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  • bb97ddfb94 Update author email for Sergey Lyskov (#228) Sergey Lyskov 2026-02-25 15:33:29 -07:00
  • 58479cd2c6 Updated the landing page for the RF3 documentation so that it links out to the README Rachel Clune 2026-02-25 09:45:57 -08:00
  • 4a70f0ef93 Docs: Designability vs. Diversity (#220) Rachel Clune 2026-02-24 10:50:29 -08:00
  • 1008159b72 fix: symmetry masking fix for parity with original. Andrew Kubaney 2026-02-22 00:32:39 -08:00
  • 7223df1f44 fix: disclude nan coords when writing mpnn cif. Andrew Kubaney 2026-02-22 00:12:47 -08:00
  • a4bacfbf68 chore: additional cli true/false option. Andrew Kubaney 2026-02-21 23:55:10 -08:00
  • b81ccd40d8 Create Issue Templates (#197) Rachel Clune 2026-02-21 22:42:28 -08:00
  • f4f3597aa8 Upload Dockerfile to examples (#222) Hope Woods 2026-02-22 00:40:06 -06:00
  • 3294b06cc6 Update na_binder_design.json (#223) Raktim Mitra 2026-02-19 09:14:49 -08:00
  • ea05d5939b Fix ligand annotatitions (#219) Jasper Butcher 2026-02-17 14:06:42 -08:00
  • 4f26b2d46a fix: switch to tmpdir otherwise hb2 won't be found (#218) Raktim Mitra 2026-02-17 14:03:21 -08:00
  • bdc0b366f7 Changed paths in example JSON files to point to new RF3 examples location Rachel Clune 2026-02-17 08:06:53 -08:00
  • 303b3573ce RF3 README update and moving RF3 examples Rachel Clune 2026-02-16 18:31:27 -08:00
  • b100462717 Fix chain break representation in input.md Rachel Clune 2026-02-12 09:45:38 -08:00
  • a814636801 Fix Slack invitation link Rohith Krishna 2026-02-06 10:49:56 -08:00
  • 976018840d remove reliance of rooutils for pip installed case (#200) Rohith Krishna 2026-02-04 19:04:54 -08:00
  • 38a83a97b1 Docs: PPI tutorial updates, RF3 and MPNN docs placeholders, minor edits (#195) v0.1.10 Rachel Clune 2026-02-02 15:33:04 -08:00
  • f682e8c801 fix: correct typo (#194) Rafael Brent 2026-02-02 11:11:58 -08:00
  • 857b6fbb51 docs: clarify is_non_loopy defaults (#193) Rafael Brent 2026-02-02 10:55:23 -08:00
  • c35837e279 fix: revert symmetry related code to the point that was stable (#179) Aiko 2026-01-22 23:50:54 -08:00
  • 06b19bdce7 Fix hbond calculation to remove produced file (#178) Jasper Butcher 2026-01-22 18:37:46 -08:00
  • a79cb953e2 Update inference command path in README.md (#169) Rohith Krishna 2026-01-16 14:51:57 -08:00
  • efa7aae8c2 remove .DS_Store files (#167) Simon Mathis 2026-01-15 22:10:44 +00:00
  • d35d8ac3c1 Make format jbutch 2026-01-14 16:59:41 -08:00
  • e94fdf63e7 Add search path for rfd3 configurations (#147) Jasper Butcher 2026-01-14 16:59:18 -08:00
  • 88d212c08d docs: update ppi docs (#159) Rafael Brent 2026-01-08 13:38:25 -08:00
  • 94eb95a004 Parallelize rc-foundry install and checkpoint downloads for colab notebook (#157) Magnus Bauer 2026-01-07 16:31:06 -08:00
  • 8bfde2381a feat: Add Intel XPU support for Foundry Models (#156) Daan Krol 2026-01-08 01:30:04 +01:00
  • d0379cea93 Fix stray rfd3 import from src (#150) Jasper Butcher 2026-01-03 22:31:45 +00:00
  • bcfa500c75 Add step to disable Jekyll in documentation build Rachel Clune 2026-01-02 11:34:48 -08:00
  • f9066e29b1 Change deployment branch from main to production Rachel Clune 2026-01-02 11:26:37 -08:00
