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/rinikerlab/amp_bms",4 "url": "https://github.com/rinikerlab/amp_bms",5 "host": "github.com",6 "commit": "935f1789d70892eab4968bc9c4b409cab1d1ae1f",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11 {12 "path": "LICENSE",13 "sha256": "97ce705c7101cac23337f40515ef4c162a9a42dc482ea9b155972f37349770ca",14 "language": "License",15 "lines": 21,16 "truncated": false,17 "block": 3,18 "row": 808819 },20 {21 "path": "README.md",22 "sha256": "cc45444e8bf1afa4dbf1b2a5891cae61ce929bdfe24b9ce165ff08cf1f84e125",23 "language": "Text",24 "lines": 67,25 "truncated": false,26 "block": 4,27 "row": 241628 },29 {30 "path": "setup.py",31 "sha256": "d2b064af92216f9bff729ee58084b2accb65c5e28533d66d87f99189854e692a",32 "language": "Python",33 "lines": 8,34 "truncated": false,35 "block": 3,36 "row": 1765637 },38 {39 "path": "source/amp/AMP.py",40 "sha256": "43458c6b18731364049dc325d30f939c3ca38fce8748319fba542cc9e4bb80d5",41 "language": "Python",42 "lines": 226,43 "truncated": false,44 "block": 3,45 "row": 2496246 },47 {48 "path": "source/amp/AMPHelpers.py",49 "sha256": "df1e7410b1fee99bf426517a43846f051be0a06e09f32755998ad46c14df3d82",50 "language": "Python",51 "lines": 72,52 "truncated": false,53 "block": 3,54 "row": 2086755 },56 {57 "path": "source/datastructures/Data.py",58 "sha256": "a84474c8b536e34be844ddac8f73e14d1967399ab15af38eb2e21e1f45627ac2",59 "language": "Python",60 "lines": 83,61 "truncated": false,62 "block": 3,63 "row": 2092364 },65 {66 "path": "source/datastructures/Graphs.py",67 "sha256": "92810aea03d8b9fc21142487633826f3e42f8e5fce571f88ca57c9ca3e5c05d0",68 "language": "Python",69 "lines": 100,70 "truncated": false,71 "block": 3,72 "row": 2126773 },74 {75 "path": "source/examples/calibration/AMPHelpers_calibration.py",76 "sha256": "6a8ab0349b95092be57589efbd92a0006465203c5fd8deaf212fb4e83e2b3c94",77 "language": "Python",78 "lines": 44,79 "truncated": false,80 "block": 3,81 "row": 2062882 },83 {84 "path": "source/examples/calibration/AMP_calibration.py",85 "sha256": "99b5efa1055e6f18c2244a356ba3aa3a03b2a26854e90cc8f513f98a909dcdf5",86 "language": "Python",87 "lines": 249,88 "truncated": false,89 "block": 3,90 "row": 2540691 },92 {93 "path": "source/examples/calibration/HFE_get_lambda_energies_ELE_LJ.py",94 "sha256": "f92a98c1e8e2fe19f538dd14b758f0708ad3f27bd08a89f2f0330364c1db502a",95 "language": "Python",96 "lines": 209,97 "truncated": false,98 "block": 3,99 "row": 24479100 },101 {102 "path": "source/examples/calibration/HFE_get_lambda_energies_POL.py",103 "sha256": "173d1ecbf2b53137288a75dec32b7192fa9a4aeb505be840bb2cfc6f39aac50f",104 "language": "Python",105 "lines": 195,106 "truncated": false,107 "block": 3,108 "row": 24165109 },110 {111 "path": "source/examples/calibration/Simulator_calibration.py",112 "sha256": "1ede934a70c79d28688859f8448f7c0518a6ebfde9c1ad0b35fe9daf81e3324c",113 "language": "Python",114 "lines": 1122,115 "truncated": false,116 "block": 3,117 "row": 27943118 },119 {120 "path": "source/examples/calibration/analysis/HFE_analysis_ELE_LJ.py",121 "sha256": "3425b2e57b3a39d2538b5a99af51efcb0db517023caf60d9eddc8b2eff608fb1",122 "language": "Python",123 "lines": 203,124 "truncated": false,125 "block": 3,126 "row": 24520127 },128 {129 "path": "source/examples/calibration/analysis/HFE_analysis_POL.py",130 "sha256": "1c2fda238ee5fcf174b8a593b83ae5d59e66dfe840362f640248d3d7d5967aee",131 "language": "Python",132 "lines": 163,133 "truncated": false,134 "block": 3,135 "row": 23581136 },137 {138 "path": "source/examples/calibration/analysis/TRP_calculate_RMSD_NOE.py",139 "sha256": "d93468316bb5f0210abafe28c73ffd022a7b85d0192b25c53a379e6885ea8f92",140 "language": "Python",141 "lines": 117,142 "truncated": false,143 "block": 3,144 "row": 24357145 },146 {147 "path": "source/examples/calibration/analysis/calculate_rdf.py",148 "sha256": "3fa8bf2ada151393e1d294ae9ebbf303e26452eec81caa27fca13eedbfc4ee88",149 "language": "Python",150 "lines": 87,151 "truncated": false,152 "block": 3,153 "row": 20859154 },155 {156 "path": "source/examples/calibration/datastructures_calibration.py",157 "sha256": "96e0aaab9c313fc327b124488c33a1f2ba2c67934203c0cf9f7d828db67c4578",158 "language": "Python",159 "lines": 85,160 "truncated": false,161 "block": 3,162 "row": 21584163 },164 {165 "path": "source/examples/calibration/examples/HFE_ELE_LJ_mol_012.py",166 "sha256": "f39261d6e16eab48ebdd7eb7d1b68a4cfef84e496f2f40cd8bc07c77cfbcca3b",167 "language": "Python",168 "lines": 88,169 "truncated": false,170 "block": 3,171 "row": 22116172 },173 {174 "path": "source/examples/calibration/examples/HFE_POL_mol_012.py",175 "sha256": "9a1991400baada972ddb45254a976ba0f397ff44fdf12b1fff56e46fca806424",176 "language": "Python",177 "lines": 101,178 "truncated": false,179 "block": 3,180 "row": 22447181 },182 {183 "path": "source/examples/calibration/examples/HFE_postprocessing_ELE_LJ_mol_012.py",184 "sha256": "80f79b6410ab0b118f4672a0297bd6cc73d9dde746298af67cd6bae5ca45cccf",185 "language": "Python",186 "lines": 74,187 "truncated": false,188 "block": 3,189 "row": 21291190 },191 {192 "path": "source/examples/calibration/examples/HFE_postprocessing_POL_mol_012.py",193 "sha256": "91d4f15e41fe1a1896e1e4368e810990e8191b78c57845cc8f9c60c82d27b587",194 "language": "Python",195 "lines": 88,196 "truncated": false,197 "block": 3,198 "row": 21343199 },200 {201 "path": "source/examples/calibration/examples/calculate_LJ_dimer_energy.py",202 "sha256": "678586f5092fa65fef0c17a420a596f403f9466cdbd7475147efea1ff7325315",203 "language": "Python",204 "lines": 151,205 "truncated": false,206 "block": 3,207 "row": 23222208 },209 {210 "path": "source/examples/calibration/examples/calculate_sapt.py",211 "sha256": "1ff93cce0b9affe25d0720188ff67bd3dc2891bcd9f0534addab542f19c05a5c",212 "language": "Python",213 "lines": 129,214 "truncated": false,215 "block": 3,216 "row": 22185217 },218 {219 "path": "source/examples/calibration/examples/charge_scaling_RDF.py",220 "sha256": "5100894a4d96206996c39f8387a9ef471f2bc91ee67898ad087c74c17a10b643",221 "language": "Python",222 "lines": 67,223 "truncated": false,224 "block": 3,225 "row": 21278226 },227 {228 "path": "source/examples/calibration/examples/filter_FreeSolv_HFE_molecules.ipynb",229 "sha256": "d24629b87978c52bfe78563b9dc35b7a5e750769df17885ac2d3d1ba86a5551f",230 "language": "Jupyter",231 "lines": 177,232 "truncated": false,233 "block": 3,234 "row": 7293235 },236 {237 "path": "source/examples/calibration/examples/pol_scaling_RDF.py",238 "sha256": "d572f8313e182735131b177f181f56d042ba16719ab6fe0289bab36d7a3a17eb",239 "language": "Python",240 "lines": 81,241 "truncated": false,242 "block": 3,243 "row": 21458244 },245 {246 "path": "source/examples/calibration/examples/pol_scaling_TRP.py",247 "sha256": "98d2db50c9a417cbe4d0be786ad122e8cd5d23a8b1eeaf2f43ca2bc73d35dc9c",248 "language": "Python",249 "lines": 78,250 "truncated": false,251 "block": 3,252 "row": 21537253 },254 {255 "path": "source/examples/calibration/helper_functions.py",256 "sha256": "1c4bdf7b2e14bcf443e5a2fbfb5da9809e25c9bfa84b984c02b40f91f2582335",257 "language": "Python",258 "lines": 137,259 "truncated": false,260 "block": 3,261 "row": 21845262 },263 {264 "path": "source/examples/calibration/main_calibration.py",265 "sha256": "fd845db1fca2a81d942b7f72340eeaf21ee9e7fe6ab4109f87232bd1b5e8de59",266 "language": "Python",267 "lines": 389,268 "truncated": false,269 "block": 3,270 "row": 26565271 },272 {273 "path": "source/examples/calibration/main_water_in_water_calibration.py",274 "sha256": "ea691bc8ca399ead67c66549277963224b0c7979b1eed2589482b10d9bb3bb92",275 "language": "Python",276 "lines": 350,277 "truncated": false,278 "block": 3,279 "row": 26135280 },281 {282 "path": "source/examples/calibration/modules_calibration.py",283 "sha256": "49ad8f1cdd52e35bc097bafdc3c4f47292ed1caaab064cf00758360f7c51e731",284 "language": "Python",285 "lines": 337,286 "truncated": false,287 "block": 3,288 "row": 26373289 },290 {291 "path": "source/examples/calibration/utilities_calibration.py",292 "sha256": "1bf4979d5c048c7e5be90527a18914d0c84792a106804f03c0ad5e3b4deae35a",293 "language": "Python",294 "lines": 336,295 "truncated": false,296 "block": 3,297 "row": 25669298 },299 {300 "path": "source/examples/calibration/write_yaml.py",301 "sha256": "d7b87d3f8a2eff7663633cf0a55576d46f6d8de637cac7f70aefd8022c61d52d",302 "language": "Python",303 "lines": 251,304 "truncated": false,305 "block": 3,306 "row": 26635307 },308 {309 "path": "source/examples/examples_analysis/calc_MELT_RMSD_DSSP.py",310 "sha256": "ff5e626bb234ad5a8be6ba5482d69e6a88257c76cd3d970949538e09b14e27f7",311 "language": "Python",312 "lines": 67,313 "truncated": false,314 "block": 3,315 "row": 19931316 },317 {318 "path": "source/examples/examples_analysis/calc_NOE_1AKI.py",319 "sha256": "5bfa092ce3a87f9474216ee8e2a0964d46b1ea8a7ecd87c4efc6e22d16ecfe7c",320 "language": "Python",321 "lines": 325,322 "truncated": false,323 "block": 3,324 "row": 25818325 },326 {327 "path": "source/examples/examples_analysis/calc_S2_1AKI.py",328 "sha256": "28b44912f1f252582b11ccbfbafd4420b01614666a59e00d0f49357d1e92acea",329 "language": "Python",330 "lines": 220,331 "truncated": false,332 "block": 3,333 "row": 23068334 },335 {336 "path": "source/examples/examples_analysis/calc_STABLE_RMSD_DSSP.py",337 "sha256": "3c742c900c57d8fa52f3f7bfca9ae3b18a6f861e4f757c7e490eb65c6ae251d9",338 "language": "Python",339 "lines": 45,340 "truncated": false,341 "block": 3,342 "row": 