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  • a3149cf18e fix small writer bug main HannesStark 2026-05-28 19:33:03 +00:00
  • 31d9d9b9c7 Version bump to 0.3.2 v0.3.2 Tim O'Donnell 2026-05-01 10:21:49 -04:00
  • f5d3c46961 Fix binding_types dropping 'binding' when combined with 'not_binding' Charlie Wang 2026-04-23 12:21:44 -04:00
  • 81b5e1da0c Merge pull request #196 from HannesStark/issue-192 v0.3.1 Tim O'Donnell 2026-03-06 15:35:08 -05:00
  • e7717aeb7a Fix the issue in #151 but still fail on malformed range tokens Tim O'Donnell 2026-03-06 15:33:04 -05:00
  • 4d2b559d7f Merge pull request #188 from ekiefl/ek/fix-gontivimab-path Tim O'Donnell 2026-03-06 15:23:48 -05:00
  • 57abea8be8 Merge pull request #175 from buerbaumer/feat/gemmi-version-compatibility Tim O'Donnell 2026-03-06 15:22:22 -05:00
  • c57461e360 Bump version to 0.3.1 and fix #192 Tim O'Donnell 2026-03-06 15:21:39 -05:00
  • 82704994e4 Fix gontivimab scaffold to reference gontivimab.cif, not sonelokimab.cif Evan Kiefl 2026-03-02 17:09:02 -08:00
  • cf201b0c3a switich to using new nanobody scaffolds HannesStark 2026-03-02 22:02:54 +00:00
  • 1d32f6aada add 3 additional nanobody scaffolds with improved developability properties compared to 8coh and 8z8v but with predicted scaffold structures HannesStark 2026-03-02 21:52:56 +00:00
  • da0f092069 Merge pull request #176 from profdocpizza/ipsae Tim O'Donnell 2026-02-17 17:16:50 -05:00
  • a145776d8b Merge branch 'main' into ipsae Tim O'Donnell 2026-02-17 13:51:36 -05:00
  • 39c87c65d6 fix: resolve inverse-fold constraint conflicts with global avoid Harald Buerbaumer 2026-02-16 18:18:40 +01:00
  • 0822cb3b71 fix: pad constraint mask for file entities, add tests and examples Harald Buerbaumer 2026-02-15 10:02:29 +01:00
  • 6d73b21d33 feat: add per-residue amino acid constraints for inverse folding Harald Buerbaumer 2026-02-14 09:54:12 +01:00
  • 33827ce0c1 Fix design insertions fix-48 Tim O'Donnell 2026-02-11 00:12:21 -05:00
  • 3eddb5a3c7 version bump v0.3.0 Tally Portnoi 2026-02-10 16:44:52 -05:00
  • 2c71c0bcac Support for symmetric IF and protein-redesign protocol Tally Portnoi 2026-02-10 16:15:30 -05:00
  • e2a9e32c12 fix bug when running inverse folding only Tally E. Portnoi 2026-02-05 22:12:08 -05:00
  • ad5d6b1413 fix off-by-one error in size bucket filtering Tally Portnoi 2026-02-05 23:12:39 -05:00
  • 1aa3a81e7d add ranking metrics to pdf Tally Portnoi 2026-02-05 22:24:00 -05:00
  • b69087552e Update comment to reflect visibility mask computation Hannes Stärk 2026-02-09 14:47:48 -05:00
  • 50be67f942 switch to templateV2 module instead of template module. During refactoring i previously accidentally took template module instead of templatemodulev2. the difference is that teamplatemodule masks out inter-chain templates (this only affects the refolding step) Hannes Stärk 2026-02-09 14:11:26 -05:00
  • 135a4a5a97 Revert "Add support for symmetric designs and protein-redesign protocol" Tally Portnoi 2026-02-05 16:43:02 -05:00
  • 8bf76220db Update src/boltzgen/data/const.py Tadas Kluonis 2026-02-05 14:25:04 +00:00
  • 83f3d5e988 Update src/boltzgen/task/filter/filter.py Tadas Kluonis 2026-02-05 14:24:19 +00:00
  • d613d36d18 removed redundant code and reused existin pae matrix for ipsae calculation profdocpizza 2026-02-05 14:23:27 +00:00
  • 49d61593f9 Update src/boltzgen/model/layers/confidence_utils.py Tadas Kluonis 2026-02-05 13:34:48 +00:00
  • a5a3705c4f Update src/boltzgen/task/filter/filter.py Tadas Kluonis 2026-02-05 13:32:35 +00:00
