caddforge-docs 0.3.0__py3-none-any.whl

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Files changed (152) hide show
  1. caddforge_docs/__init__.py +1 -0
  2. caddforge_docs/cli.py +20 -0
  3. caddforge_docs/server.py +124 -0
  4. caddforge_docs/site/404.html +2118 -0
  5. caddforge_docs/site/assets/_mkdocstrings.css +237 -0
  6. caddforge_docs/site/assets/images/favicon.png +0 -0
  7. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
  8. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
  9. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
  10. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
  11. caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
  12. caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
  13. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
  14. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
  15. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
  16. caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
  17. caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
  18. caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
  19. caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
  20. caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
  21. caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
  22. caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
  23. caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
  24. caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
  25. caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
  26. caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
  27. caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
  28. caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
  29. caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
  30. caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
  31. caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
  32. caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
  33. caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
  34. caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
  35. caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
  36. caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
  37. caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
  38. caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
  39. caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
  40. caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
  41. caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
  42. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
  43. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
  44. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
  45. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
  46. caddforge_docs/site/core/cli/index.html +2446 -0
  47. caddforge_docs/site/core/concepts/index.html +2340 -0
  48. caddforge_docs/site/core/configuration/index.html +2300 -0
  49. caddforge_docs/site/core/index.html +2170 -0
  50. caddforge_docs/site/core/jobs-results/index.html +2315 -0
  51. caddforge_docs/site/core/plugins/index.html +2200 -0
  52. caddforge_docs/site/core/slurm/index.html +2562 -0
  53. caddforge_docs/site/development/ci-publishing/index.html +2345 -0
  54. caddforge_docs/site/development/contributing/index.html +2311 -0
  55. caddforge_docs/site/development/documentation/index.html +2380 -0
  56. caddforge_docs/site/development/index.html +2201 -0
  57. caddforge_docs/site/development/release-notes/index.html +2504 -0
  58. caddforge_docs/site/development/release-readiness/index.html +2333 -0
  59. caddforge_docs/site/development/security/index.html +2181 -0
