Team Ai
Datasetpublic

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.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__choderalab__pymbar.json363 linesDownload Raw Back to 54
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/choderalab/pymbar",4 "url": "https://github.com/choderalab/pymbar/tree/4.0.3",5 "host": "github.com",6 "commit": "ed40ec3bbef03bb08938ad1a74d459b0d1ab81f7",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "b06216b25962856729369804671b10ac7daed2237597f285abc540c363c19da2",14   "language": "License",15   "lines": 7,16   "truncated": false,17   "block": 9,18   "row": 285719  },20  {21   "path": "README.md",22   "sha256": "e22f9a18d567757aa27294672561183080cb7dde1ca146cc302a9c15df3b6858",23   "language": "Text",24   "lines": 155,25   "truncated": false,26   "block": 9,27   "row": 1469228  },29  {30   "path": "devtools/conda-recipe/build.sh",31   "sha256": "77325d3647b2d5dcde886c706aa490bbdd603bcd63c71007a7af0795dbb0b3ac",32   "language": "Shell",33   "lines": 9,34   "truncated": false,35   "block": 9,36   "row": 1392737  },38  {39   "path": "devtools/travis-ci/after_success.sh",40   "sha256": "f5bb063d19e69b1b681096e22c9555ac1d5005ab77d1d1aa4df829054da5a5fd",41   "language": "Shell",42   "lines": 43,43   "truncated": false,44   "block": 9,45   "row": 1417246  },47  {48   "path": "devtools/travis-ci/install.sh",49   "sha256": "3202a142539d69708e53e89ee67a326f0d218ecf2add596ea7ae32ca9f64412c",50   "language": "Shell",51   "lines": 25,52   "truncated": false,53   "block": 9,54   "row": 1411755  },56  {57   "path": "devtools/travis-ci/push-docs-to-s3.py",58   "sha256": "ef68d48bae6c0ec554887ed0e960031e4fb56295b609dc119d5d50d535295063",59   "language": "Python",60   "lines": 48,61   "truncated": false,62   "block": 9,63   "row": 744664  },65  {66   "path": "docs/conf.py",67   "sha256": "cd801203e0dcec5c209268b52d064448a74845f490df53a6a9f50308cbf5fd60",68   "language": "Python",69   "lines": 328,70   "truncated": false,71   "block": 9,72   "row": 1092173  },74  {75   "path": "examples/constant-force-optical-trap/extract-data.py",76   "sha256": "7817545544df7ceaad64d1f6340d8554386eabe3e0b2ff0fc3bee95f67a6ab0b",77   "language": "Python",78   "lines": 109,79   "truncated": false,80   "block": 9,81   "row": 908882  },83  {84   "path": "examples/constant-force-optical-trap/force-bias-optical-trap.py",85   "sha256": "44db29e558bfde12e253c674c83971cf3d8aec9cff8fb52286ba8c8258be5672",86   "language": "Python",87   "lines": 398,88   "truncated": false,89   "block": 9,90   "row": 1148191  },92  {93   "path": "examples/harmonic-oscillators/harmonic-oscillators-distributions.py",94   "sha256": "65a887c8904dc02b3b8b930925f91f324b3a2c7d688b7037efa299fc82f5ae37",95   "language": "Python",96   "lines": 347,97   "truncated": false,98   "block": 9,99   "row": 11226100  },101  {102   "path": "examples/harmonic-oscillators/harmonic-oscillators.py",103   "sha256": "b93e8350e48008fad4d97e4bdc7f5cdef9605a29321915f534729476dbfda34e",104   "language": "Python",105   "lines": 1005,106   "truncated": false,107   "block": 9,108   "row": 12347109  },110  {111   "path": "examples/heat-capacity/heat-capacity.py",112   "sha256": "fe27324b9f459362edd4d7ce169f9e0681ea1c4a2dd441456f3e5a4dfdf97700",113   "language": "Python",114   "lines": 519,115   "truncated": false,116   "block": 9,117   "row": 11801118  },119  {120   "path": "examples/parallel-tempering-2dfes/parallel-tempering-2dfes.py",121   "sha256": "a3427ce73957c6987879d1b5fd2269fbee5f4701d196c867cd4b04e607552931",122   "language": "Python",123   "lines": 331,124   "truncated": false,125   "block": 9,126   "row": 11414127  },128  {129   "path": "examples/umbrella-sampling-fes/umbrella-sampling-advanced-fes.py",130   "sha256": "4ce9e04ff9f7c92a8f4fcbf16339907b2b0fc2bb54afbea4f5d5dfbfe798ed1d",131   "language": "Python",132   "lines": 511,133   "truncated": false,134   "block": 9,135   "row": 11828136  },137  {138   "path": "examples/umbrella-sampling-fes/umbrella-sampling.py",139   "sha256": "b641b0447673d5fc6222cc521bb90d7d6b0e5b5d16615baaee1b49a45a81ed3d",140   "language": "Python",141   "lines": 179,142   "truncated": false,143   "block": 9,144   "row": 10191145  },146  {147   "path": "examples/umbrella-sampling-fes/wham/dowham.pl",148   "sha256": "874ec716bfbc94dc6fbabcd4c5710deae7eef44a96be717cf7006709ad0c6a80",149   "language": "Perl",150   "lines": 25,151   "truncated": false,152   "block": 9,153   "row": 6034154  },155  {156   "path": "examples/umbrella-sampling-fes/wham/setupwham.pl",157   "sha256": "e817b4a773d830dfc1642439c8726e1f8a13b154a84a4546dce685117823ac39",158   "language": "Perl",159   "lines": 37,160   "truncated": false,161   "block": 9,162   "row": 6036163  },164  {165   "path": "pymbar/__init__.py",166   "sha256": "f5806f5cd9fe756c5ddcedfe245d2328d111dd1daa8eb943c63c0c061065c5f0",167   "language": "Python",168   "lines": 56,169   "truncated": false,170   "block": 9,171   "row": 7750172  },173  {174   "path": "pymbar/confidenceintervals.py",175   "sha256": "c8969356bc0ab5fb4f77079a6098029c3061ebc1312301dee7bb112b7ac23cc4",176   "language": "Python",177   "lines": 460,178   "truncated": false,179   "block": 9,180   "row": 11553181  },182  {183   "path": "pymbar/fes.py",184   "sha256": "71fb1920640e1ada15031634632d8c5688cb13d8b90cc466c270645b64f0e6ee",185   "language": "Python",186   "lines": 2477,187   "truncated": false,188   "block": 9,189   "row": 12650190  },191  {192   "path": "pymbar/mbar.py",193   "sha256": "76c85656c06504b4c4d631ca2e357de43b9666a4b303c9dffa0c5ee9edd70442",194   "language": "Python",195   "lines": 1989,196   "truncated": false,197   "block": 9,198   "row": 12623199  },200  {201   "path": "pymbar/mbar_solvers.py",202   "sha256": "e48b6a736cb29e1401a25db05c4d95f99174062bfc55a7a1841121f11586b2d1",203   "language": "Python",204   "lines": 1200,205   "truncated": false,206   "block": 9,207   "row": 12444208  },209  {210   "path": "pymbar/other_estimators.py",211   "sha256": "be596a1a1081becca4989d98eb374bb9d2175d3c9353c63f0969b9cd145b86ee",212   "language": "Python",213   "lines": 719,214   "truncated": false,215   "block": 9,216   "row": 12201217  },218  {219   "path": "pymbar/tests/test_bar.py",220   "sha256": "5d8c60a4222e16d49c1dce71b71030b1731b99ab06b667b63124fb2fef303c8b",221   "language": "Python",222   "lines": 121,223   "truncated": false,224   "block": 9,225   "row": 9222226  },227  {228   "path": "pymbar/tests/test_covariance.py",229   "sha256": "04db5232d93c07a61ea9dfadae7b438a4bf0e580eda8c946ca872689722b7817",230   "language": "Python",231   "lines": 36,232   "truncated": false,233   "block": 9,234   "row": 7283235  },236  {237   "path": "pymbar/tests/test_exp.py",238   "sha256": "11a4fbad46d16cb6f4c4e9c5abcf0199a8b17fb55771210781349064f723db6b",239   "language": "Python",240   "lines": 94,241   "truncated": false,242   "block": 9,243   "row": 8748244  },245  {246   "path": "pymbar/tests/test_fes.py",247   "sha256": "8581016ca326ba2ee3468437b54aca6e6c99192dbd18c11ebf029ee02f400136",248   "language": "Python",249   "lines": 558,250   "truncated": false,251   "block": 9,252   "row": 11745253  },254  {255   "path": "pymbar/tests/test_mbar.py",256   "sha256": "6978202990743d48b15570360c4f5bd37a433c73c61a47c6fef69c866d1127a0",257   "language": "Python",258   "lines": 578,259   "truncated": false,260   "block": 9,261   "row": 11867262  },263  {264   "path": "pymbar/tests/test_mbar_solvers.py",265   "sha256": "a4b81674c77c4262bbe2107c9c9c98dbb3e97afac43eed131f0a8a0f9473a69e",266   "language": "Python",267   "lines": 125,268   "truncated": false,269   "block": 9,270   "row": 9185271  },272  {273   "path": "pymbar/tests/test_timeseries.py",274   "sha256": "e483c912d094c38a5c275d26c898d3fc518573a79a00f4e76601b4e6062eb1ac",275   "language": "Python",276   "lines": 178,277   "truncated": false,278   "block": 9,279   "row": 10010280  },281  {282   "path": "pymbar/tests/test_utils.py",283   "sha256": "f0296bdcb9136fadf66a54298dce3af0b798da460a5550c76556052b3a296db0",284   "language": "Python",285   "lines": 241,286   "truncated": false,287   "block": 9,288   "row": 10173289  },290  {291   "path": "pymbar/testsystems/__init__.py",292   "sha256": "cc9da3cae6ab84355402d49824679e3bd26e1a282293488c4e02b47c815fcf42",293   "language": "Python",294   "lines": 13,295   "truncated": false,296   "block": 9,297   "row": 6634298  },299  {300   "path": "pymbar/testsystems/exponential_distributions.py",301   "sha256": "67858f149057734970510429f7abc0c9422d5ac3bff20cda60035224b4535b1d",302   "language": "Python",303   "lines": 246,304   "truncated": false,305   "block": 9,306   "row": 10603307  },308  {309   "path": "pymbar/testsystems/gaussian_work.py",310   "sha256": "b28a14d68bb5558fa84ddc1ed264808c587e098e5a0c8b56f8596d8c333bcb7d",311   "language": "Python",312   "lines": 105,313   "truncated": false,314   "block": 9,315   "row": 8854316  },317  {318   "path": "pymbar/testsystems/harmonic_oscillators.py",319   "sha256": "7e66ff03b6462f1c9b84edb3f176a83d9cbd4cc74c957a7267467f01685149c6",320   "language": "Python",321   "lines": 261,322   "truncated": false,323   "block": 9,324   "row": 10780325  },326  {327   "path": "pymbar/testsystems/timeseries.py",328   "sha256": "d9a5e97645ce8d59a6ffc91d4859694695133f486c70d2570a96592bf1fc832f",329   "language": "Python",330   "lines": 74,331   "truncated": false,332   "block": 9,333   "row": 8181334  },335  {336   "path": "pymbar/timeseries.py",337   "sha256": "b375525c9f3f151c006d6eb2eb7898a204c834c603eb8d48b1e8a02841dd0f2a",338   "language": "Python",339   "lines": 970,340   "truncated": false,341   "block": 9,342   "row": 12337343  },344  {345   "path": "pymbar/utils.py",346   "sha256": "faeba549fc57efe4238e83e8862dbe7b75c537b48b37396eb15a30b2c6976f42",347   "language": "Python",348   "lines": 421,349   "truncated": false,350   "block": 9,351   "row": 11258352  },353  {354   "path": "pymbar/utils_for_testing.py",355   "sha256": "f0f9b08ad7cd38bf4f4fb63796364222d0d2c40cef817b796e7b4685c1cd408b",356   "language": "Python",357   "lines": 84,358   "truncated": false,359   "block": 9,360   "row": 8356361  }362 ]363}