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• fcd37487fc Add traning (#694) Jasper Butcher 2025-11-26 00:57:45 -08:00
• 7c1a77ff0c Add enzyme example, refactor io (#688) Jasper Butcher 2025-11-25 16:45:25 -08:00
• e419028257 Update example jbutch 2025-11-23 22:54:06 -08:00
• 1251f0fcf1 Add non-hydra interface for instantiating model jbutch 2025-11-23 22:38:39 -08:00
• 22407d510c Update regression tests and defaults jbutch 2025-11-23 20:21:01 -08:00
• 12115d052b Update RFD3 regression tests jbutch 2025-11-23 19:31:45 -08:00
• e520df0a97 Update to aa_design/main latest (post loop fix) jbutch 2025-11-23 19:30:17 -08:00
• 3dba499b6d refactor source files for open sourcing (#648) Jasper Butcher 2025-11-20 16:29:47 -08:00
• aa4cb6875f fix: paths and ipd readme (#656) Nathaniel Corley 2025-11-13 17:46:04 -08:00
• 5e7b739ed3 Add initial RFD3 Files and passing tests Jasper Butcher 2025-11-11 10:07:43 -08:00
• 36f668b5ae fix: clean up logging (#587) Rafael Brent 2025-11-10 14:23:07 -08:00
• 2ee287a1d5 feat: script to predict and score (#635) Nathaniel Corley 2025-11-10 09:03:30 -08:00
• 75eb1c5b14 feat: enable jupyter notebooks (#623) Nathaniel Corley 2025-11-10 09:01:44 -08:00
• ae2bb80d02 Fix/apptainer (#629) Nathaniel Corley 2025-11-07 16:08:06 -08:00
• 8cbf11ea23 feat: predict and score (#599) Nathaniel Corley 2025-10-29 12:25:28 -07:00
• 74e879a373 refactor: move datasets to common ncorley 2025-10-27 17:40:12 -07:00
• 4325878f17 feat: Conditional application of Metrics (#585) Rafael Brent 2025-10-25 21:29:50 -07:00
• d0ea2bad5d hotfix: input parsing ncorley 2025-10-24 20:32:12 -07:00
• 44cd199837 fix: datasets (#583) Nathaniel Corley 2025-10-24 16:35:05 -07:00
• de64112d89 Feat: cyclic inference (#552) Tuscan R Thompson 2025-10-24 16:27:42 -07:00
• d10cc62c69 test: additional regression tests (#581) Nathaniel Corley 2025-10-24 14:57:12 -07:00
• 6a5c1964b0 refactor: move datasets (#579) Nathaniel Corley 2025-10-23 15:55:48 -07:00
• 8f0ac4a263 feat: Multiple GPU inference and LOCAL_MSA_DIRS env variable usage (#563) maxkazman 2025-10-20 15:06:53 -07:00
• 31deb1ab3c Wip/attention improvements (#554) Nathaniel Corley 2025-10-09 22:53:53 -07:00
• d048cc887e fix: apptainers ncorley 2025-10-08 15:45:09 -07:00
• 2abd193d47 fix: apptainers, submodule bump for atomworks ncorley 2025-10-08 13:57:07 -07:00
• f2a9d502b5 fix: MSAs for inference ncorley 2025-10-07 22:57:35 -07:00
• 30da9e6e6b fix: add symlinked apptainer ncorley 2025-10-07 17:02:31 -07:00
• 628c2bda5f update: ckpt path ncorley 2025-10-07 16:36:10 -07:00
• 423ff10a89 fix: element type bug, utils, conformers ncorley 2025-10-07 16:22:28 -07:00
• bcd3c527cd fix: updates to support latest Run10 RF3 ncorley 2025-10-07 13:49:42 -07:00
• 606420436d feat: updates from proteina pipeline, squashfs manager ncorley 2025-10-03 17:22:14 -07:00
