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  • 85c49b60d3 Explicitly specify MAMBA_ROOT_PREFIX in Dockerfile main Jacob Silterra 2025-05-02 09:58:25 -04:00
  • b4704d94de Update README.md Gabriele Corso 2024-09-04 18:44:48 -07:00
  • 9a22cbcbc7 Fix environment.yml v1.1.3 Jacob Silterra 2024-09-03 11:37:06 -04:00
  • 3e80ffd7a0 Merge pull request #241 from bamattsson/fixing_bug_in_atom_preprocessing Jacob Silterra 2024-09-03 15:57:25 -04:00
  • b65b59aa2e Merge pull request #248 from juliocesar-io/main Jacob Silterra 2024-09-03 15:56:10 -04:00
  • 5c2e633d22 Merge pull request #236 from burn-in-soul/feat/inits Jacob Silterra 2024-09-03 15:53:54 -04:00
  • 0c1ab6984a update README with GPU instructions Julio César 2024-08-30 16:54:10 +00:00
  • a95a6b8c6d fix docker build command in README.md Julio César 2024-08-30 14:13:33 +00:00
  • 8c0b943f1b changing zero to nan to allow filtering of nan in new_extract_receptor_structure Bjorn Mattsson 2024-07-15 15:17:36 +01:00
  • 6d065cd78c fix issue with different sequences and order Gabriele Corso 2024-07-08 14:12:59 +02:00
  • be0f0f59cf Add __init__ files to all python modules. There were import failures in some cases, when project not in root directory without own virtual env Alexander Schepetilnikov 2024-06-20 17:15:12 +03:00
  • a487ef897e Pin setuptools version Jacob Silterra 2024-06-07 15:40:21 -04:00
  • 9d0bf3d884 Set any nans/infs in model scores to a small value. Jacob Silterra 2024-06-06 10:25:51 -04:00
  • 5238b18d4a Merge pull request #222 from satishgaurav/patch-1 Jacob Silterra 2024-05-06 14:32:18 -04:00
  • a87faaff2b fix a typo Satish Gaurav 2024-05-05 14:48:59 +05:30
  • 561f70a897 Various bugfixes v1.1.2 Jacob Silterra 2024-04-30 10:00:31 -04:00
  • 2c867df9b8 Improve memory efficiency of graph convolution operation. v1.1.1 Jacob Silterra 2024-04-25 11:13:02 -04:00
  • 3995b24fcd Improved logging Jacob Silterra 2024-04-25 11:06:31 -04:00
  • e259429889 Add example CSV file Jacob Silterra 2024-04-09 11:03:22 -04:00
  • 6f5d4b152b Update README.md Gabriele Corso 2024-03-04 16:20:26 -08:00
  • 0b0f6765f1 Fix conda install instructions in README. Jacob Silterra 2024-03-04 12:42:16 -05:00
  • df3708b822 Break from download loop once the model has been downloaded. Jacob Silterra 2024-03-04 12:41:04 -05:00
  • ff4ad1b5f8 Merge pull request #188 from BioinfoMachineLearning/amorehead-patch-inference-args Gabriele Corso 2024-03-03 21:44:06 -05:00
  • 94a6d29ec9 Update README.md Alex Morehead 2024-03-03 18:41:24 -06:00
  • 3964223733 Rename inference_args.yaml to default_inference_args.yaml Alex Morehead 2024-03-03 18:39:54 -06:00
  • 59b9313ac3 Rename default_inference_args.yaml to inference_args.yaml Alex Morehead 2024-03-03 17:41:55 -06:00
  • d3791a885e Add examples v1.1 Jacob Silterra 2024-02-28 12:52:37 -05:00
  • ecfc98083c Minor bugfix in Dockerfile (old paths) Jacob Silterra 2024-02-28 12:48:31 -05:00
  • 8c36c48ad1 Merge pull request #182 from gcorso/dev_v1.1 Jacob Silterra 2024-02-28 11:44:07 -05:00
