| { |
| "format": "oscr-script-manifest/1", |
| "repository": "github.com/boun-tabi-lifelu/puffin", |
| "url": "https://github.com/boun-tabi-lifelu/puffin", |
| "host": "github.com", |
| "commit": "1433ef46a78bb110da1370a83b8107c034e65e91", |
| "license": "MIT", |
| "license_confirmed_by": "license file LICENSE", |
| "redistribution": "yes", |
| "files": [ |
| { |
| "path": "LICENSE", |
| "sha256": "b5e18f87829b1147701cf896d31b88423ab205612ab52fc6f89f36df5adcc206", |
| "language": "License", |
| "lines": 21, |
| "truncated": false, |
| "block": 3, |
| "row": 7938 |
| }, |
| { |
| "path": "README.md", |
| "sha256": "85ace71a3659a346ef81db6a8c88650a9bb9f9e171203df122524f04dcd33313", |
| "language": "Text", |
| "lines": 360, |
| "truncated": false, |
| "block": 4, |
| "row": 2626 |
| }, |
| { |
| "path": "configs/__init__.py", |
| "sha256": "40afe33e9461a043b773aa939b3ec32715d0031bc64114839ffc1607af407fa8", |
| "language": "Python", |
| "lines": 1, |
| "truncated": false, |
| "block": 3, |
| "row": 17485 |
| }, |
| { |
| "path": "notebooks/K_value_choice_plots.ipynb", |
| "sha256": "6428c78d4ddb49c8d59be6211581403d34db6a9586f3d0c7967cce16357fe6ec", |
| "language": "Jupyter", |
| "lines": 178, |
| "truncated": false, |
| "block": 3, |
| "row": 7370 |
| }, |
| { |
| "path": "notebooks/case_study_rdr2_analysis.ipynb", |
| "sha256": "27a3bf86d91ee6bd96233d57f129fb6490633f9b6c730d252221d496f51f6be4", |
| "language": "Jupyter", |
| "lines": 294, |
| "truncated": false, |
| "block": 3, |
| "row": 7509 |
| }, |
| { |
| "path": "notebooks/functional_organization.ipynb", |
| "sha256": "e1dd424b8885243f1c163a50cbe1378b170dfbe98ddabd1642bd22f342b21ab2", |
| "language": "Jupyter", |
| "lines": 462, |
| "truncated": false, |
| "block": 3, |
| "row": 7629 |
| }, |
| { |
| "path": "notebooks/publication.ipynb", |
| "sha256": "1c70872d58f9d573fb091846f61db368004194f80438f36781ee0adf45144e0c", |
| "language": "Jupyter", |
| "lines": 4296, |
| "truncated": false, |
| "block": 3, |
| "row": 7892 |
| }, |
| { |
| "path": "notebooks/random_pdb.ipynb", |
| "sha256": "e45df77bd2f58bd2b45e432e4f3b0451557bb2b9f132a298aadd2770171c0b8f", |
| "language": "Jupyter", |
| "lines": 1080, |
| "truncated": false, |
| "block": 3, |
| "row": 7825 |
| }, |
| { |
| "path": "notebooks/sdr_protein_family_analysis.ipynb", |
| "sha256": "c9eba9894d85b3084dfebcc009a95c8e68255fdb8016e3c6d2272c8ce5c9f2a8", |
| "language": "Jupyter", |
| "lines": 469, |
| "truncated": false, |
| "block": 3, |
| "row": 7668 |
| }, |
| { |
| "path": "notebooks/supplementary.ipynb", |
| "sha256": "4218bd07b6a924f18b3e403189a09e3b5f459a55c0a56fcaa684424ffc5cbbba", |
| "language": "Jupyter", |
| "lines": 1622, |
| "truncated": false, |
| "block": 3, |
| "row": 7856 |
| }, |
| { |
| "path": "scripts/aggreate_func_eval.sh", |
| "sha256": "b923846de4b1909ef3e2543ac890ea9a8fcaa847963ee56f94bda3a72496f2ab", |
| "language": "Shell", |
| "lines": 48, |
| "truncated": false, |