• 3e80413b0b fix: updates to fix RF3 ncorley 2025-10-03 16:01:48 -07:00
• 77c995cc11 add laproteina training and inference with new rf3 structure Kieran Didi 2025-10-02 01:26:09 +00:00
• 7a66a96a29 fix: README, environment, conftest ncorley 2025-10-02 17:38:03 -07:00
• 6891de148b chore: apptainers, ipd, rf3 runnable ncorley 2025-10-02 13:31:34 -07:00
• 592de5b488 fix: working rf3 ncorley 2025-10-01 23:52:01 -07:00
• cbbe4c6a6d wip: save before letting Claude rip ncorley 2025-10-01 12:01:05 -07:00
• ac17c5f3c8 refactor: rf3 lab ncorley 2025-09-29 16:44:02 -07:00
• b5c9685c73 Merge pull request #12 from RosettaCommons/fix/inference rc/production-legacy-safe Nathaniel Corley 2025-09-19 16:19:47 -07:00
• b124517882 fix: iptm Nathaniel Corley 2025-09-19 16:18:22 -07:00
• 7f9f5244bd Fix iptm bug, add min ipae and ipde calc and ruff formatting Kieran Didi 2025-09-18 18:43:18 -07:00
• f7289e9e5f feat: inference examples Nathaniel Corley 2025-09-17 21:42:47 -07:00
• 2e218aafc2 feat: update ligand templating, bump atomworks version ncorley 2025-09-17 21:41:57 -07:00
• b3e9466b52 chore: reomve submodules ncorley 2025-09-17 04:03:01 -07:00
• f201cfa1cc fix: inference for RF3 ncorley 2025-09-17 04:01:18 -07:00
• c0f29a80e8 clean: improve CLI error handling, auto-detect inputs= when 1+ arguments given refactor/update-atomworks-paths Simon Mathis 2025-09-09 16:28:06 -07:00
• 3a1c348875 fix: update atomworks paths to latest version Simon Mathis 2025-09-09 22:54:51 +01:00
• 5c8ba5f2a1 docs: README warning update Nathaniel Corley 2025-09-03 15:12:03 +03:00
• a6060d7a45 fix: JSON inputs and arbitrary atomic-level templating support Nathaniel Corley 2025-08-29 17:02:20 +03:00
• ce9769be79 chore: clean up inference engine Nathaniel 2025-08-29 16:59:59 +03:00
• 662605a56e chore: format Nathaniel 2025-08-29 16:58:53 +03:00
• 586ae4b28d fix: add back template selection Nathaniel 2025-08-29 16:58:38 +03:00
• c7b3a5e073 chore: commit empty .env Nathaniel 2025-08-29 16:54:30 +03:00
• d89099b752 chore: documentations, cpu compatability, JSON inputs ncorley 2025-08-29 06:51:54 -07:00
• e7430b11c5 fix(readme): formatting Nathaniel Corley 2025-08-19 21:45:41 +02:00
• 0b914395f5 docs: update README disclaimer Nathaniel Corley 2025-08-19 21:45:23 +02:00
• 849281ef99 chore: remove submodules in favor of pip package Kieran Didi 2025-08-15 11:30:19 -07:00
• 9d47095f72 chore: updated readme Kieran Didi 2025-08-15 09:30:52 -07:00
• 1ba98a9a52 fix: PDB_MIRROR variable error catching Nathaniel Corley 2025-08-15 18:26:20 +02:00
• e40c5c2168 fix: cli and inference config Kieran Didi 2025-08-15 09:17:17 -07:00
• 05ecfbf046 docs: graphics Nathaniel Corley 2025-08-15 17:27:53 +02:00
• 2f0449d016 docs: readme update and cleanup (#477) Nathaniel Corley 2025-08-15 16:37:25 +02:00
• 0e415316b7 reinit README Rohith Krishna 2025-08-15 02:07:08 -07:00
• a0ebd6b51a format Rohith Krishna 2025-08-15 02:02:36 -07:00