  • d9114a44ae Add Dockerfile for creating container. Also add web app code for simple gradio app. Refine requirements.txt/environment.yml. Automatically download models if not present. dev_v1.1 Jacob Silterra 2024-02-28 11:37:18 -05:00
  • 001c4fa46e first commit v1.1 Gabriele Corso 2024-02-28 11:21:46 -05:00
  • bc6b515145 Update README.md v1.0 Gabriele Corso 2023-10-12 14:25:03 -07:00
  • 600a23fa23 Fix ckpt path #85 Gabriele Corso 2023-07-18 01:40:55 -07:00
  • 2782769ccd added code to align apo with holo structures Gabriele Corso 2023-07-03 09:13:10 +02:00
  • 7dc84c9269 Update environment #74 Gabriele Corso 2023-06-16 02:05:26 -07:00
  • 3d45728415 fix inference_utils.py #90 Gabriele Corso 2023-06-08 05:13:04 -07:00
  • 1b9a9cb09b Update inference_utils.py for issue #90 Hannes Stärk 2023-05-12 13:58:25 -04:00
  • 6c3d8ceb6e Update evaluate.py to non-hardcoded split path Hannes Stärk 2023-05-12 13:44:27 -04:00
  • 81ff501e20 Update evaluate_files.py with non-hard coded paths Hannes Stärk 2023-05-12 13:41:34 -04:00
  • c1abe25540 Update README.md Gabriele Corso 2023-04-13 13:16:51 -07:00
  • 3c3c728cf2 Merge pull request #93 from duerrsimon/patch-1 Gabriele Corso 2023-03-27 15:37:02 -04:00
  • 23e1dba5d0 Remove hyperparameter notice Simon Duerr 2023-03-26 22:58:54 +02:00
  • f135e3baa7 Update README.md Gabriele Corso 2023-03-25 12:15:55 -07:00
  • 2c7d438516 Fix path in model parameters #80 Gabriele Corso 2023-03-09 15:12:47 -08:00
  • 73ef67ffcf fix testset csv and removed raise #77 Gabriele Corso 2023-03-04 14:16:35 -05:00
  • 3829a23af8 Update README.md Gabriele Corso 2023-02-20 11:10:19 -08:00
  • dde480d709 small fix Gabriele Corso 2023-02-11 12:39:27 -05:00
  • b7259b9584 add example Gabriele Corso 2023-02-11 12:33:49 -05:00
  • 83993e9ee5 remove odd_parity #76 Gabriele Corso 2023-02-11 12:11:18 -05:00
  • 1f63eb8b37 fix new version Gabriele Corso 2023-02-11 12:07:56 -05:00
  • 510e51690a new version: integrated ESM + ESMFold Gabriele Corso 2023-02-10 19:56:03 -05:00
  • 47bf7e5e08 added no_aminoacid_identities Gabriele Corso 2023-02-05 20:17:35 -05:00
  • fff8f0b5eb Update README.md Hannes Stärk 2023-01-09 16:32:12 -05:00
  • 382b3f0eb3 Add truncation sequence length in esm embedding generation command since the default is only 1022 Hannes Stärk 2023-01-09 09:47:18 -05:00
  • f9f2121d9d fix debug HannesStark 2022-12-16 17:59:15 -05:00
  • 452b7f7713 debug HannesStark 2022-12-16 17:55:38 -05:00
  • 8e853d6b14 Update README.md Hannes Stärk 2022-11-25 16:57:19 -05:00
  • 71c110fd7d Update README.md Hannes Stärk 2022-11-25 16:52:42 -05:00
  • cd98700f42 add additional logging to avoid confusion that repeatedly occurred HannesStark 2022-11-20 13:11:19 -05:00
  • 7d1768a505 raise error if no complexes could be preprocessed instead of saving the empty list to the pickle file since users were getting confused HannesStark 2022-11-20 12:56:24 -05:00
  • 4fb49bbf2b better log messaging HannesStark 2022-11-18 09:30:18 -05:00
  • d615844a55 Update README.md Hannes Stärk 2022-11-18 08:58:36 -05:00
  • 724da9406b logs for cache Gabriele Corso 2022-11-16 14:40:09 -05:00