| "block": 4, |
| "row": 1832 |
| }, |
| { |
| "path": "scripts/characterize_segments.sh", |
| "sha256": "de874a593094db6c85a781733183efe4c2a7975150bd411a1b980e51263e42f6", |
| "language": "Shell", |
| "lines": 240, |
| "truncated": false, |
| "block": 4, |
| "row": 2211 |
| }, |
| { |
| "path": "scripts/collect_segment_json_metrics.py", |
| "sha256": "26102f48779208a2ec381a608fdff6b128e03fb5c6e242dacafa3fdfb0dc67ab", |
| "language": "Python", |
| "lines": 156, |
| "truncated": false, |
| "block": 3, |
| "row": 23455 |
| }, |
| { |
| "path": "scripts/create_segments.sh", |
| "sha256": "6e9bc05b82d398ba29ffbd85a587e947fa57eddc749511937176254e192c1c1d", |
| "language": "Shell", |
| "lines": 73, |
| "truncated": false, |
| "block": 4, |
| "row": 1939 |
| }, |
| { |
| "path": "scripts/eval_func_puffin.sh", |
| "sha256": "8c0e43754b51e7a0026ac931d51eaaac6c531a602691f570d800fb2d15ea2852", |
| "language": "Shell", |
| "lines": 63, |
| "truncated": false, |
| "block": 4, |
| "row": 1874 |
| }, |
| { |
| "path": "scripts/full_pipeline.sh", |
| "sha256": "288e36645520d48b04dc048a7774a1ec51ca5445bf534efd20aed8c4c22357a7", |
| "language": "Shell", |
| "lines": 186, |
| "truncated": false, |
| "block": 4, |
| "row": 2173 |
| }, |
| { |
| "path": "scripts/global_prototypes.sh", |
| "sha256": "47c6cfff237dade43ce4ce5a5b4a10bcab49596cba60ff3c47fbc1222809247a", |
| "language": "Shell", |
| "lines": 176, |
| "truncated": false, |
| "block": 4, |
| "row": 2187 |
| }, |
| { |
| "path": "scripts/train_models.sh", |
| "sha256": "c858a3507198f905f50878e71a20fb05df3afdad3be50f11748e204a0b58b7aa", |
| "language": "Shell", |
| "lines": 173, |
| "truncated": false, |
| "block": 4, |
| "row": 2176 |
| }, |
| { |
| "path": "setup.py", |
| "sha256": "61b87ec09b8620cbf4e2ce8f0d14f9d3dc5bc381ba162957a159f8273e2c70af", |
| "language": "Python", |
| "lines": 21, |
| "truncated": false, |
| "block": 3, |
| "row": 18418 |
| }, |
| { |
| "path": "src/__init__.py", |
| "sha256": "ab0efeb6a5bcdbfdea1f4c0842b5bc18ba48bb93f0bb79868e3352711ffbf9eb", |
| "language": "Python", |
| "lines": 35, |
| "truncated": false, |
| "block": 3, |
| "row": 19314 |
| }, |
| { |
| "path": "src/cluster.py", |
| "sha256": "99222b715a543e4a48184f5d2de94b24ad1e255aa510f82dad1d9a0eb0973cc0", |
| "language": "Python", |
| "lines": 606, |
| "truncated": false, |
| "block": 3, |
| "row": 27150 |
| }, |
| { |
| "path": "src/cluster_compare.py", |
| "sha256": "032711a866ce80ab9222ffa032f082f546de5d3c7048a861f4390546c03ad341", |
| "language": "Python", |
| "lines": 538, |
| "truncated": false, |
| "block": 3, |
| "row": 26972 |
| }, |
| { |
| "path": "src/cluster_structural_compare.py", |
| "sha256": "68e867faca4a46d3bffcaeeb2c698db80277af16c3bb6dc0098b268101e73d97", |
| "language": "Python", |
| "lines": 728, |
| "truncated": false, |
| "block": 3, |
| "row": 27413 |
| }, |
| { |
| "path": "src/data/__init__.py", |