  60. caddforge_docs/site/development/tool-authoring/index.html +2435 -0
  61. caddforge_docs/site/examples/index.html +2465 -0
  62. caddforge_docs/site/examples/manifest.json +158 -0
  63. caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
  64. caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
  65. caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
  66. caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
  67. caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
  68. caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
  69. caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
  70. caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
  71. caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
  72. caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
  73. caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
  74. caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
  75. caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
  76. caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
  77. caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
  78. caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
  79. caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
  80. caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
  81. caddforge_docs/site/examples/quickstart/index.html +2172 -0
  82. caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
  83. caddforge_docs/site/examples/quickstart/run.py +18 -0
  84. caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
  85. caddforge_docs/site/examples/quickstart/scores.csv +7 -0
  86. caddforge_docs/site/examples/quickstart/values.csv +31 -0
  87. caddforge_docs/site/examples/run_tool.py +40 -0
  88. caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
  89. caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
  90. caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
  91. caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
  92. caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
  93. caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
  94. caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
  95. caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
  96. caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
  97. caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
  98. caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
  99. caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
  100. caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
  101. caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
  102. caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
  103. caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
  104. caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
  105. caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
  106. caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
  107. caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
  108. caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
  109. caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
  110. caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
  111. caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
  112. caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
  113. caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
  114. caddforge_docs/site/explanation/references/index.html +2218 -0
  115. caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
  116. caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
  117. caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
  118. caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
  119. caddforge_docs/site/getting-started/index.html +2200 -0
