:14:25 +07:00
  • 56277ea056 fix: formatting etowahadams 2024-11-14 13:56:26 -05:00
  • c05a35412f fix: formatting etowahadams 2024-11-14 13:16:02 -05:00
  • f1d0ae7583 try quotes etowahadams 2024-11-14 13:13:22 -05:00
  • 6a43510aac fix: formatting etowahadams 2024-11-14 13:12:45 -05:00
  • 9f09442d0a fix: formatting etowahadams 2024-11-14 13:10:46 -05:00
  • a01a60f754 docs: env variable etowahadams 2024-11-14 13:08:37 -05:00
  • e605ec81dd Merge pull request #504 from aqlaboratory/revert-502-etowahadams/install-docs ljarosch 2024-11-14 12:36:56 -05:00
  • 625ade9196 Revert "docs: Add env var instructions to install guide " Jennifer Wei 2024-11-14 13:35:43 +07:00
  • 8ece4f3c0b Merge pull request #502 from etowahadams/etowahadams/install-docs Jennifer Wei 2024-11-14 13:06:45 +07:00
  • cde001fc40 add environment variables etowahadams 2024-11-13 11:40:23 -05:00
  • b79ca29c39 Merge pull request #479 from vaclavhanzl/patch-3 Jennifer Wei 2024-11-07 15:42:32 +07:00
  • 23cf2f6107 Merge pull request #496 from vaclavhanzl/vh-fix-pl_upgrades-env Jennifer Wei 2024-11-07 08:48:43 +07:00
  • 6bdbd48fc3 Fix pl_upgrades enwironment (numpy, cuda, gcc) Vaclav Hanzl 2024-10-22 19:23:05 +02:00
  • e6ce9c937e Update Installation.md - fix pl_upgrades clone instructions Vaclav Hanzl 2024-08-24 18:15:56 +02:00
  • 6f63267114 Merge pull request #470 from rkosai/main Jennifer Wei 2024-07-18 15:29:51 +07:00
  • c48f850a98 Merge pull request #408 from rostro36/main Jennifer Wei 2024-07-18 15:29:33 +07:00
  • 7d227395d6 Merge branch 'main' into main Jannik Gut 2024-07-18 03:17:55 +02:00
  • b38b6078dc Change path of Inference.md rostro36 2024-07-18 03:11:16 +02:00
  • 0dafd62baa Update documentation. rostro36 2024-07-18 03:01:49 +02:00
  • 8b5212da72 Remove unnecessary double-load of config_json. Ryan Kosai 2024-07-16 20:48:43 -07:00
  • f37d0d964d Merge pull request #464 from ljarosch/main Jennifer Wei 2024-07-08 12:04:25 +07:00
  • d3c89fc922 Fix 3-to-1 letter conversion to use extended mapping ljarosch 2024-07-05 22:12:30 -04:00
  • f6c875b3c8 Merge pull request #448 from aqlaboratory/aux_seq_files_update Jennifer Wei 2024-05-23 16:57:46 -05:00
  • 734ebc4b9f Update Aux_seq_files.md Jennifer Wei 2024-05-23 16:37:39 -05:00
  • 74e903e5db Update OpenFold.ipynb colab-button-patch Jennifer Wei 2024-05-17 11:38:48 +02:00
  • 935f51559e Update OpenFold.ipynb Jennifer Wei 2024-05-17 11:35:25 +02:00
  • 3c1fd31ac4 Merge pull request #443 from jnwei/main Jennifer Wei 2024-05-17 09:50:16 +02:00
  • 775b57e226 Fix formatting in installation.md jnwei 2024-05-17 09:49:48 +02:00
  • 6af8158138 hotfix: Fix installation documentation Jennifer Wei 2024-05-15 23:11:13 +02:00
  • feb45a521e Merge pull request #440 from vaclavhanzl/patch-1 Jennifer Wei 2024-05-15 03:15:52 +07:00
  • d2ffb8d09c Link OpenFold repo from the docs Vaclav Hanzl 2024-05-14 21:44:09 +02:00
  • f434a2786b Merge pull request #439 from aqlaboratory/setup-improvements v.2.1.0 Jennifer Wei 2024-05-13 17:02:28 +07:00
  • d8117ce373 in scripts/utils.py account for case where no conda environment is specified. Jennifer Wei 2024-05-13 07:36:35 +00:00
  • 97dae6c68a Updates biopython version to 1.83 in colab notebook, which seems to work better jnwei 2024-05-13 16:33:50 +07:00
  • ffc9b3f65a updates biopython version to 1.80 in colab notebook jnwei 2024-05-13 16:22:15 +07:00
  • 6384d793e0 Removes mpi4py from environment.yml -- not supported for Docker builds jnwei 2024-05-13 16:06:47 +07:00
  • 49804a599a small fix to docker-image ci workflow jnwei 2024-05-13 15:39:40 +07:00
  • 6706864754 Merge branch 'main' into setup-improvements Jennifer Wei 2024-05-13 15:35:03 +07:00
  • 3eef7caab3 Merge pull request #432 from vaclavhanzl/fix-colab-change-used-commit Jennifer Wei 2024-05-13 15:34:03 +07:00
  • a3c131904b Update OpenFold.ipynb to newest pl_upgrades commit Jennifer Wei 2024-05-13 15:13:55 +07:00
  • 29b5823e8b Merge pull request #419 from aqlaboratory/setup-improvements_additional-scripts Jennifer Wei 2024-05-13 14:57:36 +07:00
  • 3bec3e9b2d Merge pull request #438 from jnwei/pl_upgrades Jennifer Wei 2024-05-13 14:51:31 +07:00
  • c07075cf72 in scripts/utils.py account for case where no conda environment is specified. Jennifer Wei 2024-05-13 07:36:35 +00:00
  • dc93d33cec remove mpipy from pip install requirements Jennifer Wei 2024-05-13 07:26:49 +00:00
  • 1647ec908d fix typo in environment.yml Jennifer Wei 2024-05-13 07:16:15 +00:00
  • 6cba403b77 fix typo in environment.yml jnwei 2024-05-13 14:14:06 +07:00
  • a8c61c6287 Merge branch 'main' into pl_upgrades Jennifer Wei 2024-05-13 12:24:37 +07:00
  • e5ce21965c Update docker-image.yml Jennifer Wei 2024-05-13 12:21:52 +07:00
  • 3ed09c63fc Update docker-image.yml Jennifer Wei 2024-05-13 12:21:35 +07:00
  • cc565fde60 Adds example directory jnwei 2024-05-10 17:21:28 +07:00
  • 0b30bb85c2 Update training OpenFold docs with correct paths. jnwei 2024-05-10 17:04:54 +07:00
  • e338f2088d adds mmseqs2 to environment.yml for clustering jnwei 2024-05-09 17:17:34 +07:00
  • 78644cdf44 Shorten README.md main page. jnwei 2024-05-09 16:48:28 +07:00
  • 89c756dac7 make space for docker CI jnwei 2024-05-06 17:24:28 +07:00
  • a744abee11 Adds mkl version to environment.yml Jennifer 2024-04-30 09:46:12 -04:00
  • 55c1e0ee56 minor language edits jnwei 2024-05-08 23:40:57 +07:00
  • 6261c95b9d small edits to main page jnwei 2024-05-08 23:36:17 +07:00
  • f1175abfb8 creates link to FAQ in documentation jnwei 2024-05-08 23:34:34 +07:00