| "sha256": "8f653e8958a327987b38459ad46a1b61cfa8e1c087ef327d369843ef7073834f", |
| "language": "Python", |
| "lines": 4, |
| "truncated": false, |
| "block": 3, |
| "row": 17679 |
| }, |
| { |
| "path": "src/data/biolip.py", |
| "sha256": "9ac70fbffcafdd263e16581af95dbeb31879d1bbb974265366614f4cd0afa89a", |
| "language": "Python", |
| "lines": 116, |
| "truncated": false, |
| "block": 3, |
| "row": 22559 |
| }, |
| { |
| "path": "src/data/check_ancestors.py", |
| "sha256": "1b64d3e180e9b83f9d8c109ba9e940f09831ede9229d139df353f0ff80f1fac4", |
| "language": "Python", |
| "lines": 17, |
| "truncated": false, |
| "block": 3, |
| "row": 18541 |
| }, |
| { |
| "path": "src/data/download_interpro.py", |
| "sha256": "973054d3ff9a97adc76fc8e38cabcde0771b06ed3ef24bc8234b4f3d8f03b15f", |
| "language": "Python", |
| "lines": 42, |
| "truncated": false, |
| "block": 3, |
| "row": 19578 |
| }, |
| { |
| "path": "src/data/ecod.py", |
| "sha256": "cdd9ddbab7128a6d48b2fa4da906622665a93dc43d182bbcf48e837e85e5583b", |
| "language": "Python", |
| "lines": 116, |
| "truncated": false, |
| "block": 3, |
| "row": 22094 |
| }, |
| { |
| "path": "src/data/filter.py", |
| "sha256": "f039815ad6a532c902140257e712da6b0036d1d494e3ecc06e412fb312c7897f", |
| "language": "Python", |
| "lines": 210, |
| "truncated": false, |
| "block": 3, |
| "row": 24178 |
| }, |
| { |
| "path": "src/data/go_datamodule.py", |
| "sha256": "7e82b41df70a5f54ce5a74593e0d77d50bf05198bf3ec1f2733b75ac451ed643", |
| "language": "Python", |
| "lines": 346, |
| "truncated": false, |
| "block": 3, |
| "row": 26000 |
| }, |
| { |
| "path": "src/data/ia.py", |
| "sha256": "c00c52a0db4fdaaf98c42b3102a8ec0ceaf5aaf701132fc487e4dc012572d46b", |
| "language": "Python", |
| "lines": 188, |
| "truncated": false, |
| "block": 3, |
| "row": 24347 |
| }, |
| { |
| "path": "src/data/interpro.py", |
| "sha256": "2c3acc76a215a9e15d34405fc44559f2c32e67da28317e0915f68bc76b497600", |
| "language": "Python", |
| "lines": 193, |
| "truncated": false, |
| "block": 3, |
| "row": 24502 |
| }, |
| { |
| "path": "src/data/manager.py", |
| "sha256": "016a37719e29ea64fe3326bc2719d5d2e6a4bded3deff5c49586356a66b77ef4", |
| "language": "Python", |
| "lines": 29, |
| "truncated": false, |
| "block": 3, |
| "row": 18673 |
| }, |
| { |
| "path": "src/data/protein_dataset.py", |
| "sha256": "a3c495df03976f045277226d01a9379778ae0368f51354efc095f0f19575082b", |
| "language": "Python", |
| "lines": 491, |
| "truncated": false, |
| "block": 3, |
| "row": 26858 |
| }, |
| { |
| "path": "src/data/rename.py", |
| "sha256": "c6d2d61a6575cf6826acc4a20eb2f05ccf149cab37bc6f2aeb4b4aa6701b0fe8", |
| "language": "Python", |
| "lines": 15, |
| "truncated": false, |
| "block": 3, |
| "row": 18486 |
| }, |
| { |
| "path": "src/data/scope.py", |
| "sha256": "89af4d1d3aa5e87bd206950d6a7aaa3861583eca0525a42e549992797781040e", |
| "language": "Python", |
| "lines": 125, |
| "truncated": false, |
| "block": 3, |
| "row": 22986 |
| }, |
| { |