  • a41f3daf8e feat: implement ipSAE metric calculation profdocpizza 2026-02-05 11:46:56 +00:00
  • fd65aa8a37 fix mmcif parsing for files with multiple modles HannesStark 2026-02-04 20:48:31 +00:00
  • f020b9db96 Add support for symmetric designs and protein-redesign protocol Tally Portnoi 2026-02-04 15:33:51 -05:00
  • db2e5ff0b9 add design mask templates option to the repo HannesStark 2026-01-24 18:57:01 +00:00
  • ffcc43764b fix mmcif parsing for files with multiple modles sync-changes HannesStark 2026-02-04 20:48:31 +00:00
  • f32ea193c0 Add support for symmetric designs and protein-redesign protocol Tally Portnoi 2026-02-04 15:33:51 -05:00
  • a85a81acef add design mask templates option to the repo HannesStark 2026-01-24 18:57:01 +00:00
  • 47528316f3 feat: add gemmi 0.6.x and 0.7.x version compatibility Harald Buerbaumer 2026-02-04 09:47:16 +01:00
  • 2f023df422 chore: loosen gemmi version constraint Harald Buerbaumer 2026-02-04 09:40:48 +01:00
  • 617e549edf fix issues related to bond len loss Yuxin Xie 2026-01-09 13:44:53 -05:00
  • 25bf683d42 Update README with video link and Slack section Hannes Stärk 2026-01-08 09:04:26 -05:00
  • 80619ae8c9 add explanations for constraint specification from the file and smiles. MinGyu Choi 2026-01-06 12:12:32 -05:00
  • 7358f4f018 add specifying covalent bonds to atoms that come from a file. Also supports atom constraints from a smiles MinGyu Choi 2026-01-05 23:32:23 -05:00
  • 247b9bbd8b Add no distillation training config 20251218 Tim O'Donnell 2025-12-18 16:33:51 -05:00
  • e83966197f Fix activation checkpointing Tim O'Donnell 2025-12-18 16:32:55 -05:00
  • cd368bc070 Fix refolding step when there are no designed residues; see #122. Note that subsequent steps will still fail when there are no designed residues. Tim O'Donnell 2025-12-17 14:44:57 -05:00
  • f3392feefd Update run.sh Tim O'Donnell 2025-12-15 12:50:02 -05:00
  • 4cb93aabfd add small molecule normalization to absolute score HannesStark 2025-12-14 17:52:41 +00:00
  • ffe9dae0f6 add absolute metrics computation HannesStark 2025-12-14 17:36:49 +00:00
  • 52a83ed5ea add per-chain sequences to metrics when designing multiple chains Tally E. Portnoi 2025-12-13 23:24:09 -05:00
  • b5d532b97a Update README.md Tim O'Donnell 2025-12-10 16:13:03 -05:00
  • db0fbdae45 Merge pull request #70 from FloWuenne/fix_dockerfile Tim O'Donnell 2025-12-10 16:11:50 -05:00
  • e4c961b55e version bump v0.2.0 HannesStark 2025-12-10 20:40:03 +00:00
  • 961ad4944d fix design chain mask for multichain Yuxin Xie 2025-12-10 14:37:39 -05:00
  • 4eb4f6bb17 version bump v0.1.9 HannesStark 2025-12-10 00:46:07 +00:00
  • ca6a038baf change delta sasa (target to ~chain design atom) Yuxin Xie 2025-12-09 19:08:04 -05:00
  • dc57019b52 change delta sasa (target to ~chain design atom) boltzgen Yuxin Xie 2025-12-09 19:08:04 -05:00
  • f76ddb3205 add option to skip Refolded cif path does not exist. This can happen if a process was interrupted between writing the refold .npz file and the refold .cif file. Hannes Stark 2025-12-09 13:21:22 -05:00
  • 4f331de0ad Only count noncovalents between design and non design chain Felix Faltings 2025-12-09 11:10:03 -05:00
  • f488e96cbd Fix residue reindexing Felix Faltings 2025-12-09 11:07:57 -05:00
  • 743236150a Make MOLDIR_ZIP_CACHE multiprocessing-safe (https://github.com/HannesStark/boltzgen/issues/40) Anton Bushuiev 2025-12-08 18:58:41 -05:00
  • 291c4633b2 Add inverse folding example (https://github.com/HannesStark/boltzgen/issues/31) Anton Bushuiev 2025-12-08 18:57:34 -05:00