19410343 },344 {345 "path": "source/examples/examples_enzymes/chorismate-mutase/smd.py",346 "sha256": "9c3590aed993f8b1893ab93023b3cad156a7178652aab2920515b658c3f1cde2",347 "language": "Python",348 "lines": 175,349 "truncated": false,350 "block": 3,351 "row": 23996352 },353 {354 "path": "source/examples/examples_enzymes/chorismate-mutase/smd.sh",355 "sha256": "6cabea856c128e9d84b7ad4acb827032a04ba356def7fd416d52a24da2839421",356 "language": "Shell",357 "lines": 3,358 "truncated": false,359 "block": 4,360 "row": 1355361 },362 {363 "path": "source/examples/examples_enzymes/chorismate-mutase/submit-all-chorismate.sh",364 "sha256": "4efba7b1e67483b6ee6fa80973c49666e27448b3af4ae95c2e36b4b8435f7ee2",365 "language": "Shell",366 "lines": 5,367 "truncated": false,368 "block": 4,369 "row": 1544370 },371 {372 "path": "source/examples/examples_enzymes/chorismate-mutase/submit-all-protein.sh",373 "sha256": "34d8e2ea58af7d3f79fa432d697e0ddb01905bcef1a91ea3781a9cdca2b9c62e",374 "language": "Shell",375 "lines": 5,376 "truncated": false,377 "block": 4,378 "row": 1552379 },380 {381 "path": "source/examples/examples_enzymes/chorismate-mutase/submit-umbrella-sampling.py",382 "sha256": "aa5a25ed6381942357213493fb9543be89fa7e3e5d998acaec3970bf44ba46d7",383 "language": "Python",384 "lines": 50,385 "truncated": false,386 "block": 3,387 "row": 20889388 },389 {390 "path": "source/examples/examples_enzymes/chorismate-mutase/umbrella-sampling.py",391 "sha256": "20b058b95c561beb08dd29fb580b351ac13e624ddaa3e04c1b77367d43edd090",392 "language": "Python",393 "lines": 184,394 "truncated": false,395 "block": 3,396 "row": 24862397 },398 {399 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/smd-5k3f-Asp134Ala.py",400 "sha256": "66491a6d22d003e28bfadef4d84b4329d9fd28a49b1405ed1dc187b071812af5",401 "language": "Python",402 "lines": 177,403 "truncated": false,404 "block": 3,405 "row": 24079406 },407 {408 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/smd-5k3f.py",409 "sha256": "676bf75d343d95444e8ca9afd2a82eafa880765255b8d598ab3741b414ce6168",410 "language": "Python",411 "lines": 181,412 "truncated": false,413 "block": 3,414 "row": 24104415 },416 {417 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/submit-5k3f-Asp134Ala.sh",418 "sha256": "38e5a0a08a1d696997c5811135ce64727ad1265b7340484e6c5eb5f7985dedcc",419 "language": "Shell",420 "lines": 5,421 "truncated": false,422 "block": 4,423 "row": 1322424 },425 {426 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/submit-5k3f.sh",427 "sha256": "01f89b531567b3091d49c93b1b189953c3f09fa7a849c191cb09ca70157923c7",428 "language": "Shell",429 "lines": 5,430 "truncated": false,431 "block": 4,432 "row": 1306433 },434 {435 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/submit.py",436 "sha256": "60f3306c3e66cb36eb78a5a9a50b070f97d074dbce7c2888199b902823eb4e66",437 "language": "Python",438 "lines": 40,439 "truncated": false,440 "block": 3,441 "row": 19935442 },443 {444 "path": "source/examples/examples_enzymes/fluoroacetate-dehalogenase/umbrella-sampling.py",445 "sha256": "7f7980d600c06e537a3d0195e65f438c15c04270ba26790a4b431b4c032e78a4",446 "language": "Python",447 "lines": 