OpenScientificCodeRegistry/Database
Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
05.6k
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/camlab-ethz/gems",4 "url": "https://github.com/camlab-ethz/GEMS",5 "host": "github.com",6 "commit": "4cc2e76b9e3559bc57d452999ad258b8a8ccaf23",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "Dataset.py",13 "sha256": "180e8e494c999f07beefa72cc6d6f601bb6cac80613b2773a426338c3478eaee",14 "language": "Python",15 "lines": 336,16 "truncated": false,17 "block": 18,18 "row": 262619 },20 {21 "path": "GEMS_dataprep_workflow.py",22 "sha256": "52ddb78cf756fb0cad3c7d48dbfa34919101e051fdef7655f535d120b14d79e8",23 "language": "Python",24 "lines": 100,25 "truncated": false,26 "block": 17,27 "row": 2628928 },29 {30 "path": "LICENSE",31 "sha256": "c43cfbcf3062a9da1561be8036e5a152837516b4e5942acd092730dcb9922f67",32 "language": "License",33 "lines": 21,34 "truncated": false,35 "block": 17,36 "row": 775537 },38 {39 "path": "PDBbind_data/read_index_into_dict.py",40 "sha256": "72b6ab026ab093cd2659def8432fd9942dca5f6cbe5b0685a3d4b8d0f2fc1206",41 "language": "Python",42 "lines": 152,43 "truncated": false,44 "block": 17,45 "row": 2922246 },47 {48 "path": "PDBbind_data/similarity/pairwise_similarity_matrix/pairwise_similarity_tanimoto.py",49 "sha256": "15082b3bb444c8f00ea45a3d13b81fbb41857b2feac1a112fcd1d57ee6bd95ba",50 "language": "Python",51 "lines": 210,52 "truncated": false,53 "block": 17,54 "row": 3187055 },56 {57 "path": "PDBbind_data/similarity/pairwise_similarity_matrix/pairwise_similarity_tm_rmsd.py",58 "sha256": "9a101cc25fcbf7edd9df2e879c889e5f0cd8a4e102137b15ae38addea9e42c5c",59 "language": "Python",60 "lines": 379,61 "truncated": false,62 "block": 18,63 "row": 237764 },65 {66 "path": "PDBbind_data/similarity/train_test_superpositions/rotate_PDB.py",67 "sha256": "1a4537791c1c579b80ae7f492d421a3b25a9dd4984ff34335f11c928353ce0d0",68 "language": "Python",69 "lines": 95,70 "truncated": false,71 "block": 17,72 "row": 2577073 },74 {75 "path": "PDBbind_dataset_filtering/remove_train_redundancy.py",76 "sha256": "da6648fc7b47a2f651ae1022644491e123af8f0ae53a8cb4957f3cd6d4500dda",77 "language": "Python",78 "lines": 225,79 "truncated": false,80 "block": 17,81 "row": 3274282 },83 {84 "path": "PDBbind_dataset_filtering/remove_train_test_sims.py",85 "sha256": "b64d1f47eee4bbb3447efaca3569bbbb1c3653a5290c5730e0979044c944e755",86 "language": "Python",87 "lines": 210,88 "truncated": false,89 "block": 17,90 "row": 3234591 },92 {93 "path": "PDBbind_search_algorithm/search_algorithm_compl.py",94 "sha256": "5a7882a98b83244bb4faceb2458ead9daeb63a539f6c15f48d1e7400e9fa1eca",95 "language": "Python",96 "lines": 137,97 "truncated": false,98 "block": 17,99 "row": 29660100 },101 {102 "path": "PDBbind_search_algorithm/search_algorithm_lig.py",103 "sha256": "b3f2c333c695998574d7e75fad1ba2c91db79a9529f87f1b61a9318fb33aba70",104 "language": "Python",105 "lines": 130,106 "truncated": false,107 "block": 17,108 "row": 29088109 },110 {111 "path": "README.md",112 "sha256": "4860b2e987991dd0a44e58784c38ea1f5b9b29bb2bb0855acb14fac7c2870f22",113 "language": "Text",114 "lines": 192,115 "truncated": false,116 "block": 18,117 "row": 11172118 },119 {120 "path": "dataprep/ankh_features.py",121 "sha256": "d3c27ee4be2affe99b608a0476604063a3e9d1930353e1b347b195ca438fa94f",122 "language": "Python",123 "lines": 152,124 "truncated": false,125 "block": 17,126 "row": 28250127 },128 {129 "path": "dataprep/chemberta_features.py",130 "sha256": "0ea36841f78b0e8953dc2206771940e8be7048d19b182d95a4ad5d233916865f",131 "language": "Python",132 "lines": 131,133 "truncated": false,134 "block": 17,135 "row": 27901136 },137 {138 "path": "dataprep/construct_dataset.py",139 "sha256": "040865fcb7db50f1805964ebcc670347169f7ea1113d3d196b5a100e9638c81e",140 "language": "Python",141 "lines": 87,142 "truncated": false,143 "block": 17,144 "row": 28117145 },146 {147 "path": "dataprep/esm_features.py",148 "sha256": "817abf64bdc925c5551d43a83d0d9aedb462be67fa06032ac1ad2648f3f5c13f",149 "language": "Python",150 "lines": 158,151 "truncated": false,152 "block": 17,153 "row": 28550154 },155 {156 "path": "dataprep/graph_construction.py",157 "sha256": "4e6e181dedc08aede25dc317a0eb867b0fde5fa3914fddea73e37b1517f64248",158 "language": "Python",159 "lines": 868,160 "truncated": false,161 "block": 18,162 "row": 5136163 },164 {165 "path": "inference.py",166 "sha256": "25929ea20165af7c7b550e7486e2eec71ab14a66c9b9072024b56621b978280a",167 "language": "Python",168 "lines": 278,169 "truncated": false,170 "block": 18,171 "row": 671172 },173 {174 "path": "model/GEMS18.py",175 "sha256": "72971a2cfd8005b15388d5ae80f505bf8558c091286c5ebff0204abfafa85a1c",176 "language": "Python",177 "lines": 269,178 "truncated": false,179 "block": 18,180 "row": 536181 },182 {183 "path": "ranking_test.py",184 "sha256": "522fa5c874eff86fdfd87d04cedfad1dd05d08c1aec4a9da6ac8e83ad25c884b",185 "language": "Python",186 "lines": 139,187 "truncated": false,188 "block": 17,189 "row": 29043190 },191 {192 "path": "test.py",193 "sha256": "49e9a259b6e6288fd25660654a52c0df643c904bef0d52929adda59457024384",194 "language": "Python",195 "lines": 200,196 "truncated": false,197 "block": 17,198 "row": 31064199 },200 {201 "path": "train.py",202 "sha256": "928ba06e267745684b51af1afb230de4932ff5406d864262e275e18ef72d7226",203 "language": "Python",204 "lines": 758,205 "truncated": false,206 "block": 18,207 "row": 4693208 },209 {210 "path": "utils/calculate_cbeta_position.py",211 "sha256": "40327679ac970ea5513b190e12d3b0ffcd410ad3b86d518b7bf6e28ace3dbdaa",212 "language": "Python",213 "lines": 45,214 "truncated": false,215 "block": 17,216 "row": 21364217 },218 {219 "path": "utils/convert_csv_to_json.py",220 "sha256": "3e628682812c4b97adc85c32cfc61b2e735d1fdc3cf20073238df25904aba4b6",221 "language": "Python",222 "lines": 59,223 "truncated": false,224 "block": 17,225 "row": 23125226 },227 {228 "path": "utils/f_parse_pdb_general.py",229 "sha256": "def0af85f209075b7b6d2c4891342ed035a48d7cc53fb665506cdc54a7565aa0",230 "language": "Python",231 "lines": 141,232 "truncated": false,233 "block": 17,234 "row": 29044235 }236 ]237}