  • 9dce49b208 Update README.md v0.1.8 Tim O'Donnell 2025-12-04 22:41:33 -05:00
  • 0048752f0b fix antibody example and docs Tim O'Donnell 2025-12-04 22:39:45 -05:00
  • b211389a58 rename Tim O'Donnell 2025-12-04 22:34:51 -05:00
  • afa51c41bf add src/boltzgen/resources/config/train/boltzgen_no_distillation.yaml train Tim O'Donnell 2025-12-04 02:12:17 +00:00
  • 3875f188a8 Merge pull request #107 from HannesStark/training-fixes Tim O'Donnell 2025-12-03 21:11:01 -05:00
  • 4cafa61e42 training fixes training-fixes Tim O'Donnell 2025-12-04 02:10:10 +00:00
  • a2d06c4526 Merge pull request #92 from keejkrej/main Tim O'Donnell 2025-12-03 20:15:32 -05:00
  • 4de4e625d0 Update README.md Tim O'Donnell 2025-12-03 17:06:57 -05:00
  • 869e4111a8 Merge pull request #106 from HannesStark/slurm Tim O'Donnell 2025-12-03 16:16:09 -05:00
  • 29c1a524a3 typos slurm Tim O'Donnell 2025-12-03 16:14:40 -05:00
  • d4183e973a Add example scripts for SLURM Tim O'Donnell 2025-12-03 16:08:12 -05:00
  • fb1d66fd5d Merge pull request #97 from rhyschappell/main Tim O'Donnell 2025-12-03 11:35:57 -05:00
  • c0b5e11e7d version bump Tim O'Donnell 2025-12-03 11:10:00 -05:00
  • abd6cd9394 merge command fixes: do not delete output dir, make hard links when possible Tim O'Donnell 2025-12-03 11:09:33 -05:00
  • bedeaf8c5a remove old scfv files Hannes Stark 2025-12-02 17:21:25 -05:00
  • ecaa5327f2 remove superfluous file. I hope noone started using them yet Hannes Stark 2025-12-02 17:16:33 -05:00
  • 9aa3769691 fix antibody changes v0.1.7 Hannes Stark 2025-12-02 17:13:05 -05:00
  • 7ac86f01f1 version bump v0.1.6 Hannes Stark 2025-12-02 14:10:48 -05:00
  • 7e8d11d9ed add scfv and fab scaffolds. Rename nanobody-anything to antibody-anything Hannes Stark 2025-12-02 14:08:32 -05:00
  • 869a449582 add 'boltzgen merge' command Tim O'Donnell 2025-12-01 17:03:36 -05:00
  • e2a33ae15c set torch num threads in analyze Rhys Chappell 2025-12-01 09:48:39 -08:00
  • e22556a099 Make '--reuse' a configure rather than an execute argument. Fixes #68 #94 Tim O'Donnell 2025-12-01 11:31:35 -05:00
  • 6578c3149f Add weights_only=False to model checkpoint loading keejkrej 2025-11-29 22:21:59 +01:00
  • cc61d42aee add missing splits files Hannes Stark 2025-11-27 11:39:00 -05:00
  • d55e0efbb4 remove superfluous files v0.1.5 Hannes Stark 2025-11-26 08:52:16 -05:00
  • 96e2377c1b small improvements and add training ids Hannes Stark 2025-11-26 08:05:44 -05:00
  • a941e4eb3d fix antibody scaffolds Tim O'Donnell 2025-11-20 14:23:03 -05:00
  • 527762d6c8 Merge pull request #73 from HannesStark/add-antibody-examples Tim O'Donnell 2025-11-20 14:04:31 -05:00
  • eb201df2ce Add antibody scaffold examples (very experimental) Tim O'Donnell 2025-11-20 12:10:07 -05:00
  • 540234e9fb Fix indexing bug for design_insertions on multiple chains Tim O'Donnell 2025-11-20 10:49:37 -05:00
  • ac86c10b47 fix:Fix python version usage in Dockerfile. FloWuenne 2025-11-20 02:58:50 +00:00
  • 8deda18e6f Remove duplicate main.py script Tim O'Donnell 2025-11-18 13:40:35 -05:00
  • d577fb2e1d Remove duplicate copy of configs Tim O'Donnell 2025-11-18 11:50:19 -05:00
  • be03083cf9 Add release instructions, fix pypi project description images, bump version Tim O'Donnell 2025-11-18 11:31:36 -05:00
  • f5275240f1 Version bump; add boltzgen -v to get package version v0.1.4 Tim O'Donnell 2025-11-18 10:46:43 -05:00
  • 159717c2f8 Create python-publish.yml Tim O'Donnell 2025-11-17 17:07:55 -05:00
  • f57e30be8e add cistation Hannes Stark 2025-11-17 08:03:45 -05:00
  • 497d9ece63 fix iiptm Hannes Stark 2025-11-17 07:29:08 -05:00