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/explanation/third-party-notices/index.html ADDED
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942
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943
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944
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945
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946
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947
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948
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949
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950
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951
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952
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953
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954
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955
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956
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957
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958
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959
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960
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961
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962
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963
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964
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965
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966
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967
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968
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969
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970
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971
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972
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973
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974
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975
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976
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977
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978
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979
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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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989
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990
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991
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992
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993
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994
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995
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996
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997
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1000
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1002
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1003
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1004
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1005
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1006
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1007
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1008
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1009
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1011
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1012
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1013
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1014
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1015
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1016
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1017
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1018
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1019
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1020
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1021
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1022
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1023
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1024
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1025
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1026
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1062
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1064
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1065
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1066
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1067
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1068
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1069
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1070
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1071
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1072
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1073
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1074
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1075
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1076
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1077
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1078
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1079
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1080
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1081
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1082
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1083
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1084
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1085
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1086
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1087
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1088
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1089
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1090
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1091
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1092
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1093
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1094
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1095
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1096
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1097
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1098
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1099
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1100
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1101
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1102
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1103
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1107
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1109
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1110
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1111
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1112
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1113
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1114
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1115
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1116
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1117
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1118
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1119
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1120
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1121
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1122
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1123
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1124
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1125
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1126
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1127
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1128
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1129
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1130
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1131
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1132
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1133
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1134
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1135
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1136
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1137
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1138
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1139
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1140
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1141
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1142
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1143
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1144
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1145
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1146
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1147
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1148
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1149
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1150
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1151
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1152
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1153
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1154
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1155
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1156
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1157
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1168
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1169
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1170
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1171
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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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1184
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1185
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1186
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1187
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1188
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1189
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1190
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1191
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1192
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1193
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1194
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1195
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1196
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1197
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1198
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1199
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1200
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1201
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1202
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1203
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1204
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1205
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1206
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1207
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1208
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1216
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1217
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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1230
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1231
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1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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1245
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1246
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1247
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1248
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1249
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1250
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1251
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1252
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1253
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1254
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1255
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1256
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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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1268
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1281
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1282
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1283
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1284
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1285
+ ML
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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1297
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1298
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1299
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1300
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1301
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1302
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1303
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1304
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1305
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1306
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1307
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1308
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1309
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1310
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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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1330
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1331
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1332
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1333
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1357
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1358
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1359
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1360
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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
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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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1400
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1401
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1402
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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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1424
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1425
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1426
