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/examples/index.html ADDED
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959
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978
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980
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981
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982
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983
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984
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985
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986
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987
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988
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1016
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1017
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1020
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1021
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1076
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1080
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1126
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1127
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1146
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1152
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1174
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1177
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1178
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1181
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1182
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1183
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1202
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1206
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1210
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1211
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1223
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1227
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1230
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1232
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1234
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1235
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1236
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1238
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1239
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1255
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1257
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1258
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1259
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1260
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1279
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1283
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1286
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1287
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1288
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1289
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1290
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1291
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1292
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1293
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1294
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1295
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1296
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1300
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1301
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1311
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1312
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1313
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1314
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1315
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1316
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1317
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1318
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1319
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1320
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1321
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1322
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1323
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1324
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1325
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1326
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1327
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1328
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1329
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1331
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1356
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1357
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1361
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1362
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1363
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1364
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1365
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1366
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1367
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1368
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1369
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1370
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1371
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1372
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1373
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1374
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1375
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1376
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1377
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1378
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1379
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1380
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1381
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1382
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1383
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1384
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1385
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1386
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1387
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1388
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1389
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1390
+ <span class="md-nav__icon md-icon"></span>
1391
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1392
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1393
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1394
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1395
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1396
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1397
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1398
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1400
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1403
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1404
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1405
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1406
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1407
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1408
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1409
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1410
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1411
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1412
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1413
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1414
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1415
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1416
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1417
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1418
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1419
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1420
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1421
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1422
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1423
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1433
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1434
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1435
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1438
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1439
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1440
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1441
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1442
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1443
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1444
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1445
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1446
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1447
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1448
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1449
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1450
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1451
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1456
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1457
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1459
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1489
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1493
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1494
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1495
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1496
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1497
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1498
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1499
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1500
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1501
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1502
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1503
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1504
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1505
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1506
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1507
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1508
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1510
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1511
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1512
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1513
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1514
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1515
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1516
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1517
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1518
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1519
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1520
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1521
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1522
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1523
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1526
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1528
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1529
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1530
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1532
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1538
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1539
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1540
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1541
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1542
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1543
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1544
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1545
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1546
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1547
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1548
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1549
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1550
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1551
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1552
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1553
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1554
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1555
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1556
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1557
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1558
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1559
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1560
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1561
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1562