| "path": "src/data/singleprotein.py", |
| "sha256": "675f0825690a701dccea2d22a531e3769965381e68ef7ab735b967c9fa0d563c", |
| "language": "Python", |
| "lines": 150, |
| "truncated": false, |
| "block": 3, |
| "row": 22754 |
| }, |
| { |
| "path": "src/esm_embed.py", |
| "sha256": "548b10d5f98de9e79418ccf59863832de2cbe32df870b7332ab35b43dba7bf34", |
| "language": "Python", |
| "lines": 170, |
| "truncated": false, |
| "block": 3, |
| "row": 23055 |
| }, |
| { |
| "path": "src/eval.py", |
| "sha256": "22b74f7285a64b28d2ce3c16fb7874198cc0ac576463193c1af4f4e72d61eaf5", |
| "language": "Python", |
| "lines": 276, |
| "truncated": false, |
| "block": 3, |
| "row": 25430 |
| }, |
| { |
| "path": "src/global_prototypes_fit.py", |
| "sha256": "1467762da2db64d2707189aa81bf99ed22832ee73f39f6ba0e4f722353a3db3c", |
| "language": "Python", |
| "lines": 1372, |
| "truncated": false, |
| "block": 3, |
| "row": 27961 |
| }, |
| { |
| "path": "src/inference.py", |
| "sha256": "774c6b4301623d64b04f3c2d8ef43d89d6bfd27c5568d26de967df69deb1b7d2", |
| "language": "Python", |
| "lines": 499, |
| "truncated": false, |
| "block": 3, |
| "row": 26996 |
| }, |
| { |
| "path": "src/interpro_proto_comp_notebook.ipynb", |
| "sha256": "92acd201b3d34f1bf72255de4f283e9042be6e8ac5ab58eb1dca472109e225bb", |
| "language": "Jupyter", |
| "lines": 112, |
| "truncated": false, |
| "block": 3, |
| "row": 7231 |
| }, |
| { |
| "path": "src/interpro_proto_go_term_comparison.py", |
| "sha256": "37c064c07d92aff9b41d7d49d9d87b8fb1ecdadd337b68ffa474a5412f61f332", |
| "language": "Python", |
| "lines": 644, |
| "truncated": false, |
| "block": 3, |
| "row": 26909 |
| }, |
| { |
| "path": "src/models/__init__.py", |
| "sha256": "3d13e2a4da697661124d0710fe6ac9f16b03dcbcb9799502978423a8fdbc87ef", |
| "language": "Python", |
| "lines": 73, |
| "truncated": false, |
| "block": 3, |
| "row": 21261 |
| }, |
| { |
| "path": "src/models/dual_model.py", |
| "sha256": "40ae4f3725c1a43a865eaa8855a7337bc7fe6d232d6319b599ccec633bb6ab13", |
| "language": "Python", |
| "lines": 401, |
| "truncated": false, |
| "block": 3, |
| "row": 26615 |
| }, |
| { |
| "path": "src/models/puffin.py", |
| "sha256": "ffedc85387de7d5ae36091e166275fd03cae9b8fd6715dbf36d7578f9065afca", |
| "language": "Python", |
| "lines": 651, |
| "truncated": false, |
| "block": 3, |
| "row": 27435 |
| }, |
| { |
| "path": "src/models/unsupervised_model.py", |
| "sha256": "f6b208e8b742bd77efa9a0e04d56ef6c4fde72db7253d0f3da67d6fd08337f2d", |
| "language": "Python", |
| "lines": 122, |
| "truncated": false, |
| "block": 3, |
| "row": 22788 |
| }, |
| { |
| "path": "src/segment_characterize.py", |
| "sha256": "ab0e3572b821331ded32dbe581f91e5d95e9852c4f2dd0a59fcbb8c0fa3c247b", |
| "language": "Python", |
| "lines": 1584, |
| "truncated": false, |
| "block": 3, |
| "row": 28000 |
| }, |
| { |
| "path": "src/segment_neighborhood.py", |
| "sha256": "6cb101d3e98fdc912ddc1560a37330b90522aa303ffe721800ca856e76af212b", |
