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/ml-jku/vnegnn",4 "url": "https://github.com/ml-jku/vnegnn",5 "host": "github.com",6 "commit": "1d1f922cb9f015d4793e7804cbc9b8b248c68498",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "7f7234b31900c3562f2595447a162c950d0d6b52a06f47c9ca2629e817dd9bb3",14 "language": "License",15 "lines": 21,16 "truncated": false,17 "block": 14,18 "row": 1696819 },20 {21 "path": "README.md",22 "sha256": "a62af832008e08684061f6de6c0dba114923d4a21db10770e5116a289a8f6b64",23 "language": "Text",24 "lines": 254,25 "truncated": false,26 "block": 16,27 "row": 761028 },29 {30 "path": "notebooks/bindingsite/analyse_preds.ipynb",31 "sha256": "01813a8735045d5e860399a9b61f51d73fdafe16f2356224a7599b6c714cf126",32 "language": "Jupyter",33 "lines": 146,34 "truncated": false,35 "block": 14,36 "row": 1523737 },38 {39 "path": "notebooks/notebook_setup.py",40 "sha256": "b6e1bdc73e36cce2266627d1dd0ed81c46dbe1ae5cd7cfa6f9343085ab121189",41 "language": "Python",42 "lines": 22,43 "truncated": false,44 "block": 15,45 "row": 684946 },47 {48 "path": "notebooks/notebook_utils.py",49 "sha256": "7d031cc3ecc966436669f10082e6597b8afb574db07d3e97ad81792abb548ec5",50 "language": "Python",51 "lines": 53,52 "truncated": false,53 "block": 15,54 "row": 1023755 },56 {57 "path": "scripts/extract_binding_atoms.py",58 "sha256": "e43f6e3e4333b8dbbd386bdb3f39d03716daa817acc6036f194d5b3cf060959a",59 "language": "Python",60 "lines": 289,61 "truncated": false,62 "block": 15,63 "row": 2139364 },65 {66 "path": "scripts/extract_binding_info.py",67 "sha256": "c113b3842e1919a24ad1bdbf5effe9cf6243ebf73b5a09f355c23250315eff18",68 "language": "Python",69 "lines": 325,70 "truncated": false,71 "block": 15,72 "row": 2208673 },74 {75 "path": "scripts/generate_esm_embeddings.py",76 "sha256": "62594f496a47f9a15d49ea78b814dde523d23f680e4c6abb4a082cc4fbc817da",77 "language": "Python",78 "lines": 499,79 "truncated": false,80 "block": 15,81 "row": 2448882 },83 {84 "path": "scripts/process_data.sh",85 "sha256": "bac2d2b727afed4e7b31c257f51a77e510c698a3ef6b78bcd5d19f150549cb61",86 "language": "Shell",87 "lines": 17,88 "truncated": false,89 "block": 16,90 "row": 502091 },92 {93 "path": "scripts/process_data_equipocket.sh",94 "sha256": "f50ce79ffd0e10cf13d0161627fe258eabf506d903c57192504d5277abeeceec",95 "language": "Shell",96 "lines": 17,97 "truncated": false,98 "block": 16,99 "row": 5014100 },101 {102 "path": "scripts/protein_feature.py",103 "sha256": "90841fdec93242a51b376b1774ee9e9fe938488b61a052cfc885cc947a587f4e",104 "language": "Python",105 "lines": 461,106 "truncated": false,107 "block": 15,108 "row": 24163109 },110 {111 "path": "src/datasets/binding_dataset.py",112 "sha256": "811bbecbd5663f28dd5d86be0d48d77b0d2f3c420cfa11cf32ca9d68b6bfa1f6",113 "language": "Python",114 "lines": 406,115 "truncated": false,116 "block": 15,117 "row": 23842118 },119 {120 "path": "src/datasets/equipocket_dataset.py",121 "sha256": "7aed88dd683e3ecf06976c1a3022ccc942455280c98632d4965b8eac87e1964a",122 "language": "Python",123 "lines": 222,124 "truncated": false,125 "block": 15,126 "row": 19948127 },128 {129 "path": "src/datasets/utils.py",130 "sha256": "037f9b9f2f6790656a7afed8a633f1033958818806d93ef2dea4784c04f3ca30",131 "language": "Python",132 "lines": 255,133 "truncated": false,134 "block": 15,135 "row": 20154136 },137 {138 "path": "src/eval.py",139 "sha256": "de9e8534666777600a73c202efdb05216ad14ce6913747ad9d18094b3e91d034",140 "language": "Python",141 "lines": 147,142 "truncated": false,143 "block": 15,144 "row": 