OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/forlilab/meeko",4 "url": "https://github.com/forlilab/Meeko",5 "host": "github.com",6 "commit": "1eac18bd6d1111f35f9f1abaa8af502c2668d054",7 "license": "LGPL-2.1",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "20c17d8b8c48a600800dfd14f95d5cb9ff47066a9641ddeab48dc54aec96e331",14   "language": "License",15   "lines": 504,16   "truncated": false,17   "block": 6,18   "row": 211419  },20  {21   "path": "README.md",22   "sha256": "6398e7c6439da189342d37c7382878df4add88a35e4d26bd2cca3e9f2b606235",23   "language": "Text",24   "lines": 75,25   "truncated": false,26   "block": 18,27   "row": 1070828  },29  {30   "path": "docs/source/conf.py",31   "sha256": "66359a02fbcac873ef492cb5421985c8f8f91fad8a0c87a57f7ae9852e4aeb7b",32   "language": "Python",33   "lines": 47,34   "truncated": false,35   "block": 17,36   "row": 2133137  },38  {39   "path": "meeko/__init__.py",40   "sha256": "d59888ee49506dd67f0945b6f0c107dadbc80ea9b5f2018230d4dfbcb915cd1b",41   "language": "Python",42   "lines": 76,43   "truncated": false,44   "block": 17,45   "row": 2360346  },47  {48   "path": "meeko/analysis/__init__.py",49   "sha256": "2fb2ce03a4011e9abb8a058d3aa611b3f89b1750f63454d547110b17739a65e5",50   "language": "Python",51   "lines": 13,52   "truncated": false,53   "block": 17,54   "row": 1850955  },56  {57   "path": "meeko/analysis/fingerprint_interactions.py",58   "sha256": "5d89dfa1d505dcfd6346b8c9db496e201b989053c4855d681953c8de04cbc031",59   "language": "Python",60   "lines": 140,61   "truncated": false,62   "block": 17,63   "row": 2817164  },65  {66   "path": "meeko/analysis/interactions.py",67   "sha256": "9fbb15e3b15a2cf86562486b2cd4d43f345d4bb7c26075660475202508576136",68   "language": "Python",69   "lines": 274,70   "truncated": false,71   "block": 18,72   "row": 100273  },74  {75   "path": "meeko/atomtyper.py",76   "sha256": "60b9f8be50f473e90de6aeacbe28b5439bceeda0b58a8d66dca6d6a16a763ce4",77   "language": "Python",78   "lines": 403,79   "truncated": false,80   "block": 18,81   "row": 250382  },83  {84   "path": "meeko/bondtyper.py",85   "sha256": "6ebbdff6b92dbbd6e5c2543b4eae16a89f72fba3370cedaf7bb989feed3cd4d2",86   "language": "Python",87   "lines": 84,88   "truncated": false,89   "block": 17,90   "row": 2541791  },92  {93   "path": "meeko/chemtempgen.py",94   "sha256": "bcbf7cf2d1fe545f344d630fe480ee580545bf219def87b026fe723cbd72ee1a",95   "language": "Python",96   "lines": 1157,97   "truncated": false,98   "block": 18,99   "row": 5266100  },101  {102   "path": "meeko/cli/mk_export.py",103   "sha256": "288af5734ba50538be5f4631d3a2b4dd24fee1c6504c43ca6f4237d9c916693a",104   "language": "Python",105   "lines": 164,106   "truncated": false,107   "block": 17,108   "row": 30519109  },110  {111   "path": "meeko/cli/mk_prepare_ligand.py",112   "sha256": "069eed4960129188bce2de9f982d5948f339c19b4852b976d47dcf1f26e965b9",113   "language": "Python",114   "lines": 697,115   "truncated": false,116   "block": 18,117   "row": 4027118  },119  {120   "path": "meeko/cli/mk_prepare_receptor.py",121   "sha256": "5daf103e1fb41159bf3f3f39fccf738cc1afd60e444d76825d89382f58f65414",122   "language": "Python",123   "lines": 1257,124   "truncated": false,125   "block": 18,126   "row": 5333127  },128  {129   "path": "meeko/covalentbuilder.py",130   "sha256": "9fd156f886161ec930bebca94382c0ca589e64c28fc8772ab8628666163cf67c",131   "language": "Python",132   "lines": 209,133   "truncated": false,134   "block": 17,135   "row": 32482136  },137  {138   "path": "meeko/espalomatyper.py",139   "sha256": "9baf638039fbbb1236a8d88ce7c9fd2db1e36cb95e03f985fd59f63ad5727fc3",140   "language": "Python",141   "lines": 123,142   "truncated": false,143   "block": 17,144   "row": 27649145  },146  {147   "path": "meeko/export_flexres.py",148   "sha256": "2bc238c4df692b804777a8c20f1e9115e5dc50cad4d4c99ab600be96b25190b1",149   "language": "Python",150   "lines": 242,151   "truncated": false,152   "block": 18,153   "row": 1042154  },155  {156   "path": "meeko/flexibility.py",157   "sha256": "68b6546d8ea0d8d165bc58c35f783a5d76588555f6a97c022b874ffcf184c741",158   "language": "Python",159   "lines": 434,160   "truncated": false,161   "block": 18,162   "row": 2584163  },164  {165   "path": "meeko/gridbox.py",166   "sha256": "a25fba9c4b4aab61502607dea6d3bc5d32415318dc6be543db15f23acdb1f3bc",167   "language": "Python",168   "lines": 160,169   "truncated": false,170   "block": 17,171   "row": 29707172  },173  {174   "path": "meeko/hydrate.py",175   "sha256": "446217179af7bc30516cc6e43b0bab20fa0effbdb33d780c2743352fa12c06fd",176   "language": "Python",177   "lines": 461,178   "truncated": false,179   "block": 18,180   "row": 2491181  },182  {183   "path": "meeko/macrocycle.py",184   "sha256": "7c056325de4644487c4ad5eee71822203db8d12121442e513256ac48a242f599",185   "language": "Python",186   "lines": 376,187   "truncated": false,188   "block": 18,189   "row": 1416190  },191  {192   "path": "meeko/molecule_pdbqt.py",193   "sha256": "3369e7f52657fedaf3d5f99df944b6269875efdefff2c824077d264b5bae3b1d",194   "language": "Python",195   "lines": 692,196   "truncated": false,197   "block": 18,198   "row": 4500199  },200  {201   "path": "meeko/molsetup.py",202   "sha256": "2604e5d435e945ee5556c306a4966e836560c103cc38c33d883d72541b527429",203   "language": "Python",204   "lines": 2150,205   "truncated": false,206   "block": 18,207   "row": 5671208  },209  {210   "path": "meeko/openff_xml_parser.py",211   "sha256": "c59d7ef517ceea9bc3f03e92cc7a6666e9a6ac2fa69c4e66c9969f46b656cf18",212   "language": "Python",213   "lines": 307,214   "truncated": false,215   "block": 18,216   "row": 212217  },218  {219   "path": "meeko/polymer.py",220   "sha256": "040ac36c0489a44ab17494ad498ebb827911c5cf9d3fc234a586ac1d1ddc389f",221   "language": "Python",222   "lines": 3747,223   "truncated": false,224   "block": 18,225   "row": 5850226  },227  {228   "path": "meeko/preparation.py",229   "sha256": "1370b86ef941ded89bbdb33785c7e645862f6516c437d59cb0f4477529d5e664",230   "language": "Python",231   "lines": 797,232   "truncated": false,233   "block": 18,234   "row": 4439235  },236  {237   "path": "meeko/rdkit_mol_create.py",238   "sha256": "9348fdefebc6b49e1db75c61065af82aee8eb53fd591333c37a579c696edd66a",239   "language": "Python",240   "lines": 455,241   "truncated": false,242   "block": 18,243   "row": 3176244  },245  {246   "path": "meeko/reactive.py",247   "sha256": "1af0440882c4c526f602112ab7a7e4fbe04378d0cd08ab0ec6ba668f9e8cb333",248   "language": "Python",249   "lines": 253,250   "truncated": false,251   "block": 17,252   "row": 32443253  },254  {255   "path": "meeko/receptor_pdbqt.py",256   "sha256": "a8185ee64c600455d8344673a2c1c28ec3b98b317dfd1c81bc0d03ff1e0b129a",257   "language": "Python",258   "lines": 261,259   "truncated": false,260   "block": 18,261   "row": 116262  },263  {264   "path": "meeko/tmp/compute_water_map.py",265   "sha256": "b2484d6b4c1b777f29b6fd6d8747c2bbeeb2fc149f1bca34cf3fc1d515937067",266   "language": "Python",267   "lines": 177,268   "truncated": false,269   "block": 17,270   "row": 29547271  },272  {273   "path": "meeko/tmp/water_builder.py",274   "sha256": "0f8d4bccd94a6fdd5d3f12d73e1acf16630ee12d0b6388070283fa62c916c8ed",275   "language": "Python",276   "lines": 672,277   "truncated": false,278   "block": 18,279   "row": 4773280  },281  {282   "path": "meeko/tmp/water_map_builder.py",283   "sha256": "b853b35d5aafb03eda03d71b64572765b39d82df47f291a85f6df1be11c2488d",284   "language": "Python",285   "lines": 271,286   "truncated": false,287   "block": 18,288   "row": 230289  },290  {291   "path": "meeko/utils/__init__.py",292   "sha256": "cb84262a5a9ffb7fe46f6547385b77223e90d70c97e32c4f66f30c1eb03f1866",293   "language": "Python",294   "lines": 5,295   "truncated": false,296   "block": 17,297   "row": 17278298  },299  {300   "path": "meeko/utils/autodock4_atom_types_elements.py",301   "sha256": "71d97e8530d8f3e65b5522fe9c099077ba825ed4bbaa847af81f5fe7dbaa56e1",302   "language": "Python",303   "lines": 48,304   "truncated": false,305   "block": 17,306   "row": 19502307  },308  {309   "path": "meeko/utils/covalent_radius_table.py",310   "sha256": "065cab31e6db6bab263daf886d5a3a08aaccc13ae4e155063a3e6f702e2dea7b",311   "language": "Python",312   "lines": 137,313   "truncated": false,314   "block": 17,315   "row": 23608316  },317  {318   "path": "meeko/utils/geomutils.py",319   "sha256": "7d9534caa044082af9a8472bda728fae3a93369be98bd014fe9b4b69e52a4ac3",320   "language": "Python",321   "lines": 483,322   "truncated": false,323   "block": 18,324   "row": 1967325  },326  {327   "path": "meeko/utils/jsonutils.py",328   "sha256": "c8aae058d0a7c684ba9ac5f4c3a5c6622d9ae56ce1587d96f6bed61fdfd2632a",329   "language": "Python",330   "lines": 178,331   "truncated": false,332   "block": 17,333   "row": 29300334  },335  {336   "path": "meeko/utils/pdbutils.py",337   "sha256": "3456f50ca0aa154d67951ce4215ff309d200f94cc148df4e8d1c54823975b8c9",338   "language": "Python",339   "lines": 20,340   "truncated": false,341   "block": 17,342   "row": 19589343  },344  {345   "path": "meeko/utils/prodyutils.py",346   "sha256": "909dd4ede08252e8b239eef0f7a5cbe73487d08f1a86df53a791dde475e3cb50",347   "language": "Python",348   "lines": 294,349   "truncated": false,350   "block": 18,351   "row": 299352  },353  {354   "path": "meeko/utils/rdkitutils.py",355   "sha256": "4e0b0089d650b7274cdfc7c1f8bdf55f1f0dc5cf8f1189cb7595c8c2bf2e7a34",356   "language": "Python",357   "lines": 528,358   "truncated": false,359   "block": 18,360   "row": 3615361  },362  {363   "path": "meeko/utils/utils.py",364   "sha256": "c1c450dac20ffaf84e90763ecdf558b998a91f189573bcf31983a882626febbc",365   "language": "Python",366   "lines": 512,367   "truncated": false,368   "block": 18,369   "row": 2613370  },371  {372   "path": "meeko/utils/van_der_waals_radius_table.py",373   "sha256": "10013e4252184e0921cde7cab22d3245fda4f2c1f2bdfe6a6901913d7d8c690d",374   "language": "Python",375   "lines": 132,376   "truncated": false,377   "block": 17,378   "row": 23243379  },380  {381   "path": "meeko/writer.py",382   "sha256": "f2474a7b21e332a93860081b2d026b47dec8d3b5739008aab030a6fb3bac6831",383   "language": "Python",384   "lines": 794,385   "truncated": false,386   "block": 18,387   "row": 4551388  },389  {390   "path": "setup.py",391   "sha256": "3a3832685ce6f0b66c3f5153da048db77284e33acce8da4d4fb6e8d1725b2f41",392   "language": "Python",393   "lines": 60,394   "truncated": false,395   "block": 17,396   "row": 22762397  },398  {399   "path": "test/adjacent_padding_test.py",400   "sha256": "326422b5dc409f2047cc9ade215d4ad0ca7d060b2e85025fae6e6fc5e40a77e7",401   "language": "Python",402   "lines": 144,403   "truncated": false,404   "block": 17,405   "row": 27396406  },407  {408   "path": "test/chemtempgen_test.py",409   "sha256": "18cfe3bf5a55d20f508dde2ca7ccdac6ad4e35c3a2597a41dbb22cb27ebcd77d",410   "language": "Python",411   "lines": 129,412   "truncated": false,413   "block": 17,414   "row": 28157415  },416  {417   "path": "test/cyclopentane_rigid_test.py",418   "sha256": "b9b4a61278033bb5a715556e2af8e70a1c7515aa2cf7d95340c8c48fa4fad225",419   "language": "Python",420   "lines": 19,421   "truncated": false,422   "block": 17,423   "row": 18798424  },425  {426   "path": "test/flexibility_test.py",427   "sha256": "4aaf9899a07d833ea20f69995881e6a6780b45e417e5e95048f3b8d86f06a888",428   "language": "Python",429   "lines": 124,430   "truncated": false,431   "block": 17,432   "row": 26010433  },434  {435   "path": "test/flexres_export_test.py",436   "sha256": "8f60a69a0eb0031030f2c67a7ab4e4c6f2951ecba522f633573005e2b1d4e62c",437   "language": "Python",438   "lines": 99,439   "truncated": false,440   "block": 17,441   "row": 26166442  },443  {444   "path": "test/json_serialization_test.py",445   "sha256": "554d3726a6e0d7fa6712387a3232beae37513956b3408e9cee0bcc13bcb099d9",446   "language": "Python",447   "lines": 792,448   "truncated": false,449   "block": 18,450   "row": 4429451  },452  {453   "path": "test/macrocycle_test.py",454   "sha256": "6e731ceb5a15818176f17c23701159d2fd5bbd10f13f901d5913c03bb1e1229a",455   "language": "Python",456   "lines": 127,457   "truncated": false,458   "block": 17,459   "row": 28500460  },461  {462   "path": "test/merge_custom_types_test.py",463   "sha256": "54f23977b54ff8d9d0a9064ed9c3c1cca37f3aab64b65f1fc82e619e3c33e2a4",464   "language": "Python",465   "lines": 83,466   "truncated": false,467   "block": 17,468   "row": 24447469  },470  {471   "path": "test/molsetup_test.py",472   "sha256": "06daedbb46c11a70d7fcf96cde29e2326aa121c52432c04c65af13274a5c9ce7",473   "language": "Python",474   "lines": 31,475   "truncated": false,476   "block": 17,477   "row": 18842478  },479  {480   "path": "test/parameterization_test.py",481   "sha256": "0ce32601c57c89d7f7aa29f53f4c7b73d2c66f86573f7e49df7870c91b5643f9",482   "language": "Python",483   "lines": 171,484   "truncated": false,485   "block": 17,486   "row": 30661487  },488  {489   "path": "test/polymer_creation_test.py",490   "sha256": "2a5b271a5a66d2ddee6eb6347920f6f24e1fc30037485411a10a82e3342b9bbc",491   "language": "Python",492   "lines": 666,493   "truncated": false,494   "block": 18,495   "row": 3827496  },497  {498   "path": "test/rdkitmol_from_docking_test.py",499   "sha256": "a317850bdc4c08b70785afcea8b412b27567403ee242fa0ab9eb22424aa3339f",500   "language": "Python",501   "lines": 185,502   "truncated": false,503   "block": 17,504   "row": 31541505  },506  {507   "path": "test/ring_detection_test.py",508   "sha256": "9d3863846feb6c72fd999e5b5c4d7ca09853a419a524d7b1f18db9689a98a886",509   "language": "Python",510   "lines": 44,511   "truncated": false,512   "block": 17,513   "row": 20958514  },515  {516   "path": "test/skip_bad_mols_test.py",517   "sha256": "7edd0ab5a7500c51b3706ee614c573d9b9a2b911b250966a88323ebf8f4d4d52",518   "language": "Python",519   "lines": 29,520   "truncated": false,521   "block": 17,522   "row": 19804523  },524  {525   "path": "test/test-oids.py",526   "sha256": "edf0af6dc5725cad10b8b4cf95828f0e2e1469a20b0a67da8a78211c1b43c5ce",527   "language": "Python",528   "lines": 48,529   "truncated": false,530   "block": 17,531   "row": 21738532  },533  {534   "path": "tools/precalculate_charges.py",535   "sha256": "0ec0cf5a37721a0428b9ce00eebfac2dc0279252c0371646ce75a660670dd9a1",536   "language": "Python",537   "lines": 156,538   "truncated": false,539   "block": 17,540   "row": 28470541  }542 ]543}