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1563
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1564
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1565
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1566
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1567
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1568
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1569
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1570
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
+
1582
+ Example Library
1583
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1584
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1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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1594
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1595
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1596
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1597
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1598
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1599
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1600
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1601
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1602
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1603
+
1604
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1605
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1606
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1607
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1608
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1609
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1610
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1611
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1612
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1613
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1614
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1615
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1616
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1617
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1618
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1619
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1620
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1621
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1622
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1623
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
1624
+
1625
+ <li class="md-nav__item">
1626
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1627
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1628
+
1629
+ Scientific configuration templates
1630
+
1631
+ </span>
1632
+ </a>
1633
+
1634
+ </li>
1635
+
1636
+ <li class="md-nav__item">
1637
+ <a href="#run-a-downloaded-template" class="md-nav__link">
1638
+ <span class="md-ellipsis">
1639
+
1640
+ Run a downloaded template
1641
+
1642
+ </span>
1643
+ </a>
1644
+
1645
+ </li>
1646
+
1647
+ <li class="md-nav__item">
1648
+ <a href="#units-and-preparation" class="md-nav__link">
1649
+ <span class="md-ellipsis">
1650
+
1651
+ Units and preparation
1652
+
1653
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1654
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1655
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1656
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1657
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1658
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1659
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1660
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1661
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1663
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1664
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1665
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1666
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1667
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1668
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1669
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1670
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1671
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1672
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1673
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1674
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1675
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1676
+
1677
+
1678
+ <span class="md-ellipsis">
1679
+
1680
+
1681
+ Example Data Provenance
1682
+
1683
+
1684
+
1685
+ </span>
1686
+
1687
+
1688
+
1689
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1690
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1691
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1692
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1693
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1694
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1695
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1696
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1697
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1699
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1704
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1706
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1707
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1708
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1709
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1710
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1711
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1712
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1713
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1714
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1715
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1716
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1717
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1718
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1719
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1720
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1721
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1722
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1723
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1724
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1725
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1726
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1727
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1728