16184145 },146 {147 "path": "src/models/equipocket/__init__.py",148 "sha256": "d410deeed2dc360aa1f882b6003caeb018c34367e197456dedec09779d2dcec8",149 "language": "Python",150 "lines": 3,151 "truncated": false,152 "block": 15,153 "row": 5647154 },155 {156 "path": "src/models/equipocket/baseline_models.py",157 "sha256": "e5677f25da1a0f4bce034676a61a23e7ed6116b6f0cf5f2c9c08f3dd33b45d82",158 "language": "Python",159 "lines": 252,160 "truncated": false,161 "block": 15,162 "row": 20988163 },164 {165 "path": "src/models/equipocket/egnn_clean.py",166 "sha256": "ccb4abe92ac530ec4c50d1c2e65639ef6089f4dbd667473d405355a35c1aa0fe",167 "language": "Python",168 "lines": 347,169 "truncated": false,170 "block": 15,171 "row": 22662172 },173 {174 "path": "src/models/equipocket/equipocket.py",175 "sha256": "79bb3b3ca112d5230ddb4c1a5a90973ebbdbfc17806bb975ee7d69df5324713d",176 "language": "Python",177 "lines": 212,178 "truncated": false,179 "block": 15,180 "row": 20799181 },182 {183 "path": "src/models/equipocket/surface_egnn.py",184 "sha256": "d2bccde7851884b8a18ba57784f51b641f5c43337fccb25cfe31bfb6094ff2d6",185 "language": "Python",186 "lines": 269,187 "truncated": false,188 "block": 15,189 "row": 21164190 },191 {192 "path": "src/models/vnegnn/__init__.py",193 "sha256": "a7fc39d42c37984a62500bba480e5506eebd131b9315e392d80eac0b6da32bf4",194 "language": "Python",195 "lines": 4,196 "truncated": false,197 "block": 15,198 "row": 6015199 },200 {201 "path": "src/models/vnegnn/aggregation.py",202 "sha256": "72e925ccf4bfaae83d50c795263a782ff887cc57d0d4cea9eb3ccfa0ed6b5d08",203 "language": "Python",204 "lines": 66,205 "truncated": false,206 "block": 15,207 "row": 10968208 },209 {210 "path": "src/models/vnegnn/utils.py",211 "sha256": "ce627e5d04fd1fb96263cf751b6e8f8d1b811838b20a4015db3e0ce8a7988278",212 "language": "Python",213 "lines": 42,214 "truncated": false,215 "block": 15,216 "row": 9064217 },218 {219 "path": "src/models/vnegnn/vnegnn.py",220 "sha256": "6a2f946a813aad3c1d7ae54afb532c76385950423ef997a4f2bf42e1520c7bb5",221 "language": "Python",222 "lines": 412,223 "truncated": false,224 "block": 15,225 "row": 23305226 },227 {228 "path": "src/modules/callbacks.py",229 "sha256": "efdad6c14ceed3033654aec502ecbe92146d7d1fea47597bf1600d624a6bffd2",230 "language": "Python",231 "lines": 30,232 "truncated": false,233 "block": 15,234 "row": 8688235 },236 {237 "path": "src/modules/cluster.py",238 "sha256": "b6add4e95ddb3b7c8b596dd03295a09d6194a1835e33b5a5a619fa0e33ea79d6",239 "language": "Python",240 "lines": 19,241 "truncated": false,242 "block": 15,243 "row": 6756244 },245 {246 "path": "src/modules/ema.py",247 "sha256": "46dc860024c0680b34fc9a578d1bedfe576cb839d2326b1bbf51b836c4f999ca",248 "language": "Python",249 "lines": 101,250 "truncated": false,251 "block": 15,252 "row": 14400253 },254 {255 "path": "src/modules/losses.py",256 "sha256": "0486fb09527b6157d766f48d3b02879d5e8a6338be1413e36df22c96d376b013",257 "language": "Python",258 "lines": 56,259 "truncated": false,260 "block": 15,261 "row": 9788262 },263 {264 "path": "src/modules/metrics.py",265 "sha256": "0db656dd4433ffa7837510f912a5be95f9ca23f77a4c3683009e579971a20890",266 "language": "Python",267 "lines": 169,268 "truncated": false,269 "block": 15,270 "row": 19001271 },272 {273 "path": "src/modules/schedulers.py",274 "sha256": "4607ceb927a36526babb1d3ac690b151b9c318f9b297c467f952397117f8c092",275 "language": "Python",276 "lines": 52,277 "truncated": false,278 "block": 15,279 "row": 9768280 },281 {282 "path": "src/train.py",283 "sha256": "a51c866b5c5d2ca35877e8e72474fbc91345d3b407aae6a22985f2eebb67745d",284 "language": "Python",285 "lines": 138,286 "truncated": false,287 "block": 15,288 "row": 16018289 },290 {291 "path": "src/utils/__init__.py",292 "sha256": "b8a7151208cb000d79d02dcee34d5ded49f572b090f5d6cd026cae0e542519d1",293 "language": "Python",294 "lines": 28,295 "truncated": false,296 "block": 15,297 "row": 7538298 },299 {300 "path": "src/utils/constants.py",301 "sha256": "a1eb483c3a866411f2371267772d4ee74685fa4a9cdbdc90fa963c7c0e30266b",302 "language": "Python",303 "lines": 23,304 "truncated": false,305 "block": 15,306 "row": 6387307 },308 {309 "path": "src/utils/graph.py",310 "sha256": "0b474e84058166f7031924e6cfca442828b0def7bb9efd6e70c3f2e8e70ef562",311 "language": "Python",312 "lines": 118,313 "truncated": false,314 "block": 15,315 "row": 14728316 },317 {318 "path": "src/utils/instantiators.py",319 "sha256": "98c5283b858452c0a31fe1556e097fe08b706c12d8873fe3e46be9aa0272c3be",320 "language": "Python",321 "lines": 56,322 "truncated": false,323 "block": 15,324 "row": 10280325 },326 {327 "path": "src/utils/logging_utils.py",328 "sha256": "2d4a3f00fdfc32a7cce2dc62c99d53b22400c84f9f7382e8b90e4a0bff1a8512",329 "language": "Python",330 "lines": 76,331 "truncated": false,332 "block": 15,333 "row": 11744334 },335 {336 "path": "src/utils/misc.py",337 "sha256": "8b7771e7547a6f41b70a9b8aa3dace83bd4ce064d41ad625762459d530cb9f98",338 "language": "Python",339 "lines": 379,340 "truncated": false,341 "block": 15,342 "row": 23809343 },344 {345 "path": "src/utils/protein.py",346 "sha256": "cb3d0b5a5cc639181bb82025e86d178661fdd0d068e7c214764f98f999f17e48",347 "language": "Python",348 "lines": 109,349 "truncated": false,350 "block": 15,351 "row": 15527352 },353 {354 "path": "src/utils/pylogger.py",355 "sha256": "795c750bb2de58f962f39a29c04c795d426fa46f43e7d4554e58cb6caa4b42b4",356 "language": "Python",357 "lines": 67,358 "truncated": false,359 "block": 15,360 "row": 12990361 },362 {363 "path": "src/utils/rich_utils.py",364 "sha256": "79fe3df736f3b779942729d119db3e65e5b53d4c1ab78f16e76a91ec86e22c9e",365 "language": "Python",366 "lines": 108,367 "truncated": false,368 "block": 15,369 "row": 14069370 },371 {372 "path": "src/utils/tensor_utils.py",373 "sha256": "eb82e68f65648546daed3b6924ce8c653d62ddfeaa3f6a43fae97c5b08570465",374 "language": "Python",375 "lines": 113,376 "truncated": false,377 "block": 15,378 "row": 14551379 },380 {381 "path": "src/utils/torch_utils.py",382 "sha256": "4c9977dd2732c315a852fc0eea775c1da620b44223cd1eab6d88a5879f851f55",383 "language": "Python",384 "lines": 125,385 "truncated": false,386 "block": 15,387 "row": 15672388 },389 {390 "path": "src/utils/utils.py",391 "sha256": "3c7cdcd2deb3e7322cfdce0522268058353ec3d80fc597b28ddf67ab963c2bb5",392 "language": "Python",393 "lines": 214,394 "truncated": false,395 "block": 15,396 "row": 20055397 },398 {399 "path": "src/wrappers/base.py",400 "sha256": "33c445c484eab79e3724d3b8a826070852ad58aead9f44bafbbb92751c755119",401 "language": "Python",402 "lines": 124,403 "truncated": false,404 "block": 15,405 "row": 15861406 },407 {408 "path": "src/wrappers/bindingsites.py",409 "sha256": "0e795d4bb4ed3fc50771e8f9c1aa9a41b5d717d76f139d5b0b2e354d224ae04b",410 "language": "Python",411 "lines": 306,412 "truncated": false,413 "block": 15,414 "row": 22201415 },416 {417 "path": "src/wrappers/equipocket.py",418 "sha256": "fba8d599662d7bc97e63096ea5a6b24a0d266631399ca2b3a60ff08b3b55ca8c",419 "language": "Python",420 "lines": 126,421 "truncated": false,422 "block": 15,423 "row": 15231424 }425 ]426}