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  • a321fa8801 deploy: 39671441e6 gh-pages woodsh17 2026-06-03 21:14:08 +00:00
  • 39671441e6 refactor(mypy): clear 8 easy rfd3 modules off the ignore ratchet (#298) production lyskov-ai 2026-06-03 15:13:41 -06:00
  • 3ae4ee81e6 chore(mypy): bring models/rfd3 into scope behind an ignore_errors ratchet (#297) lyskov-ai 2026-06-03 14:48:39 -06:00
  • 3fdf9f4c78 refactor(mypy): un-ignore trainers/fabric (ratchet complete) (#296) lyskov-ai 2026-06-03 14:13:37 -06:00
  • 5200cfb363 refactor(mypy): un-ignore callbacks/health_logging (#295) lyskov-ai 2026-06-03 13:54:33 -06:00
  • 7d70c32abb refactor(mypy): un-ignore utils/{ddp,rigid,datasets} (#294) lyskov-ai 2026-06-03 13:12:46 -06:00
  • b8a81f88da Update binder_design_tutorial.md docs_rfd3_binder_tutorial Rachel Clune 2026-06-03 11:03:56 -07:00
  • 9fbeffc590 Minor binder design tutorial edits Rachel Clune 2026-06-03 10:00:59 -07:00
  • 497307e81f refactor(mypy): un-ignore metrics/metric module (#288) lyskov-ai 2026-06-03 11:00:47 -06:00
  • 1def4e2ee2 refactor(mypy): un-ignore 7 medium-tier modules (#287) lyskov-ai 2026-06-03 10:49:53 -06:00
  • bb8c084c03 Added small molecule example Rachel Clune 2026-06-02 16:05:02 -07:00
  • d8b0be6015 fix: make weighted_rigid_align dtype-agnostic (accept float64) (#286) lyskov-ai 2026-06-02 15:45:33 -06:00
  • 2d66d998ce test: unit tests for foundry geometry utils (alignment, rotation augmentation) (#285) lyskov-ai 2026-06-02 14:26:39 -06:00
  • b69bed5e4c test: bootstrap mypy + pytest + coverage CI gates (#284) lyskov-ai 2026-06-02 12:51:28 -06:00
  • 4bdc24c7aa First draft of binder design tutorial Rachel Clune 2026-05-30 10:40:50 -07:00
  • cd4d94fb0c Issue with ORI token in partial diffusion (#275) Jonathan Funk 2026-05-25 05:19:43 +02:00
  • 07e9ace471 Fix: stop dropping nucleic acid residues in partial diffusion (#281) Raktim Mitra 2026-05-23 05:25:13 -07:00
  • cee116dc55 fix: infer ori edge case (#273) Rafael Brent 2026-04-23 13:31:16 -07:00
  • 2e3f2edde2 rfd3na (#269) Raktim Mitra 2026-04-16 09:52:02 -07:00
  • b071919caa Docs rfd3 instsallation tutorial (#262) Rachel Clune 2026-04-08 08:26:11 -07:00
  • 4e3feffc12 Docs add analytics (#264) Rachel Clune 2026-04-07 10:15:21 -07:00
  • 8c739d3221 docs: streamline tutorial — remove Section 4, consolidate Section 6 docs/rf3-antibody-tutorial-public Nathaniel Corley 2026-04-07 06:02:43 +00:00
  • 41c07d164d docs: replace cross-approach comparison with templating confidence note Nathaniel Corley 2026-04-07 05:49:09 +00:00
  • 9a454738d6 docs: add RF3 Overview and Tutorial Overview headers to intro Nathaniel Corley 2026-04-07 05:47:41 +00:00
  • 632c68732d docs: re-execute notebook (57/57 cells, 0 errors, 0 warnings) Nathaniel Corley 2026-04-07 05:41:13 +00:00
  • e318045a47 docs: streamline Section 5, remove contact analysis, add FoldBench Nathaniel Corley 2026-04-07 05:37:02 +00:00
  • 398cf8e4ee fix: suppress all warnings in notebook outputs Nathaniel Corley 2026-04-07 05:21:26 +00:00
  • 77a2027f56 docs: add RF3 antibody/antigen structure prediction tutorial Nathaniel Corley 2026-04-07 04:48:04 +00:00
  • 60ef1d9bcb Put MSA example into external docs docs-rac-rf3-updates Rachel Clune 2026-04-06 09:46:26 -07:00
  • 7dd7b31a0a Improve PTM bond handling in RFdiffusion3 (#256) Jasper Butcher 2026-04-04 22:11:59 -07:00