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1427
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1428
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1429
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1437
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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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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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1471
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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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1484
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1485
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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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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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1524
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1525
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1526
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1527
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1528
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1529
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1530
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1531
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1532
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1533
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1534
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1535
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1536
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1537
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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
+
1543
+ Public Python API
1544
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1545
+
1546
+
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
+ Example Library
1572
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1573
+
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
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1582
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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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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
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1604
+
1605
+
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
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1624
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1625
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1626
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1627
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1628
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1629
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1630
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1631
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1632
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1633
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1634
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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
+
1652
+
1653
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1654
+
1655
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1656
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1657
+ <span class="md-ellipsis">
1658
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1659
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1660
+ Explanation
1661
+
1662
+
1663
+
1664
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1665
+
1666
+
1667
+
1668
+ <span class="md-nav__icon md-icon"></span>
1669
+ </label>
1670
+
1671
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="true">
1672
+ <label class="md-nav__title" for="__nav_9">
1673
+ <span class="md-nav__icon md-icon"></span>
1674
+
1675
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1676
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1677
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1678
+
1679
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1680
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1681
+
1682
+
1683
+
1684
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1685
+
1686
+
1687
+
1688
+ <li class="md-nav__item">
1689
+ <a href="../reproducibility/" class="md-nav__link">
1690
+
1691
+
1692
+
1693
+ <span class="md-ellipsis">
1694
+
1695
+
1696
+ Reproducibility
1697
+
1698
+
1699
+
1700
+ </span>
1701
+
1702
+
1703
+
1704
+ </a>
1705
+ </li>
1706
+
1707
+
1708
+
1709
+
1710
+
1711
+
1712
+
1713
+
1714
+
1715
+
1716
+ <li class="md-nav__item">
1717
+ <a href="../references/" class="md-nav__link">
1718
+
1719
+
1720
+
1721
+ <span class="md-ellipsis">
1722
+
1723
+
1724
+ Method References
1725
+
1726
+
1727
+
1728
+ </span>
1729
+
1730
+
1731
+
1732
+ </a>
1733
+ </li>
1734
+
1735
+
1736
+
1737
+
1738
+
1739
+
1740
+
1741
+
1742
+
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
+ <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
+
1761
+ Third-party Notices
1762
+
1763
+
1764
+
1765
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1766
+
1767
+
1768
+
1769
+ <span class="md-nav__icon md-icon"></span>
1770
+ </label>
1771
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1772
+ <a href="./" class="md-nav__link md-nav__link--active">
1773
+
1774
+
1775
+
1776
+ <span class="md-ellipsis">
1777
+
1778
+
1779
+ Third-party Notices
1780
+
1781
+
1782
+
1783
+ </span>
1784
+
1785
+
1786
+
1787
+ </a>
1788
+
1789
+
1790
+
1791
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
1792
+
1793
+
1794
+
1795
+
1796
+
1797
+
1798
+ <label class="md-nav__title" for="__toc">
1799
+ <span class="md-nav__icon md-icon"></span>
1800
+ Table of contents
1801
+ </label>
1802
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
1803
+
1804
+ <li class="md-nav__item">
1805
+ <a href="#theme-and-rendered-documentation" class="md-nav__link">
1806
+ <span class="md-ellipsis">
1807
+
1808
+ Theme and rendered documentation
1809
+
1810
+ </span>
1811
+ </a>
1812
+
1813
+ </li>
1814
+
1815
+ <li class="md-nav__item">
1816
+ <a href="#javascript-and-styles" class="md-nav__link">
1817
+ <span class="md-ellipsis">
1818
+
1819
+ JavaScript and styles
1820
+
1821
+ </span>
1822
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1823
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1824
+ </li>
1825
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1826
+ <li class="md-nav__item">
1827
+ <a href="#icons" class="md-nav__link">
1828
+ <span class="md-ellipsis">
1829
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1830
+ Icons
1831
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1832
+ </span>
1833
+ </a>
1834
+
1835
+ </li>
1836
+
1837
+ <li class="md-nav__item">
1838
+ <a href="#scientific-runtime-dependencies" class="md-nav__link">
1839
+ <span class="md-ellipsis">
1840
+
1841
+ Scientific runtime dependencies
1842
+
1843
+ </span>
1844
+ </a>
1845
+
1846
+ </li>
1847
+
1848
+ <li class="md-nav__item">
1849
+ <a href="#other-caddforge-packages" class="md-nav__link">
1850
+ <span class="md-ellipsis">
1851
+
1852
+ Other CADDForge packages
1853
+
1854
+ </span>
1855
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1856
+
1857
+ </li>
1858
+
1859
+ </ul>
1860
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1861