  • 5393a8cafc fix confidence ckpt and improve memory Gabriele Corso 2022-11-16 14:13:42 -05:00
  • 4c60e5b7ee fix center convolution index #34 Gabriele Corso 2022-11-16 14:00:39 -05:00
  • f8d67b5b2b correct skipping of complexes in inference from files HannesStark 2022-10-26 08:38:32 -04:00
  • b1b9b46541 improve logging HannesStark 2022-10-26 08:35:32 -04:00
  • c32ec5b433 add logging to eval-files.py HannesStark 2022-10-26 08:31:49 -04:00
  • 21fadc2a37 skip molecules if preprocessing ligands does not work out. HannesStark 2022-10-25 17:41:45 -04:00
  • cdb6a0e8cb skip molecules if preprocessing ligands does not work out. HannesStark 2022-10-25 17:40:26 -04:00
  • b60807224f fix user inference mistake that Rachel found HannesStark 2022-10-25 17:14:28 -04:00
  • 4cd8ee1bb9 add more logging HannesStark 2022-10-25 16:58:13 -04:00
  • 63f9c33afa raise instead of return #26 Gabriele Corso 2022-10-23 22:22:10 -04:00
  • a6c527536d remove debugging raise in the inference file HannesStark 2022-10-14 17:30:46 -04:00
  • 5cf22913e1 correct num predictions in the readme Hannes Stärk 2022-10-14 17:04:40 -04:00
  • 2221adbeb3 Fixed the inference script Gabriele Corso 2022-10-13 09:22:36 -07:00
  • be1dcde594 Update README.md Gabriele Corso 2022-10-12 11:04:07 -07:00
  • 6795f8f2e2 Remove unnecessary parameters from readme confidence train Hannes Stärk 2022-10-11 10:01:15 -04:00
  • 7b68ba2483 Update README.md Gabriele Corso 2022-10-10 14:55:39 -07:00
  • d935c51c64 Update README.md Gabriele Corso 2022-10-09 21:05:33 -07:00
  • 1754dfbaf7 fix typo HannesStark 2022-10-09 18:02:29 -04:00
  • c56d0d3632 different paper number reproduction HannesStark 2022-10-09 17:29:55 -04:00
  • 67750afe1b fix typo dev HannesStark 2022-10-09 18:02:29 -04:00
  • 0b0240cd90 different paper number reproduction HannesStark 2022-10-09 17:29:55 -04:00
  • 80c374e99b Merge pull request #16 from yufengwhy/main Bowen Jing 2022-10-09 07:11:35 -04:00
  • 664f0e0d19 fix data protein_ligand_example_csv yufeng.yu 2022-10-08 17:43:38 +08:00
  • f6094e7471 remove unwanted raise #13 Gabriele Corso 2022-10-07 18:33:34 -04:00
  • 0b3a1f8d1a fix lm embedding preparation file if protein was not preprocessed HannesStark 2022-10-07 09:06:37 -04:00
  • 7178a57aa1 Remove separate schedule arguments from readme Hannes Stärk 2022-10-07 08:07:55 -04:00
  • d6a10b5724 Update Zenodo Link to point to the newer dataset version Hannes Stärk 2022-10-07 08:04:19 -04:00
  • addd0e9756 avoid failure in case of unreadable molecules Gabriele Corso 2022-10-06 19:00:20 -04:00
  • 7c1117ec6c Merge pull request #7 from duerrsimon/patch-1 Gabriele Corso 2022-10-06 18:25:55 -04:00
  • 6f19de8af4 Update process_mols.py Simon Duerr 2022-10-06 13:13:37 -07:00
  • 0f9c419107 improve README HannesStark 2022-10-05 16:42:49 -04:00
  • 7efe528abd fix old parameter names in README HannesStark 2022-10-05 16:34:47 -04:00
  • a60b3b7380 Create LICENSE Gabriele Corso 2022-10-04 23:44:32 -07:00
  • 0da902786b Update README.md Gabriele Corso 2022-10-04 23:42:54 -07:00
  • ac5612da4f first commit Gabriele Corso 2022-10-04 20:11:55 -04:00