| { |
| "format": "oscr-script-manifest/1", |
| "repository": "github.com/bjing2016/alphaflow", |
| "url": "https://github.com/bjing2016/alphaflow", |
| "host": "github.com", |
| "commit": "0408d7c89dac444a43a9089d7427ce470b0a5e67", |
| "license": "MIT", |
| "license_confirmed_by": "license file LICENSE", |
| "redistribution": "yes", |
| "files": [ |
| { |
| "path": "LICENSE", |
| "sha256": "2dbdbaa3390007d29c403e9367c7cd0cd41cb15ec0ce2ea3c4b25c2be1b164a8", |
| "language": "License", |
| "lines": 21, |
| "truncated": false, |
| "block": 6, |
| "row": 1860 |
| }, |
| { |
| "path": "README.md", |
| "sha256": "67ca277d1504f3e7ffb6d53945ab7d0e346b4dae0ea4b2a2d0d6c72df6c6a7b5", |
| "language": "Text", |
| "lines": 214, |
| "truncated": false, |
| "block": 8, |
| "row": 10806 |
| }, |
| { |
| "path": "alphaflow/config.py", |
| "sha256": "1882205763df612db95305e1f0c25b042e8f5dba046eaa25d1332e7a3073e1b8", |
| "language": "Python", |
| "lines": 677, |
| "truncated": false, |
| "block": 7, |
| "row": 9889 |
| }, |
| { |
| "path": "alphaflow/data/data_modules.py", |
| "sha256": "9db5ad1b695e443ea7c43a27e4bb3e21fa4b6cf609284fab9e0abe2bfb9310ea", |
| "language": "Python", |
| "lines": 679, |
| "truncated": false, |
| "block": 7, |
| "row": 9826 |
| }, |
| { |
| "path": "alphaflow/data/data_pipeline.py", |
| "sha256": "7d2a4d3d402103b5a4e4dbeed3bd736148522f76bae7990798ab5e95dcfd04c4", |
| "language": "Python", |
| "lines": 809, |
| "truncated": false, |
| "block": 7, |
| "row": 10376 |
| }, |
| { |
| "path": "alphaflow/data/feature_pipeline.py", |
| "sha256": "4fc2d877c4fdb461c2edc51edcd2891622aeaeed3af8153ded724858992609b2", |
| "language": "Python", |
| "lines": 131, |
| "truncated": false, |
| "block": 6, |
| "row": 38026 |
| }, |
| { |
| "path": "alphaflow/data/inference.py", |
| "sha256": "c7526bc687c90899a526b118679bb47a59646ed0ced44148aa688818719935de", |
| "language": "Python", |
| "lines": 90, |
| "truncated": false, |
| "block": 6, |
| "row": 37373 |
| }, |
| { |
| "path": "alphaflow/data/input_pipeline.py", |
| "sha256": "5c9051e98c7ec0226a41d7a0875b612dfad7b37d86b41a82531b27052475f139", |
| "language": "Python", |
| "lines": 320, |
| "truncated": false, |
| "block": 7, |
| "row": 2583 |
| }, |
| { |
| "path": "alphaflow/model/alphafold.py", |
| "sha256": "0cd2e5b0b20bda15af85c07d474da026c22a997dabe96cf5131b81f92b0fe249", |
| "language": "Python", |
| "lines": 445, |
| "truncated": false, |
| "block": 7, |
| "row": 7439 |
| }, |
| { |
| "path": "alphaflow/model/esmfold.py", |
| "sha256": "e6330465c37f8bb1311478b9a1bf77e9127cbf1ef6c30e2c4081eb65e01c82ad", |
| "language": "Python", |
| "lines": 436, |
| "truncated": false, |
| "block": 7, |
| "row": 7750 |
| }, |
| { |
| "path": "alphaflow/model/input_stack.py", |