  120. caddforge_docs/site/getting-started/installation/index.html +2541 -0
  121. caddforge_docs/site/gui/index.html +2267 -0
  122. caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
  123. caddforge_docs/site/gui/walkthrough/index.html +2181 -0
  124. caddforge_docs/site/how-to/jobs/index.html +2195 -0
  125. caddforge_docs/site/how-to/scatter/index.html +2193 -0
  126. caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
  127. caddforge_docs/site/index.html +2359 -0
  128. caddforge_docs/site/objects.inv +0 -0
  129. caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
  130. caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
  131. caddforge_docs/site/pipelines/examples/index.html +3186 -0
  132. caddforge_docs/site/pipelines/index.html +2164 -0
  133. caddforge_docs/site/pipelines/specification/index.html +2278 -0
  134. caddforge_docs/site/plugins/datascience/index.html +2405 -0
  135. caddforge_docs/site/plugins/descriptors/index.html +2609 -0
  136. caddforge_docs/site/plugins/docking/index.html +2480 -0
  137. caddforge_docs/site/plugins/fep/index.html +2508 -0
  138. caddforge_docs/site/plugins/index.html +2216 -0
  139. caddforge_docs/site/plugins/md/index.html +3795 -0
  140. caddforge_docs/site/plugins/ml/index.html +2815 -0
  141. caddforge_docs/site/plugins/qm/index.html +2309 -0
  142. caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
  143. caddforge_docs/site/reference/api/index.html +4414 -0
  144. caddforge_docs/site/reference/index.html +2166 -0
  145. caddforge_docs/site/search/search_index.json +1 -0
  146. caddforge_docs/site/sitemap.xml +191 -0
  147. caddforge_docs/site/sitemap.xml.gz +0 -0
  148. caddforge_docs-0.3.0.dist-info/METADATA +158 -0
  149. caddforge_docs-0.3.0.dist-info/RECORD +152 -0
  150. caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
  151. caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
  152. caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
caddforge_docs/site/index.html ADDED
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+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
947
+
948
+
949
+ <div class="md-nav__link md-nav__container">
950
+ <a href="pipelines/" class="md-nav__link ">
951
+
952
+
953
+
954
+ <span class="md-ellipsis">
955
+
956
+
957
+ Pipelines
958
+
959
+
960
+
961
+ </span>
962
+
963
+
964
+
965
+ </a>
966
+
967
+
968
+ <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
969
+ <span class="md-nav__icon md-icon"></span>
970
+ </label>
971
+
972
+ </div>
973
+
974
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
975
+ <label class="md-nav__title" for="__nav_5">
976
+ <span class="md-nav__icon md-icon"></span>
977
+
978
+
979
+ Pipelines
980
+
981
+
982
+ </label>
983
+ <ul class="md-nav__list" data-md-scrollfix>
984
+
985
+
986
+
987
+
988
+
989
+
990
+
991
+ <li class="md-nav__item">
992
+ <a href="pipelines/specification/" class="md-nav__link">
993
+
994
+
995
+
996
+ <span class="md-ellipsis">
997
+
998
+
999
+ Specification
1000
+
1001
+
1002
+
1003
+ </span>
1004
+
1005
+
1006
+
1007
+ </a>
1008
+ </li>
1009
+
1010
+
1011
+
1012
+
1013
+
1014
+
1015
+
1016
+
1017
+
1018
+
1019
+ <li class="md-nav__item">
1020
+ <a href="pipelines/artifacts/" class="md-nav__link">
1021
+
1022
+
1023
+
1024
+ <span class="md-ellipsis">
1025
+
1026
+
1027
+ Artifacts
1028
+
1029
+
1030
+
1031
+ </span>
1032
+
1033
+
1034
+
1035
+ </a>
1036
+ </li>
1037
+
1038
+
1039
+
1040
+
1041
+
1042
+
1043
+
1044
+
1045
+
1046
+
1047
+ <li class="md-nav__item">
1048
+ <a href="pipelines/built-ins/" class="md-nav__link">
1049
+
1050
+
1051
+
1052
+ <span class="md-ellipsis">
1053
+
1054
+
1055
+ Built-in Stages
1056
+
1057
+
1058
+
1059