• 7707677613 enable rf3 fold syntax Rohith Krishna 2025-08-15 01:59:08 -07:00
• a36db88321 default to rf3 Rohith Krishna 2025-08-15 01:27:13 -07:00
• 40d55d95c9 point checkpoint to rf_latest.pt Rohith Krishna 2025-08-14 23:57:10 -07:00
• 64c4270aa0 rename to rf3 Rohith Krishna 2025-08-14 23:17:50 -07:00
• b0e917afb4 rename inference engine to rf3 Rohith Krishna 2025-08-14 22:57:20 -07:00
• 73790f3b37 enable running the code without a PDB_MIRROR Rohith Krishna 2025-08-14 22:50:53 -07:00
• f48eb39574 enable inference to run from pip installing Rohith Krishna 2025-08-14 22:15:30 -07:00
• 5363649731 update pyproject toml Rohith Krishna 2025-08-14 18:44:15 -07:00
• 43ae6ea526 clean Simon Mathis 2025-08-15 00:29:29 +01:00
• 09dec44401 fix: dependencies Simon Mathis 2025-08-14 15:09:03 -07:00
• 9ec23cd32e clean Simon Mathis 2025-08-14 14:43:47 -07:00
• 9338d8bdc4 clean Simon Mathis 2025-08-14 14:42:13 -07:00
• cd36068cd7 clean: make pip installable, remove unused files, ruff, add license Simon Mathis 2025-08-14 14:34:42 -07:00
• da0a3b45e7 chore: ruff & remove outdated files Simon Mathis 2025-08-14 13:53:20 -07:00
• c7e588518b clean: swap cifutils/datahub backend for atomworks Simon Mathis 2025-08-14 13:44:38 -07:00
• 77eef3d818 fix some import errors Rohith Krishna 2025-08-13 22:55:13 -07:00
• 1622312e9c replace every instance of cifutils and datahub Rohith Krishna 2025-08-13 21:38:20 -07:00
• 0ba86f4826 fix: add missing index Simon Mathis 2025-08-14 13:07:19 -07:00
• 0db0856858 build: update toml Simon Mathis 2025-08-13 01:31:08 +01:00
• 739f09c820 clean: remove chemdata reliance Simon Mathis 2025-08-13 01:30:57 +01:00
• f793be8c94 clean: remove unused auxiliary predictors Simon Mathis 2025-08-13 00:54:16 +01:00
• 598b6019f7 clean: remove unused loss functions Simon Mathis 2025-08-13 00:52:00 +01:00
• 7cb2ed3e54 clean: remove legacy symmetry resolution Simon Mathis 2025-08-13 00:45:54 +01:00
• 8dc8a91761 chore: ruff Simon Mathis 2025-08-13 00:34:16 +01:00
• 4b474b5458 clean: clean further unused modules Simon Mathis 2025-08-13 00:33:25 +01:00
• 2893a73ebb clean: remove unused embedding blocks Simon Mathis 2025-08-13 00:25:29 +01:00
• 277966e017 clean: remove remaining util reference Simon Mathis 2025-08-13 00:23:04 +01:00
• 0b5f045b23 cleanup: util Simon Mathis 2025-08-13 00:17:43 +01:00
• 0d1e9d65b5 clean: clean up unused functions in util_module Simon Mathis 2025-08-12 23:59:58 +01:00
• 521fb53103 chore: ruff Simon Mathis 2025-08-12 23:33:44 +01:00
• d6225dfcce tmp: activate CI Simon Mathis 2025-08-12 23:31:01 +01:00
• edbf6b5a34 wip: step 1 Simon Mathis 2025-08-12 23:28:00 +01:00
• 1a9b71da2d tests: regression test ncorley 2025-08-11 16:06:08 -07:00
• 7d32dcecf3 wip: stage 2, al working ncorley 2025-08-10 15:20:32 -07:00
• 07aa1765d6 wip: intermediary save; all working ncorley 2025-08-10 14:24:34 -07:00