| "sha256": "84e58e6e788fa12120e8b5a1c5020c0418370ba99fb941c59ad921dc1083d470", |
| "language": "Python", |
| "lines": 284, |
| "truncated": false, |
| "block": 7, |
| "row": 1071 |
| }, |
| { |
| "path": "alphaflow/model/layers.py", |
| "sha256": "322e2be7c4c2388fc607177bec12855c6834cf33e45b97125d6c8dbdef23f651", |
| "language": "Python", |
| "lines": 188, |
| "truncated": false, |
| "block": 6, |
| "row": 43173 |
| }, |
| { |
| "path": "alphaflow/model/tri_self_attn_block.py", |
| "sha256": "30430c16f2b0ec02839b105250aa6bc07690ca66a8c17697526eff969f9cd784", |
| "language": "Python", |
| "lines": 160, |
| "truncated": false, |
| "block": 6, |
| "row": 43682 |
| }, |
| { |
| "path": "alphaflow/model/trunk.py", |
| "sha256": "213ff448864597290cc9cc4c2ff2ed19d6d9b349fde2058bcfa2c353896ae06e", |
| "language": "Python", |
| "lines": 195, |
| "truncated": false, |
| "block": 6, |
| "row": 44342 |
| }, |
| { |
| "path": "alphaflow/model/wrapper.py", |
| "sha256": "dcb5c0d76af0769dc0f80b7eb84b878061ee2d001b9aad8c6cddab81aa361071", |
| "language": "Python", |
| "lines": 514, |
| "truncated": false, |
| "block": 7, |
| "row": 8345 |
| }, |
| { |
| "path": "alphaflow/utils/diffusion.py", |
| "sha256": "2c19a0ab1ea55e3939bbfeee9295be975f12629682e8f01a5863f641dd977f90", |
| "language": "Python", |
| "lines": 147, |
| "truncated": false, |
| "block": 6, |
| "row": 42265 |
| }, |
| { |
| "path": "alphaflow/utils/logging.py", |
| "sha256": "e18ed11cf194b46ba5e0356ecd8de975f5aee170827fa92e8abe8ffa0c6d0904", |
| "language": "Python", |
| "lines": 43, |
| "truncated": false, |
| "block": 6, |
| "row": 28725 |
| }, |
| { |
| "path": "alphaflow/utils/loss.py", |
| "sha256": "40fe77976f8428f11643ded8657397f87435ac7a6c783c154de27bd72274316e", |
| "language": "Python", |
| "lines": 1617, |
| "truncated": false, |
| "block": 8, |
| "row": 396 |
| }, |
| { |
| "path": "alphaflow/utils/misc.py", |
| "sha256": "a9c6ee8f6f6c72a76aa8789a8a2fac237cf66d999f37508c2cc3cd9b0cb433e3", |
| "language": "Python", |
| "lines": 182, |
| "truncated": false, |
| "block": 6, |
| "row": 43569 |
| }, |
| { |
| "path": "alphaflow/utils/parsing.py", |
| "sha256": "e034d1a60869ffde4adc7005ff8a49fac6738386bd46a841c8451796471a92b4", |
| "language": "Python", |
| "lines": 74, |
| "truncated": false, |
| "block": 6, |
| "row": 37092 |
| }, |
| { |
| "path": "alphaflow/utils/protein.py", |
| "sha256": "35aa4d71bcda33a0fa446c72bc156273d32a45933124e717016a09842cae7030", |
| "language": "Python", |
| "lines": 282, |
| "truncated": false, |
| "block": 7, |
| "row": 3495 |
| }, |
| { |
| "path": "alphaflow/utils/tensor_utils.py", |
| "sha256": "16a1ff69545cdc25a01737f0c6a997c3dc2ec23fa0a27b094c72a7daecb9dc28", |
| "language": "Python", |
| "lines": 118, |
| "truncated": false, |
| "block": 6, |
| "row": 37590 |
| }, |
| { |