+ </span>
1060
+
1061
+
1062
+
1063
+ </a>
1064
+ </li>
1065
+
1066
+
1067
+
1068
+
1069
+
1070
+
1071
+
1072
+
1073
+
1074
+
1075
+ <li class="md-nav__item">
1076
+ <a href="pipelines/examples/" class="md-nav__link">
1077
+
1078
+
1079
+
1080
+ <span class="md-ellipsis">
1081
+
1082
+
1083
+ Examples
1084
+
1085
+
1086
+
1087
+ </span>
1088
+
1089
+
1090
+
1091
+ </a>
1092
+ </li>
1093
+
1094
+
1095
+
1096
+
1097
+ </ul>
1098
+ </nav>
1099
+
1100
+ </li>
1101
+
1102
+
1103
+
1104
+
1105
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1106
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1107
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1108
+
1109
+
1110
+
1111
+
1112
+
1113
+
1114
+
1115
+
1116
+
1117
+
1118
+
1119
+
1120
+
1121
+
1122
+
1123
+
1124
+
1125
+
1126
+
1127
+
1128
+
1129
+
1130
+
1131
+
1132
+
1133
+
1134
+
1135
+
1136
+
1137
+
1138
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1139
+
1140
+
1141
+
1142
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
1143
+
1144
+
1145
+ <div class="md-nav__link md-nav__container">
1146
+ <a href="plugins/" class="md-nav__link ">
1147
+
1148
+
1149
+
1150
+ <span class="md-ellipsis">
1151
+
1152
+
1153
+ Plugins
1154
+
1155
+
1156
+
1157
+ </span>
1158
+
1159
+
1160
+
1161
+ </a>
1162
+
1163
+
1164
+ <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
1165
+ <span class="md-nav__icon md-icon"></span>
1166
+ </label>
1167
+
1168
+ </div>
1169
+
1170
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
1171
+ <label class="md-nav__title" for="__nav_6">
1172
+ <span class="md-nav__icon md-icon"></span>
1173
+
1174
+
1175
+ Plugins
1176
+
1177
+
1178
+ </label>
1179
+ <ul class="md-nav__list" data-md-scrollfix>
1180
+
1181
+
1182
+
1183
+
1184
+
1185
+
1186
+
1187
+ <li class="md-nav__item">
1188
+ <a href="plugins/version-matrix/" class="md-nav__link">
1189
+
1190
+
1191
+
1192
+ <span class="md-ellipsis">
1193
+
1194
+
1195
+ Version Matrix
1196
+
1197
+
1198
+
1199
+ </span>
1200
+
1201
+
1202
+
1203
+ </a>
1204
+ </li>
1205
+
1206
+
1207
+
1208
+
1209
+
1210
+
1211
+
1212
+
1213
+
1214
+
1215
+ <li class="md-nav__item">
1216
+ <a href="plugins/docking/" class="md-nav__link">
1217
+
1218
+
1219
+
1220
+ <span class="md-ellipsis">
1221
+
1222
+
1223
+ Docking
1224
+
1225
+
1226
+
1227
+ </span>
1228
+
1229
+
1230
+
1231
+ </a>
1232
+ </li>
1233
+
1234
+
1235
+
1236
+
1237
+
1238
+
1239
+
1240
+
1241
+
1242
+
1243
+ <li class="md-nav__item">
1244
+ <a href="plugins/descriptors/" class="md-nav__link">
1245
+
1246
+
1247
+
1248
+ <span class="md-ellipsis">
1249
+
1250
+
1251
+ Descriptors
1252
+
1253
+
1254
+
1255
+ </span>
1256
+
1257
+
1258
+
1259
+ </a>
1260
+ </li>
1261
+
1262
+
1263
+
1264
+
1265
+
1266
+
1267
+
1268
+
1269
+
1270
+
1271
+ <li class="md-nav__item">
1272
+ <a href="plugins/md/" class="md-nav__link">
1273
+
1274
+
1275
+
1276
+ <span class="md-ellipsis">
1277
+
1278
+
1279
+ MD
1280
+
1281
+
1282
+
1283
+ </span>
1284
+
1285
+
1286
+
1287
+ </a>
1288
+ </li>
1289
+
1290
+
1291
+
1292
+
1293
+
1294
+
1295
+
1296
+
1297
+
1298
+
1299
+ <li class="md-nav__item">
1300
+ <a href="plugins/fep/" class="md-nav__link">
1301
+
1302
+
1303
+
1304
+ <span class="md-ellipsis">
1305
+
1306
+
1307
+ FEP
1308
+
1309
+
1310
+
1311
+ </span>
1312
+
1313
+
1314
+
1315
+ </a>
1316
+ </li>
1317
+
1318
+
1319
+
1320
+
1321
+
1322
+
1323
+
1324
+
1325
+
1326
+
1327
+ <li class="md-nav__item">
1328
+ <a href="plugins/qm/" class="md-nav__link">
1329
+
1330
+
1331
+
1332
+ <span class="md-ellipsis">
1333
+
1334
+
1335
+ QM
1336
+
1337
+
1338
+
1339
+ </span>
1340
+
1341
+
1342
+
1343
+ </a>
1344
+ </li>
1345
+
1346
+
1347
+
1348
+
1349
+
1350
+
1351
+
1352
+
1353
+
1354