  • 73865046c5 Creating the external foundry documentation structure and first round of documentation for RFD3 (#143) Rachel Clune 2026-01-02 11:21:10 -08:00
  • 2bfcd663bc Fix skip existing not working (#140) Jasper Butcher 2025-12-27 19:57:29 +00:00
  • 122f39b7e8 Bugfix to Partial diffusion where partial_t doesn't affect output (#138) Jasper Butcher 2025-12-27 12:27:19 +00:00
  • c260885159 fix: mpnn fasta output refactor/improvements. Andrew Kubaney 2025-12-23 21:30:38 -08:00
  • 48c8966345 Improve 'unindex' field description in input_parsing.py (#129) Jasper Butcher 2025-12-23 10:19:48 +01:00
  • ffa9411a56 Fix symmetry issues (#126) Jasper Butcher 2025-12-22 15:59:36 +01:00
  • a36d29c5c0 Pr/lorenzo tarricone/98 (#125) v0.1.9 Rohith Krishna 2025-12-20 11:42:25 -08:00
  • 1184ddb7fc Merge pull request #124 from RosettaCommons/fix/config_path Rohith Krishna 2025-12-20 11:01:37 -08:00
  • e0d149f6e8 chore: ruff Rohith Krishna 2025-12-20 10:56:29 -08:00
  • 58e03a1035 fix to cli to enable running from pip installed package, cleanuo Rohith Krishna 2025-12-19 23:50:38 -08:00
  • 9a3e717978 fix: use relative paths for rf3 config path Rohith Krishna 2025-12-19 20:10:37 -08:00
  • cc327b4ad0 Merge pull request #118 from RosettaCommons/fix/inputspecification Jasper Butcher 2025-12-19 09:26:29 +01:00
  • e50a652252 Update models/rfd3/src/rfd3/inference/input_parsing.py Jasper Butcher 2025-12-19 09:25:57 +01:00
  • 123ff20eae Make format jbutch 2025-12-19 00:24:44 -08:00
  • d5617048e2 Update models/rfd3/src/rfd3/engine.py Jasper Butcher 2025-12-19 09:22:10 +01:00
  • 4e32d39e7c Update models/rfd3/src/rfd3/inference/input_parsing.py Jasper Butcher 2025-12-19 09:21:30 +01:00
  • 1f30d87dd3 Update models/rfd3/src/rfd3/inference/input_parsing.py Jasper Butcher 2025-12-19 09:21:17 +01:00
  • e34d31c491 Make format Ubiquinone-dot 2025-12-18 16:21:28 +01:00
  • 4637117e1d Fix circlar imports Ubiquinone-dot 2025-12-18 16:20:43 +01:00
  • e89bf0c732 Make format Ubiquinone-dot 2025-12-18 16:11:29 +01:00
  • ed4c8208c4 Delete benchmarks symlink Ubiquinone-dot 2025-12-18 16:08:53 +01:00
  • eebbf34968 Handle input specification in multiply specifications Ubiquinone-dot 2025-12-18 16:06:57 +01:00
  • d7107b7289 Merge pull request #119 from RosettaCommons/copilot/sub-pr-118 Jasper Butcher 2025-12-18 16:00:35 +01:00
  • 2d13bf3feb Update models/rfd3/src/rfd3/utils/inference.py Jasper Butcher 2025-12-18 15:46:51 +01:00
  • 31183dbac8 Fix logic error in path validation copilot-swe-agent[bot] 2025-12-18 14:09:58 +00:00
  • 5016e7d015 Add missing DesignInputSpecification import copilot-swe-agent[bot] 2025-12-18 14:08:36 +00:00
  • daea7fcf6f Initial plan copilot-swe-agent[bot] 2025-12-18 14:04:43 +00:00
  • 89f39a0be9 Fix symmetry & abspath issues Ubiquinone-dot 2025-12-18 10:22:52 +01:00
  • 6866d610a9 Added line to all.ipynb to fix KeyError: 'extra' issue Rachel Clune 2025-12-17 08:34:30 -08:00
  • ec4065f2e7 Merge pull request #111 from RosettaCommons/fix/chunkedPLL Jasper Butcher 2025-12-17 11:49:16 +01:00
  • cea652a73b chore: format Aiko Muraishi 2025-12-16 13:22:11 -08:00
  • 49187c311f fix: the cause of the slow inference using low_memory_mode Aiko Muraishi 2025-12-16 13:04:59 -08:00
  • 25e48fe8d8 Add Slack link Jasper Butcher 2025-12-13 07:59:02 +00:00