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1729
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1730
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1731
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1732
+
1733
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1734
+
1735
+
1736
+
1737
+ <span class="md-ellipsis">
1738
+
1739
+
1740
+ Explanation
1741
+
1742
+
1743
+
1744
+ </span>
1745
+
1746
+
1747
+
1748
+ <span class="md-nav__icon md-icon"></span>
1749
+ </label>
1750
+
1751
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1752
+ <label class="md-nav__title" for="__nav_9">
1753
+ <span class="md-nav__icon md-icon"></span>
1754
+
1755
+
1756
+ Explanation
1757
+
1758
+
1759
+ </label>
1760
+ <ul class="md-nav__list" data-md-scrollfix>
1761
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1762
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1763
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1764
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1765
+
1766
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1767
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1768
+ <li class="md-nav__item">
1769
+ <a href="../explanation/reproducibility/" class="md-nav__link">
1770
+
1771
+
1772
+
1773
+ <span class="md-ellipsis">
1774
+
1775
+
1776
+ Reproducibility
1777
+
1778
+
1779
+
1780
+ </span>
1781
+
1782
+
1783
+
1784
+ </a>
1785
+ </li>
1786
+
1787
+
1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
+ <li class="md-nav__item">
1797
+ <a href="../explanation/references/" class="md-nav__link">
1798
+
1799
+
1800
+
1801
+ <span class="md-ellipsis">
1802
+
1803
+
1804
+ Method References
1805
+
1806
+
1807
+
1808
+ </span>
1809
+
1810
+
1811
+
1812
+ </a>
1813
+ </li>
1814
+
1815
+
1816
+
1817
+
1818
+
1819
+
1820
+
1821
+
1822
+
1823
+
1824
+ <li class="md-nav__item">
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+ <a href="../explanation/third-party-notices/" class="md-nav__link">
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+
1827
+
1828
+
1829
+ <span class="md-ellipsis">
1830
+
1831
+
1832
+ Third-party Notices
1833
+
1834
+
1835
+
1836
+ </span>
1837
+
1838
+
1839
+
1840
+ </a>
1841
+ </li>
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+ </ul>
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+ </nav>
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+ </li>
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+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+
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+
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+
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+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
1890
+
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+
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+ <div class="md-nav__link md-nav__container">
1893
+ <a href="../development/" class="md-nav__link ">
1894
+
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+
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+
1897
+ <span class="md-ellipsis">
1898
+
1899
+
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+ Development
1901
+
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+
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+
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+ </span>
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+
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+
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+
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+ </a>
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+
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+
1911
+ <label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
1912
+ <span class="md-nav__icon md-icon"></span>
1913
+ </label>
1914
+
1915
+ </div>
1916
+
1917
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
1918
+ <label class="md-nav__title" for="__nav_10">
1919
+ <span class="md-nav__icon md-icon"></span>
1920
+
1921
+
1922
+ Development
1923
+
1924
+
1925
+ </label>
1926
+ <ul class="md-nav__list" data-md-scrollfix>
1927
+
1928
+
1929
+
1930
+
1931
+
1932
+
1933
+
1934
+ <li class="md-nav__item">
1935
+ <a href="../development/release-notes/" class="md-nav__link">
1936
+
1937
+
1938
+
1939
+ <span class="md-ellipsis">
1940
+
1941
+
1942
+ Release Notes
1943
+
1944
+
1945
+
1946
+ </span>
1947
+
1948
+
1949
+
1950
+ </a>
1951
+ </li>
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+
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+
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+
1955
+
1956
+
1957
+
1958
+
1959
+
1960
+
1961
+
1962
+ <li class="md-nav__item">
1963
+ <a href="../development/tool-authoring/" class="md-nav__link">
1964
+
1965
+
1966
+
1967
+ <span class="md-ellipsis">
1968
+
1969
+
1970
+ Tool Authoring
1971
+
1972
+
1973
+
1974
+ </span>
1975
+
1976
+
1977
+
1978
+ </a>
1979
+ </li>
1980
+
1981
+
1982
+
1983
+
1984
+
1985
+
1986
+
1987
+
1988
+
1989
+
1990
+ <li class="md-nav__item">
1991
+ <a href="../development/documentation/" class="md-nav__link">
1992
+
1993
+
1994
+
1995
+ <span class="md-ellipsis">
1996
+
1997
+
1998
+ Documentation
1999
+
2000
+
2001
+
2002
+ </span>
2003
+
2004
+
2005
+
2006
+ </a>
2007
+ </li>
2008
+
2009
+
2010
+
2011
+
2012
+
2013
+
2014
+
2015
+
2016
+
2017
+
2018
+ <li class="md-nav__item">
2019
+ <a href="../development/contributing/" class="md-nav__link">
2020
+
2021
+
2022
+
2023
+ <span class="md-ellipsis">
2024
+
2025
+
2026
+ Contributing
2027
+
2028
+
2029
+
2030
+ </span>
2031
+
2032
+
2033
+
2034
+ </a>
2035
+ </li>
2036
+
2037
+
2038
+
2039
+
2040
+
2041
+
2042
+
2043
+
2044
+
2045
+
2046
+ <li class="md-nav__item">
2047
+ <a href="../development/security/" class="md-nav__link">
2048
+
2049
+
2050
+
2051
+ <span class="md-ellipsis">
2052
+
2053
+
2054
+ Security Reporting
2055
+
2056
+
2057
+
2058
+ </span>
2059
+
2060
+
2061
+
2062
+ </a>
2063
+ </li>
2064
+
2065
+
2066
+
2067
+
2068
+
2069
+
2070
+
2071
+
2072
+
2073
+
2074
+ <li class="md-nav__item">
2075
+ <a href="../development/release-readiness/" class="md-nav__link">
2076
+
2077
+
2078
+
2079
+ <span class="md-ellipsis">
2080
+
2081
+
2082
+ Release Readiness
2083
+
2084
+
2085
+
2086
+ </span>
2087
+
2088
+
2089
+
2090
+ </a>
2091
+ </li>
2092
+
2093
+
2094
+
2095
+
2096
+
2097
+
2098
+
2099
+
2100
+
2101
+
2102
+ <li class="md-nav__item">
2103
+ <a href="../development/ci-publishing/" class="md-nav__link">
2104
+
2105
+
2106