+
1355
+ <li class="md-nav__item">
1356
+ <a href="plugins/ml/" class="md-nav__link">
1357
+
1358
+
1359
+
1360
+ <span class="md-ellipsis">
1361
+
1362
+
1363
+ ML
1364
+
1365
+
1366
+
1367
+ </span>
1368
+
1369
+
1370
+
1371
+ </a>
1372
+ </li>
1373
+
1374
+
1375
+
1376
+
1377
+
1378
+
1379
+
1380
+
1381
+
1382
+
1383
+ <li class="md-nav__item">
1384
+ <a href="plugins/datascience/" class="md-nav__link">
1385
+
1386
+
1387
+
1388
+ <span class="md-ellipsis">
1389
+
1390
+
1391
+ Data Science
1392
+
1393
+
1394
+
1395
+ </span>
1396
+
1397
+
1398
+
1399
+ </a>
1400
+ </li>
1401
+
1402
+
1403
+
1404
+
1405
+ </ul>
1406
+ </nav>
1407
+
1408
+ </li>
1409
+
1410
+
1411
+
1412
+
1413
+
1414
+
1415
+
1416
+
1417
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1418
+
1419
+
1420
+
1421
+
1422
+
1423
+
1424
+
1425
+
1426
+
1427
+
1428
+
1429
+
1430
+
1431
+
1432
+
1433
+
1434
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1435
+
1436
+
1437
+
1438
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" >
1439
+
1440
+
1441
+ <div class="md-nav__link md-nav__container">
1442
+ <a href="gui/" class="md-nav__link ">
1443
+
1444
+
1445
+
1446
+ <span class="md-ellipsis">
1447
+
1448
+
1449
+ GUI
1450
+
1451
+
1452
+
1453
+ </span>
1454
+
1455
+
1456
+
1457
+ </a>
1458
+
1459
+
1460
+ <label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
1461
+ <span class="md-nav__icon md-icon"></span>
1462
+ </label>
1463
+
1464
+ </div>
1465
+
1466
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
1467
+ <label class="md-nav__title" for="__nav_7">
1468
+ <span class="md-nav__icon md-icon"></span>
1469
+
1470
+
1471
+ GUI
1472
+
1473
+
1474
+ </label>
1475
+ <ul class="md-nav__list" data-md-scrollfix>
1476
+
1477
+
1478
+
1479
+
1480
+
1481
+
1482
+
1483
+ <li class="md-nav__item">
1484
+ <a href="gui/walkthrough/" class="md-nav__link">
1485
+
1486
+
1487
+
1488
+ <span class="md-ellipsis">
1489
+
1490
+
1491
+ Walkthrough
1492
+
1493
+
1494
+
1495
+ </span>
1496
+
1497
+
1498
+
1499
+ </a>
1500
+ </li>
1501
+
1502
+
1503
+
1504
+
1505
+
1506
+
1507
+
1508
+
1509
+
1510
+
1511
+ <li class="md-nav__item">
1512
+ <a href="gui/plugin-authoring/" class="md-nav__link">
1513
+
1514
+
1515
+
1516
+ <span class="md-ellipsis">
1517
+
1518
+
1519
+ Plugin GUI Authoring
1520
+
1521
+
1522
+
1523
+ </span>
1524
+
1525
+
1526
+
1527
+ </a>
1528
+ </li>
1529
+
1530
+
1531
+
1532
+
1533
+ </ul>
1534
+ </nav>
1535
+
1536
+ </li>
1537
+
1538
+
1539
+
1540
+
1541
+
1542
+
1543
+
1544
+
1545
+
1546
+
1547
+
1548
+
1549
+
1550
+
1551
+
1552
+
1553
+
1554
+
1555
+
1556
+
1557
+
1558
+
1559
+
1560
+
1561
+
1562
+
1563
+
1564
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1565
+
1566
+
1567
+
1568
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" >
1569
+
1570
+
1571
+ <div class="md-nav__link md-nav__container">
1572
+ <a href="reference/" class="md-nav__link ">
1573
+
1574
+
1575
+
1576
+ <span class="md-ellipsis">
1577
+
1578
+
1579
+ Reference
1580
+
1581
+
1582
+
1583
+ </span>
1584
+
1585
+
1586
+
1587
+ </a>
1588
+
1589
+
1590
+ <label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
1591
+ <span class="md-nav__icon md-icon"></span>
1592
+ </label>
1593
+
1594
+ </div>
1595
+
1596
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
1597
+ <label class="md-nav__title" for="__nav_8">
1598
+ <span class="md-nav__icon md-icon"></span>
1599
+
1600
+
1601
+ Reference
1602
+
1603
+
1604
+ </label>
1605
+ <ul class="md-nav__list" data-md-scrollfix>
1606
+
1607
+
1608
+
1609
+
1610
+
1611
+
1612
+
1613
+ <li class="md-nav__item">
1614
+ <a href="reference/api/" class="md-nav__link">
1615
+
1616
+
1617
+
1618
+ <span class="md-ellipsis">
1619
+
1620
+