| "language": "Python", |
| "lines": 1070, |
| "truncated": false, |
| "block": 3, |
| "row": 27774 |
| }, |
| { |
| "path": "src/train.py", |
| "sha256": "2bd3d479162696188a9e62533bac439d2ac075182be4954b2c4a4659cff1a1aa", |
| "language": "Python", |
| "lines": 299, |
| "truncated": false, |
| "block": 3, |
| "row": 25746 |
| }, |
| { |
| "path": "src/unit_func_eval.py", |
| "sha256": "6920b3d3cefaaf462bbc40ff276839e5b265887982c87e7f74d3ee00867a7a6c", |
| "language": "Python", |
| "lines": 695, |
| "truncated": false, |
| "block": 3, |
| "row": 27306 |
| }, |
| { |
| "path": "src/utils/__init__.py", |
| "sha256": "53c89d14f10dc118d52ecc0122763b4a447325aed03354c70cc9d95cfed289b7", |
| "language": "Python", |
| "lines": 5, |
| "truncated": false, |
| "block": 3, |
| "row": 17878 |
| }, |
| { |
| "path": "src/utils/cluster_utils.py", |
| "sha256": "b9a64a4f811ba5675b555a3759f2cc4c90ff4f25cf3d017eb16a2633e83cfdc7", |
| "language": "Python", |
| "lines": 564, |
| "truncated": false, |
| "block": 3, |
| "row": 26982 |
| }, |
| { |
| "path": "src/utils/eval_utils.py", |
| "sha256": "1a602c97047fc74050c0aa5e2ca39f1c58abde5ec8d4855e39944e9e52b1dfdb", |
| "language": "Python", |
| "lines": 632, |
| "truncated": false, |
| "block": 3, |
| "row": 27100 |
| }, |
| { |
| "path": "src/utils/instantiators.py", |
| "sha256": "2fa9e7f3ca1fba4c5639ff51e3d20e93fce58cde027ebd3e22dc0303b677f3b4", |
| "language": "Python", |
| "lines": 55, |
| "truncated": false, |
| "block": 3, |
| "row": 19916 |
| }, |
| { |
| "path": "src/utils/logging_utils.py", |
| "sha256": "6d6b96f53484f62aee94fd1de8f2dc591f35f2745c277ebe328dcb23e8fcb8a7", |
| "language": "Python", |
| "lines": 56, |
| "truncated": false, |
| "block": 3, |
| "row": 19901 |
| }, |
| { |
| "path": "src/utils/metrics.py", |
| "sha256": "1c505137f4d90038f5ce60f83edd4df2effd3b714ecffadc18c11f75aaefeb3f", |
| "language": "Python", |
| "lines": 176, |
| "truncated": false, |
| "block": 3, |
| "row": 23733 |
| }, |
| { |
| "path": "src/utils/model_utils.py", |
| "sha256": "20da5a929a17c76cb35d042126dc0a82e7973ff5e7ceb9def3363bf7f22ae244", |
| "language": "Python", |
| "lines": 50, |
| "truncated": false, |
| "block": 3, |
| "row": 19994 |
| }, |
| { |
| "path": "src/utils/pylogger.py", |
| "sha256": "b23f0ac101671ce8bbd04769df8a2c69ac8c75d2c38a0dc501e6564a75193519", |
| "language": "Python", |
| "lines": 51, |
| "truncated": false, |
| "block": 3, |
| "row": 20659 |
| }, |
| { |
| "path": "src/utils/rich_utils.py", |
| "sha256": "b0e3853cba28589fd6647b1faad09cca9a2ef506323854f63f95f5688b57f19d", |
| "language": "Python", |
| "lines": 99, |
| "truncated": false, |
| "block": 3, |
| "row": 21542 |
| }, |
| { |
| "path": "src/utils/utils.py", |
| "sha256": "c74b5c90f342822615a329bcbd7feb418fe76922ac5e17182ad2504369b5d211", |
| "language": "Python", |
| "lines": 119, |
| "truncated": false, |
| "block": 3, |
| "row": 22424 |
| } |
| ] |
| } |