+ </nav>
1862
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1863
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1864
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1865
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1866
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1867
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1868
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1869
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1870
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1871
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1872
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1877
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1879
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1900
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1907
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1908
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1911
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
1912
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+ <div class="md-nav__link md-nav__container">
1915
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1916
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1917
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1918
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1919
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1920
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1921
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1922
+ Development
1923
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1924
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1925
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1926
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1927
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1928
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1929
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1930
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1931
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1932
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1933
+ <label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
1934
+ <span class="md-nav__icon md-icon"></span>
1935
+ </label>
1936
+
1937
+ </div>
1938
+
1939
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
1940
+ <label class="md-nav__title" for="__nav_10">
1941
+ <span class="md-nav__icon md-icon"></span>
1942
+
1943
+
1944
+ Development
1945
+
1946
+
1947
+ </label>
1948
+ <ul class="md-nav__list" data-md-scrollfix>
1949
+
1950
+
1951
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1952
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1954
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1955
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1956
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1957
+ <a href="../../development/release-notes/" class="md-nav__link">
1958
+
1959
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1960
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1961
+ <span class="md-ellipsis">
1962
+
1963
+
1964
+ Release Notes
1965
+
1966
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1967
+
1968
+ </span>
1969
+
1970
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1971
+
1972
+ </a>
1973
+ </li>
1974
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1975
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1976
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1977
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1978
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1979
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1980
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1981
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1982
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1983
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1984
+ <li class="md-nav__item">
1985
+ <a href="../../development/tool-authoring/" class="md-nav__link">
1986
+
1987
+
1988
+
1989
+ <span class="md-ellipsis">
1990
+
1991
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1992
+ Tool Authoring
1993
+
1994
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1995
+
1996
+ </span>
1997
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1998
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1999
+
2000
+ </a>
2001
+ </li>
2002
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2005
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2008
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2013
+ <a href="../../development/documentation/" class="md-nav__link">
2014
+
2015
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2017
+ <span class="md-ellipsis">
2018
+
2019
+
2020
+ Documentation
2021
+
2022
+
2023
+
2024
+ </span>
2025
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2026
+
2027
+
2028
+ </a>
2029
+ </li>
2030
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2031
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2032
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2033
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2034
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2035
+
2036
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2037
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2038
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2039
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2040
+ <li class="md-nav__item">
2041
+ <a href="../../development/contributing/" class="md-nav__link">
2042
+
2043
+
2044
+
2045
+ <span class="md-ellipsis">
2046
+
2047
+
2048
+ Contributing
2049
+
2050
+
2051
+
2052
+ </span>
2053
+
2054
+
2055
+
2056
+ </a>
2057
+ </li>
2058
+
2059
+
2060
+
2061
+
2062
+
2063
+
2064
+
2065
+
2066
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2067
+
2068
+ <li class="md-nav__item">
2069
+ <a href="../../development/security/" class="md-nav__link">
2070
+
2071
+
2072
+
2073
+ <span class="md-ellipsis">
2074
+
2075
+
2076
+ Security Reporting
2077
+
2078
+
2079
+
2080
+ </span>
2081
+
2082
+
2083
+
2084
+ </a>
2085
+ </li>
2086
+
2087
+
2088
+
2089
+
2090
+
2091
+
2092
+
2093
+
2094
+
2095
+
2096
+ <li class="md-nav__item">
2097
+ <a href="../../development/release-readiness/" class="md-nav__link">
2098
+
2099
+
2100
+
2101
+ <span class="md-ellipsis">
2102
+
2103
+
2104
+ Release Readiness
2105
+
2106
+
2107
+
2108
+ </span>
2109
+
2110
+
2111
+
2112
+ </a>
2113
+ </li>
2114
+
2115
+
2116
+
2117
+
2118
+
2119
+
2120
+
2121
+
2122
+
2123
+
2124
+ <li class="md-nav__item">
2125
+ <a href="../../development/ci-publishing/" class="md-nav__link">
2126
+
2127
+
2128
+
2129
+ <span class="md-ellipsis">
2130
+
2131
+
2132
+ CI and Publishing
2133
+
2134
+
2135
+
2136
+ </span>
2137
+
2138
+
2139
+
2140
+ </a>
2141
+ </li>
2142
+
2143
+
2144
+
2145
+
2146
+ </ul>
2147
+ </nav>
2148
+
2149
+ </li>
2150
+
2151
+
2152
+
2153
+ </ul>
2154
+ </nav>
2155
+ </div>
2156
+ </div>
2157
+ </div>
2158
+
2159
+
2160
+
2161
+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2162
+ <div class="md-sidebar__scrollwrap">
2163
+ <div class="md-sidebar__inner">
2164
+
2165
+
2166
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2167
+
2168
+
2169
+
2170
+
2171
+
2172
+
2173
+ <label class="md-nav__title" for="__toc">
2174
+ <span class="md-nav__icon md-icon"></span>
2175
+ Table of contents
2176
+ </label>
2177
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2178
+
2179
+ <li class="md-nav__item">
2180
+ <a href="#theme-and-rendered-documentation" class="md-nav__link">