  • b5395e43a8 Fix ligand res_id offset to match AF3 convention (#261) Jasper Butcher 2026-04-04 21:49:41 -07:00
  • dacd4894ec Docs: Creating a contribution guide for Foundry (#215) Rachel Clune 2026-04-04 18:43:12 -07:00
  • 54a8d721c1 Expose n_recycle as inference sampler parameter (#259) Jasper Butcher 2026-04-04 16:37:44 -07:00
  • 9fa9ba2f27 Add MPS (Apple Silicon) support for RFD3, RF3, and ProteinMPNN (#260) Jasper Butcher 2026-04-04 16:36:44 -07:00
  • 2b938016f4 Optimize attention computation with local window bias (#254) kaistroh 2026-04-05 00:04:27 +02:00
  • 6462d22ecf main readme updates foundry-atom23 Raktim Mitra 2026-03-28 12:04:48 -07:00
  • 24e92c0b43 cleanup Raktim Mitra 2026-03-28 11:57:37 -07:00
  • b04cc1d727 more extensive documentation Raktim Mitra 2026-03-28 11:51:34 -07:00
  • da7b89cc14 docs and json progress Raktim Mitra 2026-03-27 12:27:56 -07:00
  • 28d1375f96 cleanup debug comment Raktim Mitra 2026-03-27 11:32:08 -07:00
  • 3da4cdfe19 ruff_format_2 Raktim Mitra 2026-03-27 11:25:56 -07:00
  • b9e050c35b ruff format Raktim Mitra 2026-03-27 11:22:23 -07:00
  • c5a9fbefde Fix broken PPI tutorial link in RFdiffusion3 README (#252) Jane 2026-03-26 12:08:05 -05:00
  • 257d20ca88 Docs: Intermediate enzyme design tutorial (#250) Rachel Clune 2026-03-24 13:37:21 -07:00
  • fdf3f98a9f cleanup configs Raktim Mitra 2026-03-23 13:33:50 -07:00
  • 67921fa6c7 leftover rebase bugs cleanup, atom14 inference demo working Raktim Mitra 2026-03-20 16:48:45 -07:00
  • f10771f98d debug cleanup Raktim Mitra 2026-03-20 16:11:19 -07:00
  • e94ea147a6 remove extra rfd3na configs Raktim Mitra 2026-03-20 16:07:07 -07:00
  • 001709433c remove rf3 config which tagegd along Raktim Mitra 2026-03-20 16:04:16 -07:00
  • fe817ccc7a unindex train fix Raktim Mitra 2026-03-20 11:15:25 -07:00
  • 5a73df5c2f unindex fix final for real Raktim Mitra 2026-03-19 12:56:45 -07:00
  • 42680bdf1e cfg for bp_partners feature Raktim Mitra 2026-02-27 15:17:09 -08:00
  • bfe513ab17 refactor ss metric computatino section to be called during inference to write in the json Raktim Mitra 2026-02-26 12:25:41 -08:00
  • 60b18c281b mc: yaml changes Raktim Mitra 2026-02-26 10:41:52 -08:00
  • ad3d95f351 extra filter for huge base pair centroid distances, and also cleaned inference specification code afavor 2026-02-25 21:03:30 -08:00
  • d04989f65f add failsafe for nucleic ss metric Raktim Mitra 2026-02-19 01:59:11 -08:00
  • 212082581b time to fix ss metric line 242 Raktim Mitra 2026-02-18 17:47:44 -08:00
  • 84648be95a fix: permute U in association_schemes_stripped Raktim Mitra 2026-02-19 00:05:08 -08:00
  • 3d016cd389 fix atom14 scheme cases Raktim Mitra 2026-02-18 22:51:57 -08:00
  • 3578002956 fixed na ss metric calculation afavor 2026-02-18 21:53:29 -08:00
  • c8d1e6be10 time to fix ss metric line 242 Raktim Mitra 2026-02-18 17:47:44 -08:00
  • bcaa6b79a8 run time fixes; inference fix for readout seq from struct Raktim Mitra 2026-02-18 12:59:23 -08:00
  • de06df8cbf cleanup; aptamer metric; monomer dist on; send trainininggit status Raktim Mitra 2026-02-17 12:26:13 -08:00
  • 91a0eb22ec skip ss computation when not ss example Raktim Mitra 2026-02-17 11:06:26 -08:00
  • 3dfa04ac20 prevalidate on Raktim Mitra 2026-02-16 19:19:29 -08:00
  • 1f0d9115f6 val metric logging fix Raktim Mitra 2026-02-16 18:53:46 -08:00