+
2107
+ <span class="md-ellipsis">
2108
+
2109
+
2110
+ CI and Publishing
2111
+
2112
+
2113
+
2114
+ </span>
2115
+
2116
+
2117
+
2118
+ </a>
2119
+ </li>
2120
+
2121
+
2122
+
2123
+
2124
+ </ul>
2125
+ </nav>
2126
+
2127
+ </li>
2128
+
2129
+
2130
+
2131
+ </ul>
2132
+ </nav>
2133
+ </div>
2134
+ </div>
2135
+ </div>
2136
+
2137
+
2138
+
2139
+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2140
+ <div class="md-sidebar__scrollwrap">
2141
+ <div class="md-sidebar__inner">
2142
+
2143
+
2144
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2145
+
2146
+
2147
+
2148
+
2149
+
2150
+
2151
+ <label class="md-nav__title" for="__toc">
2152
+ <span class="md-nav__icon md-icon"></span>
2153
+ Table of contents
2154
+ </label>
2155
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2156
+
2157
+ <li class="md-nav__item">
2158
+ <a href="#scientific-configuration-templates" class="md-nav__link">
2159
+ <span class="md-ellipsis">
2160
+
2161
+ Scientific configuration templates
2162
+
2163
+ </span>
2164
+ </a>
2165
+
2166
+ </li>
2167
+
2168
+ <li class="md-nav__item">
2169
+ <a href="#run-a-downloaded-template" class="md-nav__link">
2170
+ <span class="md-ellipsis">
2171
+
2172
+ Run a downloaded template
2173
+
2174
+ </span>
2175
+ </a>
2176
+
2177
+ </li>
2178
+
2179
+ <li class="md-nav__item">
2180
+ <a href="#units-and-preparation" class="md-nav__link">
2181
+ <span class="md-ellipsis">
2182
+
2183
+ Units and preparation
2184
+
2185
+ </span>
2186
+ </a>
2187
+
2188
+ </li>
2189
+
2190
+ </ul>
2191
+
2192
+ </nav>
2193
+ </div>
2194
+ </div>
2195
+ </div>
2196
+
2197
+
2198
+
2199
+ <div class="md-content" data-md-component="content">
2200
+
2201
+ <article class="md-content__inner md-typeset">
2202
+
2203
+
2204
+
2205
+
2206
+
2207
+
2208
+
2209
+
2210
+ <h1 id="example-library">Example Library<a class="headerlink" href="#example-library" title="Permanent link">&para;</a></h1>
2211
+ <p>Start with the <a href="../getting-started/first-workflow/">local workflow</a> and <a href="../getting-started/first-pipeline/">small pipeline</a>. Their synthetic inputs and expected outputs are included and exercised by integration tests. See <a href="quickstart/">data provenance</a>.</p>
2212
+ <h2 id="scientific-configuration-templates">Scientific configuration templates<a class="headerlink" href="#scientific-configuration-templates" title="Permanent link">&para;</a></h2>
2213
+ <p>These templates accompany the public plugin pages. They need prepared inputs and the scientific runtimes listed below. They are schema-checked against the tagged components in the <a href="../plugins/version-matrix/">version matrix</a>; engine execution is not part of the docs-only CI. Replace placeholders, check molecular preparation, and scale compute settings before running a scientific job. They do not download experimental data.</p>
2214
+ <table>
2215
+ <thead>
2216
+ <tr>
2217
+ <th>Workflow</th>
2218
+ <th>Configuration</th>
2219
+ <th>Runtime / preparation</th>
2220
+ </tr>
2221
+ </thead>
2222
+ <tbody>
2223
+ <tr>
2224
+ <td><a href="../plugins/docking/#unidock"><code>docking/unidock</code></a></td>
2225
+ <td><a href="tools/docking-unidock.yaml">YAML</a></td>
2226
+ <td>Uni-Dock executable, supported GPU; prepared PDBQT receptor and ligand SDF; replace box center/size</td>
2227
+ </tr>
2228
+ <tr>
2229
+ <td><a href="../plugins/docking/#idockya"><code>docking/idockya</code></a></td>
2230
+ <td><a href="tools/docking-idockya.yaml">YAML</a></td>
2231
+ <td>pyocl-idor/OpenChemLib (Java 21+); receptor and native ligand SDF in the same frame</td>
2232
+ </tr>
2233
+ <tr>
2234
+ <td><a href="../plugins/docking/#gnina"><code>docking/gnina</code></a></td>
2235
+ <td><a href="tools/docking-gnina.yaml">YAML</a></td>
2236
+ <td>GNINA executable; prepared receptor and ligands; review CNN/GPU settings</td>
2237
+ </tr>
2238
+ <tr>
2239
+ <td><a href="../plugins/descriptors/#ani-psa"><code>descriptors/ani-psa</code></a></td>
2240
+ <td><a href="tools/descriptors-ani-psa.yaml">YAML</a></td>
2241
+ <td>RDKit, TorchANI and model weights; check allowed elements and conformer settings</td>
2242
+ </tr>
2243
+ <tr>
2244
+ <td><a href="../plugins/descriptors/#phesa"><code>descriptors/phesa</code></a></td>
2245
+ <td><a href="tools/descriptors-phesa.yaml">YAML</a></td>
2246
+ <td>pyocl-idor/OpenChemLib (Java 21+); validated reference chemistry and coordinate-frame handling</td>
2247
+ </tr>
2248
+ <tr>
2249
+ <td><a href="../plugins/descriptors/#ani-conformers"><code>descriptors/ani-conformers</code></a></td>
2250
+ <td><a href="tools/descriptors-ani-conformers.yaml">YAML</a></td>
2251
+ <td>RDKit, TorchANI and model weights; SMILES and supported elements</td>
2252
+ </tr>
2253
+ <tr>
2254
+ <td><a href="../plugins/descriptors/#cluster-molecules"><code>descriptors/cluster-molecules</code></a></td>
2255
+ <td><a href="tools/descriptors-cluster-molecules.yaml">YAML</a></td>
2256
+ <td>RDKit and declared clustering dependencies; CSV/SMILES/SDF inputs; select a sensible cluster count</td>
2257
+ </tr>
2258
+ <tr>
2259
+ <td><a href="../plugins/md/#fix-structure"><code>md/fix-structure</code></a></td>
2260
+ <td><a href="tools/md-fix-structure.yaml">YAML</a></td>
2261
+ <td>OpenMM/PDBFixer and matching force fields; check protonation, termini, and untouched cofactors</td>
2262
+ </tr>
2263
+ <tr>
2264
+ <td><a href="../plugins/md/#center-and-align"><code>md/center-and-align</code></a></td>
2265
+ <td><a href="tools/md-center-and-align.yaml">YAML</a></td>
2266
+ <td>MDAnalysis; matching topology and trajectory, atom selections</td>
2267
+ </tr>
2268
+ <tr>
2269
+ <td><a href="../plugins/md/#extract-frames"><code>md/extract-frames</code></a></td>
2270
+ <td><a href="tools/md-extract-frames.yaml">YAML</a></td>
2271
+ <td>MDAnalysis and applicable trajectory readers; frame/time selections</td>
2272
+ </tr>
2273
+ <tr>
2274
+ <td><a href="../plugins/md/#cluster-representative"><code>md/cluster-representative</code></a></td>
2275
+ <td><a href="tools/md-cluster-representative.yaml">YAML</a></td>
2276
+ <td>MDAnalysis and clustering stack; matching topology/trajectory and representative criteria</td>
2277
+ </tr>
2278
+ <tr>
2279
+ <td><a href="../plugins/md/#plain-md"><code>md/plain-md</code></a></td>
2280
+ <td><a href="tools/md-plain-md.yaml">YAML</a></td>
2281
+ <td>OpenMM and preparation/parameterization stack; authoritative protein/ligand chemistry</td>
2282
+ </tr>
2283
+ <tr>
2284