1621
+ Public Python API
1622
+
1623
+
1624
+
1625
+ </span>
1626
+
1627
+
1628
+
1629
+ </a>
1630
+ </li>
1631
+
1632
+
1633
+
1634
+
1635
+
1636
+
1637
+
1638
+
1639
+
1640
+
1641
+ <li class="md-nav__item">
1642
+ <a href="examples/" class="md-nav__link">
1643
+
1644
+
1645
+
1646
+ <span class="md-ellipsis">
1647
+
1648
+
1649
+ Example Library
1650
+
1651
+
1652
+
1653
+ </span>
1654
+
1655
+
1656
+
1657
+ </a>
1658
+ </li>
1659
+
1660
+
1661
+
1662
+
1663
+
1664
+
1665
+
1666
+
1667
+
1668
+
1669
+ <li class="md-nav__item">
1670
+ <a href="examples/quickstart/" class="md-nav__link">
1671
+
1672
+
1673
+
1674
+ <span class="md-ellipsis">
1675
+
1676
+
1677
+ Example Data Provenance
1678
+
1679
+
1680
+
1681
+ </span>
1682
+
1683
+
1684
+
1685
+ </a>
1686
+ </li>
1687
+
1688
+
1689
+
1690
+
1691
+ </ul>
1692
+ </nav>
1693
+
1694
+ </li>
1695
+
1696
+
1697
+
1698
+
1699
+
1700
+
1701
+
1702
+
1703
+
1704
+
1705
+
1706
+
1707
+
1708
+
1709
+
1710
+
1711
+
1712
+
1713
+
1714
+
1715
+
1716
+
1717
+
1718
+
1719
+
1720
+
1721
+
1722
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1723
+
1724
+
1725
+
1726
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
1727
+
1728
+
1729
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1730
+
1731
+
1732
+
1733
+ <span class="md-ellipsis">
1734
+
1735
+
1736
+ Explanation
1737
+
1738
+
1739
+
1740
+ </span>
1741
+
1742
+
1743
+
1744
+ <span class="md-nav__icon md-icon"></span>
1745
+ </label>
1746
+
1747
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1748
+ <label class="md-nav__title" for="__nav_9">
1749
+ <span class="md-nav__icon md-icon"></span>
1750
+
1751
+
1752
+ Explanation
1753
+
1754
+
1755
+ </label>
1756
+ <ul class="md-nav__list" data-md-scrollfix>
1757
+
1758
+
1759
+
1760
+
1761
+
1762
+
1763
+
1764
+ <li class="md-nav__item">
1765
+ <a href="explanation/reproducibility/" class="md-nav__link">
1766
+
1767
+
1768
+
1769
+ <span class="md-ellipsis">
1770
+
1771
+
1772
+ Reproducibility
1773
+
1774
+
1775
+
1776
+ </span>
1777
+
1778
+
1779
+
1780
+ </a>
1781
+ </li>
1782
+
1783
+
1784
+
1785
+
1786
+
1787
+
1788
+
1789
+
1790
+
1791
+
1792
+ <li class="md-nav__item">
1793
+ <a href="explanation/references/" class="md-nav__link">
1794
+
1795
+
1796
+
1797
+ <span class="md-ellipsis">
1798
+
1799
+
1800
+ Method References
1801
+
1802
+
1803
+
1804
+ </span>
1805
+
1806
+
1807
+
1808
+ </a>
1809
+ </li>
1810
+
1811
+
1812
+
1813
+
1814
+
1815
+
1816
+
1817
+
1818
+
1819
+
1820
+ <li class="md-nav__item">
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+ <a href="explanation/third-party-notices/" class="md-nav__link">
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+
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+ <h1 id="caddforge">CADDForge<a class="headerlink" href="#caddforge" title="Permanent link">&para;</a></h1>
2207
+ <p>CADDForge is the central CADD toolbox framework for running computational chemistry and modelling
2208
+ workflows through a consistent Python API, CLI, plugin system, job model, and pipeline layer.</p>
2209
+ <p>The project is split into a lightweight core package and tool-specific plugin packages:</p>
2210
+ <table>
2211
+ <thead>
2212
+ <tr>
2213
+ <th>Package</th>
2214
+ <th>Purpose</th>
2215
+ </tr>
2216
+ </thead>
2217
+ <tbody>
2218
+ <tr>
2219
+ <td><code>caddforge</code></td>
2220
+ <td>Metadata-only installer for the complete public toolbox.</td>
2221
+ </tr>
2222
+ <tr>
2223
+ <td><code>caddforge-core</code></td>
2224
+ <td>Core abstractions, CLI, job execution, backends, pipeline engine, plugin registry.</td>
2225
+ </tr>
2226
+ <tr>
2227
+ <td><code>caddforge-docking</code></td>
2228
+ <td>Docking and rescoring workflows.</td>