  • fbd07421ec Merge pull request #99 from RosettaCommons/fix/rfd3_sym_readme Rohith Krishna 2025-12-12 11:29:12 -08:00
  • 5f0681976c fix: is_non_loopy=true only for unconditional Aiko Muraishi 2025-12-11 17:32:59 -08:00
  • a1f00e6db9 fix: include is_non_loopy=true to the example Aiko Muraishi 2025-12-11 16:59:20 -08:00
  • 27bf3f3e29 Merge pull request #93 from RosettaCommons/fix/ppi-docs Rohith Krishna 2025-12-10 20:54:56 -08:00
  • 50b9c4be46 Merge pull request #95 from RosettaCommons/fix/rfd3_sym Rohith Krishna 2025-12-10 20:54:11 -08:00
  • 092f2f5555 Merge pull request #96 from timkartar/patch-2 Rohith Krishna 2025-12-10 20:53:34 -08:00
  • 0f32b77908 Update na_binder_design.json Raktim Mitra 2025-12-10 18:49:26 -08:00
  • 7e9022deac Update na_binder_design.md Raktim Mitra 2025-12-10 18:47:20 -08:00
  • cc4c89dd21 chore: format Aiko Muraishi 2025-12-10 18:45:04 -08:00
  • 02a2d6be42 Update demo.json Raktim Mitra 2025-12-10 18:42:55 -08:00
  • bbe16117ea fix: bugs in assertion Aiko Muraishi 2025-12-10 18:38:32 -08:00
  • 845b99d8fa docs: update the ppi docs to reflect best practices Rafi Brent 2025-12-10 00:28:17 -08:00
  • 676b4a95f3 Fix formatting of pip install command in README Rachel Clune 2025-12-09 17:36:21 -06:00
  • 8da6dc7e9d Merge pull request #66 from LorenzoTarricone/patch-1 v0.1.8 Rohith Krishna 2025-12-08 10:26:47 -08:00
  • 2568e98761 Merge pull request #72 from RosettaCommons/Ubiquinone-dot-patch-1 Jasper Butcher 2025-12-07 21:21:02 -08:00
  • 667800f392 Fix string quotes in engine.py Jasper Butcher 2025-12-07 21:19:50 -08:00
  • f135630997 Add 'extra' key to example specifications Jasper Butcher 2025-12-07 20:57:42 -08:00
  • 7f8f9f0ead Import apply_symmetry_to_xyz_atomwise function Lorenzo Tarricone 2025-12-06 16:26:41 +00:00
  • 8aeacba747 Fix: Exact python versioning jbutch 2025-12-05 14:56:17 -08:00
  • 73d43c50e1 Fix import error for cfg jbutch 2025-12-05 14:51:37 -08:00
  • 0fb924882a Update pyproject.toml v0.1.7 test-build jbutch 2025-12-05 12:05:45 -08:00
  • 946b724abb Merge branch 'feat/multiple-checkpoint-directories' into production jbutch 2025-12-04 21:38:20 -08:00
  • 2895eb0069 Shorten .env jbutch 2025-12-04 21:34:12 -08:00
  • 569b0d5635 Merge pull request #58 from RosettaCommons/feat/multiple-checkpoint-directories Jasper Butcher 2025-12-04 21:34:27 -08:00
  • 0a8348f42a Update src/foundry_cli/download_checkpoints.py Jasper Butcher 2025-12-04 21:31:22 -08:00
  • b66aa4324a Update src/foundry/inference_engines/checkpoint_registry.py Jasper Butcher 2025-12-04 21:26:02 -08:00
  • 5c766cdde8 Add backward compatibility jbutch 2025-12-04 21:23:40 -08:00
  • 0404d6ae9e Rewind .env jbutch 2025-12-04 21:10:03 -08:00
  • 3313cdfa47 Add multiple checkpoint directories optioning and rename env var jbutch 2025-12-04 21:06:10 -08:00
  • 798fd9c405 Merge pull request #56 from RosettaCommons/fix/install-cmds Jasper Butcher 2025-12-04 20:04:45 -08:00
  • 4fcafb3862 Mv .env jbutch 2025-12-04 20:02:12 -08:00
  • 857e3d4fdc Update src/foundry_cli/download_checkpoints.py Jasper Butcher 2025-12-04 20:01:00 -08:00
  • 9d5c4f193d Update .env Jasper Butcher 2025-12-04 19:59:46 -08:00
  • 8988b1ef77 Make format jbutch 2025-12-04 19:56:10 -08:00
  • 273e2dd4fe Update input.md jbutch 2025-12-04 19:50:04 -08:00
  • da6310d78c Minor fixes jbutch 2025-12-04 19:35:31 -08:00