| "path": "predict.py", |
| "sha256": "216a6e6114c46f6cb873510d78dfac5a251cf3a63439c4a5a6d119453fc251ae", |
| "language": "Python", |
| "lines": 133, |
| "truncated": false, |
| "block": 6, |
| "row": 41839 |
| }, |
| { |
| "path": "scripts/add_msa_info.py", |
| "sha256": "a7ef84725af7b74ad4de02979cc70bdf6a598d22f3bfdac8550d0002939e41ac", |
| "language": "Python", |
| "lines": 58, |
| "truncated": false, |
| "block": 6, |
| "row": 30805 |
| }, |
| { |
| "path": "scripts/analyze_ensembles.py", |
| "sha256": "379b0631956a3816d5c6b0b425b4e7d1100cab3df5ae63d5fc49e894162e18ae", |
| "language": "Python", |
| "lines": 286, |
| "truncated": false, |
| "block": 7, |
| "row": 4727 |
| }, |
| { |
| "path": "scripts/cluster_chains.py", |
| "sha256": "f0d70aecb68894aeea7defb9b6f3f012811468b74a4852c47378122cb8afc8ef", |
| "language": "Python", |
| "lines": 43, |
| "truncated": false, |
| "block": 6, |
| "row": 29095 |
| }, |
| { |
| "path": "scripts/download_atlas.sh", |
| "sha256": "ff8440c76d7be6e2e10ebb5276e32fb750659a5a06dbc6cc825a7d416e24a9da", |
| "language": "Shell", |
| "lines": 6, |
| "truncated": false, |
| "block": 8, |
| "row": 6690 |
| }, |
| { |
| "path": "scripts/mmseqs_query.py", |
| "sha256": "f39627d6bc7bec7629146b751aaf4f636c870739a5edaf56a2e883967d6e773e", |
| "language": "Python", |
| "lines": 294, |
| "truncated": false, |
| "block": 7, |
| "row": 2952 |
| }, |
| { |
| "path": "scripts/mmseqs_search.py", |
| "sha256": "ff188461d6a5f626e8abd61226e6b181d681919a4f635d363af6dd6bfe8db72f", |
| "language": "Python", |
| "lines": 634, |
| "truncated": false, |
| "block": 7, |
| "row": 9824 |
| }, |
| { |
| "path": "scripts/mmseqs_search_helper.py", |
| "sha256": "6429696a63bf149e0c4fcb69a7d847b62ce9843e44a099493c15b6a42f06e90a", |
| "language": "Python", |
| "lines": 30, |
| "truncated": false, |
| "block": 6, |
| "row": 25328 |
| }, |
| { |
| "path": "scripts/prep_atlas.py", |
| "sha256": "386880888ade8c684d8dcbb47ceff1add7af9dae7a8ea9818effc0566e4abe17", |
| "language": "Python", |
| "lines": 60, |
| "truncated": false, |
| "block": 6, |
| "row": 32488 |
| }, |
| { |
| "path": "scripts/print_analysis.py", |
| "sha256": "bf046f025ef46fdf70aad0eac471f75836b6e0967bb738e6d3914a973e3ab72f", |
| "language": "Python", |
| "lines": 111, |
| "truncated": false, |
| "block": 6, |
| "row": 40377 |
| }, |
| { |
| "path": "scripts/unpack_mmcif.py", |
| "sha256": "00c7e3e3b43cf18c92083c699191bbb1cc6718d1b17c0c7e58cd6f91f60d28f9", |
| "language": "Python", |
| "lines": 73, |
| "truncated": false, |
| "block": 6, |
| "row": 32659 |
| }, |
| { |
| "path": "train.py", |
| "sha256": "059364fcdbf439989b2e17987a77fe2da2f71060fd446001051005e198cddc2f", |
| "language": "Python", |
| "lines": 163, |
| "truncated": false, |
| "block": 6, |
| "row": 42849 |
| } |
| ] |
| } |