2229
+ </tr>
2230
+ <tr>
2231
+ <td><code>caddforge-descriptors</code></td>
2232
+ <td>Molecular descriptor and property workflows.</td>
2233
+ </tr>
2234
+ <tr>
2235
+ <td><code>caddforge-md</code></td>
2236
+ <td>Molecular dynamics setup and execution workflows.</td>
2237
+ </tr>
2238
+ <tr>
2239
+ <td><code>caddforge-fep</code></td>
2240
+ <td>Absolute and relative free-energy workflows.</td>
2241
+ </tr>
2242
+ <tr>
2243
+ <td><code>caddforge-qm</code></td>
2244
+ <td>COSMO-RS transfer-free-energy workflow.</td>
2245
+ </tr>
2246
+ <tr>
2247
+ <td><code>caddforge-ml</code></td>
2248
+ <td>Machine-learning workflows and model utilities.</td>
2249
+ </tr>
2250
+ <tr>
2251
+ <td><code>caddforge-datascience</code></td>
2252
+ <td>Generic data-science utilities exposed as CADDForge tools.</td>
2253
+ </tr>
2254
+ <tr>
2255
+ <td><code>caddforge-gui</code></td>
2256
+ <td>Web GUI and plugin GUI extension runtime.</td>
2257
+ </tr>
2258
+ <tr>
2259
+ <td><code>caddforge-docs</code></td>
2260
+ <td>Installed documentation and optional browser command.</td>
2261
+ </tr>
2262
+ </tbody>
2263
+ </table>
2264
+ <h2 id="design-goals">Design goals<a class="headerlink" href="#design-goals" title="Permanent link">&para;</a></h2>
2265
+ <ul>
2266
+ <li>Standardize CADD workflow execution without putting tool-specific science into core.</li>
2267
+ <li>Keep workflows backend-agnostic through local and HPC backends.</li>
2268
+ <li>Store configs, logs, metadata, and results in predictable run directories.</li>
2269
+ <li>Let plugins declare their inputs, outputs, and pipeline contracts.</li>
2270
+ <li>Support large-scale file and path-collection scatter through the central pipeline executor.</li>
2271
+ </ul>
2272
+ <h2 id="choose-a-starting-point">Choose a starting point<a class="headerlink" href="#choose-a-starting-point" title="Permanent link">&para;</a></h2>
2273
+ <ul>
2274
+ <li>New users: <a href="getting-started/installation/">install selected components</a>, then
2275
+ run the <a href="getting-started/first-workflow/">local workflow tutorial</a>.</li>
2276
+ <li>Pipeline users: follow the <a href="getting-started/first-pipeline/">small pipeline tutorial</a>
2277
+ before adapting scientific templates.</li>
2278
+ <li>Python users: consult the <a href="reference/api/">public API</a> and <a href="examples/">example library</a>.</li>
2279
+ <li>Contributors: read <a href="development/contributing/">development guidance</a>.</li>
2280
+ </ul>
2281
+ <p>The planned <code>caddforge</code> distribution installs the complete public bundle, including
2282
+ <code>caddforge-docs</code> and its offline viewer. Its updated public release is still pending;
2283
+ install published components individually in the meantime. <code>caddforge-core</code> owns
2284
+ Python imports and the CLI, and docs remain optional for selective installations.
2285
+ These pages describe the tagged public component set; check the
2286
+ <a href="plugins/version-matrix/">version matrix</a> and <a href="development/release-readiness/">release prerequisites</a>
2287
+ for availability.</p>
2288
+ <h2 id="quick-links">Quick links<a class="headerlink" href="#quick-links" title="Permanent link">&para;</a></h2>
2289
+ <ul>
2290
+ <li><a href="getting-started/installation/">Installation</a></li>
2291
+ <li><a href="getting-started/first-workflow/">First workflow</a></li>
2292
+ <li><a href="core/cli/">CLI reference</a></li>
2293
+ <li><a href="pipelines/">Pipeline documentation</a></li>
2294
+ <li><a href="plugins/">Plugin catalog</a></li>
2295
+ <li><a href="development/tool-authoring/">Tool authoring</a></li>
2296
+ </ul>
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