157,448 "truncated": false,449 "block": 3,450 "row": 24035451 },452 {453 "path": "source/examples/examples_md/example-simulation.ipynb",454 "sha256": "0b57c489a4e560323d7eb78815e88616a1b7eedb534e05c4e776be302fe3042a",455 "language": "Jupyter",456 "lines": 26,457 "truncated": false,458 "block": 3,459 "row": 7043460 },461 {462 "path": "source/examples/examples_scripts/run_melting_curve_md.py",463 "sha256": "0d9fa97588c30f8712f347b19311ad95b1f9739b3bb746df344213fe381f31fd",464 "language": "Python",465 "lines": 41,466 "truncated": false,467 "block": 3,468 "row": 19386469 },470 {471 "path": "source/examples/examples_scripts/run_stable_protein_md.py",472 "sha256": "9ecca07a65b111724e52a2939dbe2f5ab1d3fabd84fa3832c388cf28b6a15779",473 "language": "Python",474 "lines": 41,475 "truncated": false,476 "block": 3,477 "row": 19380478 },479 {480 "path": "source/md/Simulator.py",481 "sha256": "a86a8b090810fb75bf2d3051e43662a1a76b2bfc45a984dc614b23bcc1860e7d",482 "language": "Python",483 "lines": 642,484 "truncated": false,485 "block": 3,486 "row": 27431487 },488 {489 "path": "source/md/TorchForce.py",490 "sha256": "1bb6410bdddeb32eae2cc8ec470f5873b5377ad40c9ce47d2ff805874601bd2a",491 "language": "Python",492 "lines": 354,493 "truncated": false,494 "block": 3,495 "row": 26368496 },497 {498 "path": "source/modules/D4DispersionScaling.py",499 "sha256": "e39f36bf3137c863d59e5c2dcc3471efe430ce97b9285a094880af313aeb81a5",500 "language": "Python",501 "lines": 91,502 "truncated": false,503 "block": 3,504 "row": 21605505 },506 {507 "path": "source/modules/Modules.py",508 "sha256": "c915e537868f62c02dccf843dba2a323f256bfc7266a17158caffd033eb82aad",509 "language": "Python",510 "lines": 291,511 "truncated": false,512 "block": 3,513 "row": 25311514 },515 {516 "path": "source/modules/MolecularMultipoles.py",517 "sha256": "bfc770aa1522206016dddffb5589f36bf152ec41e4f95a5d2622d003fd2b53dc",518 "language": "Python",519 "lines": 77,520 "truncated": false,521 "block": 3,522 "row": 21386523 },524 {525 "path": "source/utilities/Element.py",526 "sha256": "a37ac25dc2d3424033ed32fb0590c160173efe050f1d311273c901ec3ab4a427",527 "language": "Python",528 "lines": 315,529 "truncated": false,530 "block": 3,531 "row": 25986532 },533 {534 "path": "source/utilities/Helpers.py",535 "sha256": "f539e4dbc11880452ad6bb143267e69481ca3ba60143c14d696427fc024daa78",536 "language": "Python",537 "lines": 207,538 "truncated": false,539 "block": 3,540 "row": 23981541 },542 {543 "path": "source/utilities/Scatter.py",544 "sha256": "b8edd9b82e3316b5c4ff9e17f71cfd486d37a6de8f3a0d901b7a16952893a15f",545 "language": "Python",546 "lines": 80,547 "truncated": false,548 "block": 3,549 "row": 20749550 },551 {552 "path": "source/utilities/Training.py",553 "sha256": "8805d150252d76d851d5343a662ee69817f5d68b9ecec6f5ec63ca8d560077ae",554 "language": "Python",555 "lines": 208,556 "truncated": false,557 "block": 3,558 "row": 24580559 },560 {561 "path": "source/utilities/Utilities.py",562 "sha256": "152b2311de530d41180396d51b24a6b919fbad333f61ba0b4764437f0299d850",563 "language": "Python",564 "lines": 78,565 "truncated": false,566 "block": 3,567 "row": 20357568 }569 ]570}