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/gui/plugin-authoring/index.html ADDED
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950
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951
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953
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959
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960
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978
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1006
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1021
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1076
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1080
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1126
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1128
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1139
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1146
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1151
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1152
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1153
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1154
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1166
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1167
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1169
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1170
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1172
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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1195
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1199
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1201
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1202
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1210
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1211
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1222
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1223
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1226
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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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1238
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1258
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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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1285
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1286
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1290
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1294
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1295
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1311
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1313
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1314
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1317
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1321
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1322
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1328
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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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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
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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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1399
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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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1424
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1427
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1428
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1448
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1449
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1450
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1451
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1452
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1453
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1454
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1462
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1463
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1464
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1465
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1466
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1467
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1468
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1469
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1470
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1471
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1472
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1473
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1474
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1475
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1476
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1477
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1478
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1479
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1480
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1481
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1482
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1483
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1486
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1487
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1488
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1489
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1490
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1491
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1492
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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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1509
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1510
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1511
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1512
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1514
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1520
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1527
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1530
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1558
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1562
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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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1580
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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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1597
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1598
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1599
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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
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1624
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1635
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1636
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1637
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1638
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1639
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1640
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1641
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1642
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1643
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1644
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1645
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1646
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1647
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1648
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1649
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1650
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1651
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1652
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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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1662
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1663
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1664
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1665
+
1666
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1667
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1668
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1669
+
1670
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1671
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1672
+
1673
+
1674
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1675
+
1676
+
1677
+
1678
+ </a>
1679
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1680
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1681
+
1682
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1683
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1684
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1685
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1686
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1687
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1688
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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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1698
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1699
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1700
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1701
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1702
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1703
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1704
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1705
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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
+
1725
+
1726
+ <span class="md-ellipsis">
1727
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1728
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1729
+ Explanation
1730
+
1731
+
1732
+
1733
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1734
+
1735
+
1736
+
1737
+ <span class="md-nav__icon md-icon"></span>
1738
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1739
+
1740
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1741
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1742
+ <span class="md-nav__icon md-icon"></span>
1743
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1744
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1745
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1746
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1747
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1748
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1749
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1750
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1751
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1752
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1755
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1757
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1758
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1759
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1760
+
1761
+
1762
+ <span class="md-ellipsis">
1763
+
1764
+
1765
+ Reproducibility
1766
+
1767
+
1768
+
1769
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1770
+
1771
+
1772
+
1773
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1774
+ </li>
1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
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1784
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1785
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1786
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1787
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1788
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1789
+
1790
+ <span class="md-ellipsis">
1791
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1792
+
1793
+ Method References
1794
+
1795
+
1796
+
1797
+ </span>
1798
+
1799
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1800
+
1801
+ </a>
1802
+ </li>
1803
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1804
+
1805
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1806
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1807
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1808
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1809
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1810
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1811
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1812
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1813
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1814
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2141
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2145
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2147
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2148
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2149
+
2150
+ Frontend helpers
2151
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2152
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2153
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2154
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2155
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2156
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2157
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2158
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2159
+ <span class="md-ellipsis">
2160
+
2161
+ Backend helpers
2162
+
2163
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2164
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2165
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2166
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2167
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2168
+ </ul>
2169
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2170
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2173
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2174
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2177
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2178
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2179
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2180
+
2181
+
2182
+
2183
+
2184
+
2185
+
2186
+
2187
+
2188
+ <h1 id="plugin-gui-authoring">Plugin GUI Authoring<a class="headerlink" href="#plugin-gui-authoring" title="Permanent link">&para;</a></h1>
2189
+ <p>Plugin GUI extensions should use the shared GUI runtime instead of duplicating common upload,
2190
+ staging, path-token, and job-listing behavior.</p>
2191
+ <h2 id="frontend-helpers">Frontend helpers<a class="headerlink" href="#frontend-helpers" title="Permanent link">&para;</a></h2>
2192
+ <p>Import shared primitives from the plugin UI kit:</p>
2193
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="k">import</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="nx">field</span><span class="p">,</span><span class="w"> </span><span class="nx">row</span><span class="p">,</span><span class="w"> </span><span class="nx">section</span><span class="p">,</span><span class="w"> </span><span class="nx">createFilePicker</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="kr">from</span><span class="w"> </span><span class="s2">"../../assets/plugin_uikit.js"</span><span class="p">;</span>
2194
+ </code></pre></div>
2195
+ <p>Common helpers include:</p>
2196
+ <ul>
2197
+ <li><code>stepSection</code></li>
2198
+ <li><code>modeSwitchSection</code></li>
2199
+ <li><code>backendSection</code></li>
2200
+ <li><code>submitBar</code></li>
2201
+ <li><code>createPathOrFileInput</code></li>
2202
+ </ul>
2203
+ <p>Docking and pose-analysis pages can reuse the Mol* viewer helper:</p>
2204
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="k">import</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="nx">createDockingMolstarViewer</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="kr">from</span><span class="w"> </span><span class="s2">"../../assets/molstar_viewer.js"</span><span class="p">;</span>
2205
+ </code></pre></div>
2206
+ <h2 id="backend-helpers">Backend helpers<a class="headerlink" href="#backend-helpers" title="Permanent link">&para;</a></h2>
2207
+ <p>Extension routers can use:</p>
2208
+ <ul>
2209
+ <li><code>encode_path_token</code></li>
2210
+ <li><code>decode_path_token</code></li>
2211
+ <li><code>list_tool_jobs</code></li>
2212
+ <li><code>make_staging_dir</code></li>
2213
+ <li><code>store_upload</code></li>
2214
+ <li><code>move_to_directory</code></li>
2215
+ <li><code>ensure_job_within_run_dir</code></li>
2216
+ </ul>
2217
+ <p>For runtime concerns such as backend construction and job submission, use <code>caddforge.core.execution</code>.</p>
2218
+
2219
+
2220
+
2221
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2222
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2223
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2224
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2225
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2226
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