  • fc8514bb04 fixed behavior for conditional sampling of NA SS condition afavor 2026-02-16 18:15:42 -08:00
  • d8b8d0c047 cleaned up NA-SS conditioning code before rebase afavor 2026-02-16 13:34:07 -08:00
  • 4478253fa9 dll bug fix Raktim Mitra 2026-02-16 12:48:48 -08:00
  • 22d24edc5b make 2oken_2d_features/embedder optional Raktim Mitra 2026-02-16 12:13:11 -08:00
  • d7fe89b8f5 ligand chain fix; add ori_jitter option in new dialect Raktim Mitra 2026-02-10 18:25:01 -08:00
  • cff03801ed inference fixes Raktim Mitra 2026-02-09 11:37:38 -08:00
  • 335e580390 fix: tiny legacy parsing bug Raktim Mitra 2026-02-06 11:45:31 -08:00
  • 45e8f837ce mor einference fixes Raktim Mitra 2026-02-05 12:40:50 -08:00
  • 4caba95d32 fix: atom23 constants import error Raktim Mitra 2026-02-03 15:45:00 -08:00
  • 129efbf590 feat: atom23 porting Raktim Mitra 2026-01-18 15:41:00 -08:00
  • b5beff039e inference fixes for legacy_input_parsing Raktim Mitra 2026-02-03 12:54:16 -08:00
  • f0ab0fedae train and inference atom23 with custom datasets and na ss transform Raktim Mitra 2026-01-31 16:14:06 -08:00
  • 716c16a7ec Add nucleic SS metrics + conditioning + pseudoknot dataset config afavor 2026-01-30 13:32:46 -08:00
  • 3952c976a3 add .env, can remove paths later Raktim Mitra 2026-01-20 14:50:40 -08:00
  • c2ec302745 feat: atom23 inference changes and training fixes Raktim Mitra 2026-01-20 14:44:19 -08:00
  • 94d9d635cd feat: atom23 porting Raktim Mitra 2026-01-18 15:41:00 -08:00
  • ebec466e4f feat: atom23 inference changes and training fixes Raktim Mitra 2026-01-20 14:44:19 -08:00
  • 4a7aaf8793 feat: atom23 porting Raktim Mitra 2026-01-18 15:41:00 -08:00
  • ece2498c5d Bugfixes for confidence training fdimaio 2026-01-05 17:56:52 -08:00
  • 688d049775 Install bug Jasper Butcher 2026-01-11 00:04:32 +00:00
  • a94de86df9 Revert "Adding Google Analytics to the Foundry documentation" (#244) Rachel Clune 2026-03-19 09:02:39 -07:00
  • d746dc56a3 Adding Google Analytics to the Foundry documentation (#243) Rachel Clune 2026-03-18 19:07:18 -07:00
  • 6ab4add581 Fixed broken links in tutorials (#242) Rachel Clune 2026-03-12 19:50:52 -07:00
  • 146c2be7ac Creation of a NA binder tutorial (#232) Rachel Clune 2026-03-12 19:36:36 -07:00
  • 711d950d3d Started recreating relevant examples from RFD1 docs_recreate_rfd1_examples Rachel Clune 2026-03-12 16:18:02 -07:00
  • 4686f7300c fix: reference conformers (#235) Nathaniel Corley 2026-03-06 12:56:10 -08:00
  • c88dc56588 fix: turn off checkpointing in inference. fix/mpnn-fasta-output Andrew Kubaney 2026-03-04 14:14:43 -08:00
  • 75986084a6 fix: restore python version constraint (==3.12) (#227) David Hyunyoo Jang 2026-03-04 00:49:50 +09:00
  • 38d0989cb7 Docs: RF3 README update and moving RF3 examples (#216) Rachel Clune 2026-02-27 15:35:02 -08:00
  • 2f905c59b4 Delete models/rfd3/docs/enzyme_tutorial_files directory Rachel Clune 2026-02-25 21:29:58 -08:00
  • 290b2fd0bb fix: weight initialization bug in chunked P_LL (#229) Aiko 2026-02-25 16:29:51 -08:00
  • 99a0cb773a Enzyme Design Tutorial (#210) Rachel Clune 2026-02-25 16:13:05 -08:00
  • 9f609e8758 Docs: update repository URL in README (#226) David Hyunyoo Jang 2026-02-26 07:39:22 +09:00
  • 3b262b742b Update na_binder_design.md (#230) Raktim Mitra 2026-02-25 14:34:33 -08:00