+ <td><a href="../plugins/md/#minimize"><code>md/minimize</code></a></td>
2285
+ <td><a href="tools/md-minimize.yaml">YAML</a></td>
2286
+ <td>OpenMM, ParmEd and AmberTools for automatic preparation; or validated prepared topology and mapping</td>
2287
+ </tr>
2288
+ <tr>
2289
+ <td><a href="../plugins/md/#openbpmd"><code>md/openbpmd</code></a></td>
2290
+ <td><a href="tools/md-openbpmd.yaml">YAML</a></td>
2291
+ <td>OpenMM, OpenBPMD preparation stack and AmberTools; complete complex and ligand chemistry</td>
2292
+ </tr>
2293
+ <tr>
2294
+ <td><a href="../plugins/md/#grand"><code>md/grand</code></a></td>
2295
+ <td><a href="tools/md-grand.yaml">YAML</a></td>
2296
+ <td>grand, OpenMM, OpenMMTools/force fields and OpenFF; ligand-centered pocket and parameterized complex</td>
2297
+ </tr>
2298
+ <tr>
2299
+ <td><a href="../plugins/md/#inducia"><code>md/inducia</code></a></td>
2300
+ <td><a href="tools/md-inducia.yaml">YAML</a></td>
2301
+ <td>Public descriptor/docking dependencies, GNINA, grand, OpenMM, AmberTools and OpenBPMD; prepared inputs</td>
2302
+ </tr>
2303
+ <tr>
2304
+ <td><a href="../plugins/fep/#openfe-abfe"><code>fep/openfe-abfe</code></a></td>
2305
+ <td><a href="tools/fep-openfe-abfe.yaml">YAML</a></td>
2306
+ <td>OpenFE, OpenFF and parameterization stack; prepared complex, convergence assessment</td>
2307
+ </tr>
2308
+ <tr>
2309
+ <td><a href="../plugins/fep/#openfe-rbfe-septop"><code>fep/openfe-rbfe-septop</code></a></td>
2310
+ <td><a href="tools/fep-openfe-rbfe-septop.yaml">YAML</a></td>
2311
+ <td>OpenFE/SepTop runtime, ligand mapping and parameterization; scientifically suitable paired systems</td>
2312
+ </tr>
2313
+ <tr>
2314
+ <td><a href="../plugins/qm/#transfer-free-energy"><code>qm/transfer-free-energy</code></a></td>
2315
+ <td><a href="tools/qm-transfer-free-energy.yaml">YAML</a></td>
2316
+ <td>PySCF/openCOSMO-RS stack; conformers, solvent structures, and standard state</td>
2317
+ </tr>
2318
+ <tr>
2319
+ <td><a href="../plugins/ml/#simple-gp"><code>ml/simple-gp</code></a></td>
2320
+ <td><a href="tools/ml-simple-gp.yaml">YAML</a></td>
2321
+ <td>Declared GP/ML stack; numeric CSV features and training/prediction split</td>
2322
+ </tr>
2323
+ <tr>
2324
+ <td><a href="../plugins/ml/#pca"><code>ml/pca</code></a></td>
2325
+ <td><a href="tools/ml-pca.yaml">YAML</a></td>
2326
+ <td>Declared ML stack; numeric CSV and appropriate preprocessing</td>
2327
+ </tr>
2328
+ <tr>
2329
+ <td><a href="../plugins/ml/#model-zoo"><code>ml/model-zoo</code></a></td>
2330
+ <td><a href="tools/ml-model-zoo.yaml">YAML</a></td>
2331
+ <td>Dependencies for selected registry models; leakage-free training/validation data</td>
2332
+ </tr>
2333
+ <tr>
2334
+ <td><a href="../plugins/ml/#model-factory"><code>ml/model-factory</code></a></td>
2335
+ <td><a href="tools/ml-model-factory.yaml">YAML</a></td>
2336
+ <td>Dependencies for selected registry models; explicit target/task and split</td>
2337
+ </tr>
2338
+ <tr>
2339
+ <td><a href="../plugins/ml/#explore-classifier"><code>ml/explore-classifier</code></a></td>
2340
+ <td><a href="tools/ml-explore-classifier.yaml">YAML</a></td>
2341
+ <td>Interactive UI dependencies and prepared classification data</td>
2342
+ </tr>
2343
+ <tr>
2344
+ <td><a href="../plugins/datascience/#csv-scatter"><code>datascience/csv-scatter</code></a></td>
2345
+ <td><a href="tools/datascience-csv-scatter.yaml">YAML</a></td>
2346
+ <td>pandas/Bokeh; CSV columns and optional RDKit for molecule hover</td>
2347
+ </tr>
2348
+ <tr>
2349
+ <td><a href="../plugins/datascience/#distribution-diagnostics"><code>datascience/distribution-diagnostics</code></a></td>
2350
+ <td><a href="tools/datascience-distribution-diagnostics.yaml">YAML</a></td>
2351
+ <td>pandas/SciPy/Matplotlib; numeric CSV column; runnable synthetic tutorial also supplied</td>
2352
+ </tr>
2353
+ </tbody>
2354
+ </table>
2355
+ <h2 id="run-a-downloaded-template">Run a downloaded template<a class="headerlink" href="#run-a-downloaded-template" title="Permanent link">&para;</a></h2>
2356
+ <p>Save <a href="run_tool.py">run_tool.py</a> beside a chosen configuration. Supply all input files,
2357
+ then run from that directory so relative workflow paths resolve consistently:</p>
2358
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics
2359
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics<span class="w"> </span>--config<span class="w"> </span>diagnostics.yaml
2360
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>python<span class="w"> </span>run_tool.py<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics<span class="w"> </span>diagnostics.yaml
2361
+ </code></pre></div>
2362
+ <p>Use your template's section, tool, and filename in these commands. The Python runner
2363
+ uses <code>get_tool</code> and <code>submit_workflow</code>, passes declared input ports for runtime staging,
2364
+ and checks the canonical result. For Slurm, it prints the submitted job ID; inspect
2365
+ status before reading completed outputs. Per-plugin pages explain expected files and
2366
+ result keys. No generic CLI command validates the scientific suitability of inputs.</p>
2367
+ <h2 id="units-and-preparation">Units and preparation<a class="headerlink" href="#units-and-preparation" title="Permanent link">&para;</a></h2>
2368
+ <table>
2369
+ <thead>
2370
+ <tr>
2371
+ <th>Family</th>
2372
+ <th>Quantities to record</th>
2373
+ </tr>
2374
+ </thead>
2375
+ <tbody>
2376
+ <tr>
2377
+ <td>Docking / alignment</td>
2378
+ <td>Coordinate frame and distance units; score definition, not an inferred affinity unit</td>
2379
+ </tr>
2380
+ <tr>
2381
+ <td>MD / minimization</td>
2382
+ <td>Length/time/temperature units in field names; engine energy units, force field, and restraint definitions</td>
2383
+ </tr>
2384
+ <tr>
2385
+ <td>FEP / QM</td>
2386
+ <td>Energy units reported by the selected engine, temperature, standard state, uncertainty/convergence</td>
2387
+ </tr>
2388
+ <tr>
2389
+ <td>Descriptors</td>
2390
+ <td>Descriptor/model definition; PheSA frame behavior; dimensionless similarities where appropriate</td>
2391
+ </tr>
2392
+ <tr>
2393
+ <td>ML / data science</td>
2394
+ <td>Feature/target units, transformations, split and seed; synthetic examples are dimensionless</td>
2395
+ </tr>
2396
+ </tbody>
2397
+ </table>
2398
+ <p>See <a href="../explanation/reproducibility/">scientific interpretation</a> and
2399
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2400
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