2181
+ <span class="md-ellipsis">
2182
+
2183
+ Theme and rendered documentation
2184
+
2185
+ </span>
2186
+ </a>
2187
+
2188
+ </li>
2189
+
2190
+ <li class="md-nav__item">
2191
+ <a href="#javascript-and-styles" class="md-nav__link">
2192
+ <span class="md-ellipsis">
2193
+
2194
+ JavaScript and styles
2195
+
2196
+ </span>
2197
+ </a>
2198
+
2199
+ </li>
2200
+
2201
+ <li class="md-nav__item">
2202
+ <a href="#icons" class="md-nav__link">
2203
+ <span class="md-ellipsis">
2204
+
2205
+ Icons
2206
+
2207
+ </span>
2208
+ </a>
2209
+
2210
+ </li>
2211
+
2212
+ <li class="md-nav__item">
2213
+ <a href="#scientific-runtime-dependencies" class="md-nav__link">
2214
+ <span class="md-ellipsis">
2215
+
2216
+ Scientific runtime dependencies
2217
+
2218
+ </span>
2219
+ </a>
2220
+
2221
+ </li>
2222
+
2223
+ <li class="md-nav__item">
2224
+ <a href="#other-caddforge-packages" class="md-nav__link">
2225
+ <span class="md-ellipsis">
2226
+
2227
+ Other CADDForge packages
2228
+
2229
+ </span>
2230
+ </a>
2231
+
2232
+ </li>
2233
+
2234
+ </ul>
2235
+
2236
+ </nav>
2237
+ </div>
2238
+ </div>
2239
+ </div>
2240
+
2241
+
2242
+
2243
+ <div class="md-content" data-md-component="content">
2244
+
2245
+ <article class="md-content__inner md-typeset">
2246
+
2247
+
2248
+
2249
+
2250
+
2251
+
2252
+
2253
+
2254
+ <h1 id="third-party-notices">Third-party Notices<a class="headerlink" href="#third-party-notices" title="Permanent link">&para;</a></h1>
2255
+ <p>CADDForge's own code is MIT licensed. Components included in the rendered
2256
+ documentation retain their upstream copyright and licence terms. The complete
2257
+ texts below accompany the site, its wheel, and its source distribution.</p>
2258
+ <h2 id="theme-and-rendered-documentation">Theme and rendered documentation<a class="headerlink" href="#theme-and-rendered-documentation" title="Permanent link">&para;</a></h2>
2259
+ <table>
2260
+ <thead>
2261
+ <tr>
2262
+ <th>Component</th>
2263
+ <th>Upstream</th>
2264
+ <th>Licence text</th>
2265
+ </tr>
2266
+ </thead>
2267
+ <tbody>
2268
+ <tr>
2269
+ <td>Material for MkDocs</td>
2270
+ <td><a href="https://github.com/squidfunk/mkdocs-material">squidfunk/mkdocs-material</a></td>
2271
+ <td><a href="../../assets/licenses/mkdocs-material-LICENSE.txt">MIT</a></td>
2272
+ </tr>
2273
+ <tr>
2274
+ <td>ProperDocs</td>
2275
+ <td><a href="https://github.com/properdocs/properdocs">properdocs/properdocs</a></td>
2276
+ <td><a href="../../assets/licenses/properdocs-LICENSE.txt">BSD</a></td>
2277
+ </tr>
2278
+ <tr>
2279
+ <td>mkdocstrings</td>
2280
+ <td><a href="https://github.com/mkdocstrings/mkdocstrings">mkdocstrings/mkdocstrings</a></td>
2281
+ <td><a href="../../assets/licenses/mkdocstrings-LICENSE.txt">ISC</a></td>
2282
+ </tr>
2283
+ <tr>
2284
+ <td>mkdocstrings-python</td>
2285
+ <td><a href="https://github.com/mkdocstrings/python">mkdocstrings/python</a></td>
2286
+ <td><a href="../../assets/licenses/mkdocstrings-python-LICENSE.txt">ISC</a></td>
2287
+ </tr>
2288
+ <tr>
2289
+ <td>Section Index</td>
2290
+ <td><a href="https://github.com/oprypin/mkdocs-section-index">oprypin/mkdocs-section-index</a></td>
2291
+ <td><a href="../../assets/licenses/mkdocs-section-index-LICENSE.txt">MIT</a></td>
2292
+ </tr>
2293
+ <tr>
2294
+ <td>PyMdown Extensions</td>
2295
+ <td><a href="https://github.com/facelessuser/pymdown-extensions">facelessuser/pymdown-extensions</a></td>
2296
+ <td><a href="../../assets/licenses/pymdown-extensions-LICENSE.txt">MIT and upstream notices</a></td>
2297
+ </tr>
2298
+ <tr>
2299
+ <td>Material Extensions</td>
2300
+ <td><a href="https://github.com/facelessuser/mkdocs-material-extensions">facelessuser/mkdocs-material-extensions</a></td>
2301
+ <td><a href="../../assets/licenses/mkdocs-material-extensions-LICENSE.txt">MIT</a></td>
2302
+ </tr>
2303
+ </tbody>
2304
+ </table>
2305
+ <h2 id="javascript-and-styles">JavaScript and styles<a class="headerlink" href="#javascript-and-styles" title="Permanent link">&para;</a></h2>
2306
+ <p>The reviewed theme assets come from Material for MkDocs 9.7.7. Its
2307
+ <a href="https://github.com/squidfunk/mkdocs-material/blob/9.7.7/package-lock.json">upstream dependency lockfile</a>
2308
+ records the component versions. Dependencies used only to compile the theme are
2309
+ not themselves shipped as executable build tools.</p>
2310
+ <p>Documentation build dependencies pin this theme version, and the asset hook
2311
+ rejects a different installed version. When upgrading, review the actual bundled
2312
+ components and update the dependency pins, <code>scripts/site_assets.py</code>, this
2313
+ inventory, and the full licence texts together. These build dependencies are not
2314
+ required to view the installed documentation.</p>
2315
+ <table>
2316
+ <thead>
2317
+ <tr>
2318
+ <th>Component</th>
2319
+ <th>Version</th>
2320
+ <th>Upstream</th>
2321
+ <th>Licence text</th>
2322
+ </tr>
2323
+ </thead>
2324
+ <tbody>
2325
+ <tr>
2326
+ <td>clipboard.js</td>
2327
+ <td>2.0.11</td>
2328
+ <td><a href="https://github.com/zenorocha/clipboard.js">zenorocha/clipboard.js</a></td>
2329
+ <td><a href="../../assets/licenses/clipboard-LICENSE.txt">MIT</a></td>
2330
+ </tr>
2331
+ <tr>
2332
+ <td>good-listener / delegate / select</td>
2333
+ <td>1.2.2 / 3.2.0 / 1.1.2</td>
2334
+ <td><a href="https://github.com/zenorocha">Zeno Rocha</a></td>
2335
+ <td><a href="../../assets/licenses/zeno-rocha-components-LICENSE.txt">MIT</a></td>
2336
+ </tr>
2337
+ <tr>
2338
+ <td>tiny-emitter</td>
2339
+ <td>2.1.0</td>
2340
+ <td><a href="https://github.com/scottcorgan/tiny-emitter">scottcorgan/tiny-emitter</a></td>
2341
+ <td><a href="../../assets/licenses/tiny-emitter-LICENSE.txt">MIT</a></td>
2342
+ </tr>
2343
+ <tr>
2344
+ <td>escape-html</td>
2345
+ <td>1.0.3</td>
2346
+ <td><a href="https://github.com/component/escape-html">component/escape-html</a></td>
2347
+ <td><a href="../../assets/licenses/escape-html-LICENSE.txt">MIT</a></td>
2348
+ </tr>
2349
+ <tr>
2350
+ <td>focus-visible</td>
2351
+ <td>5.2.1</td>
2352
+ <td><a href="https://github.com/WICG/focus-visible">WICG/focus-visible</a></td>
2353
+ <td><a href="../../assets/licenses/focus-visible-LICENSE.txt">Upstream notice</a>, <a href="../../assets/licenses/W3C-Software-and-Document-2015.txt">W3C terms</a></td>
2354
+ </tr>
2355
+ <tr>
2356
+ <td>fuzzaldrin-plus</td>
2357
+ <td>0.6.0</td>
2358
+ <td><a href="https://github.com/jeancroy/fuzzaldrin-plus">jeancroy/fuzzaldrin-plus</a></td>
2359
+ <td><a href="../../assets/licenses/fuzzaldrin-plus-LICENSE.txt">MIT</a></td>
2360
+ </tr>
2361
+ <tr>
2362
+ <td>Lunr</td>
2363
+ <td>2.3.9</td>
2364
+ <td><a href="https://github.com/olivernn/lunr.js">olivernn/lunr.js</a></td>
2365
+ <td><a href="../../assets/licenses/lunr-LICENSE.txt">MIT</a></td>
2366
+ </tr>
2367
+ <tr>
2368
+ <td>RxJS</td>
2369
+ <td>7.8.2</td>
2370
+ <td><a href="https://github.com/ReactiveX/rxjs">ReactiveX/rxjs</a></td>
2371
+ <td><a href="../../assets/licenses/rxjs-LICENSE.txt">Apache 2.0</a></td>
2372
+ </tr>
2373
+ <tr>
2374
+ <td>tslib helpers</td>
2375
+ <td>2.7.0</td>
2376
+ <td><a href="https://github.com/microsoft/tslib">microsoft/tslib</a></td>
2377
+ <td><a href="../../assets/licenses/tslib-LICENSE.txt">0BSD</a></td>
2378
+ </tr>
2379
+ <tr>
2380
+ <td>Preact</td>
2381
+ <td>10.28.2</td>
2382
+ <td><a href="https://github.com/preactjs/preact">preactjs/preact</a></td>
2383
+ <td><a href="../../assets/licenses/preact-LICENSE.txt">MIT</a></td>
2384
+ </tr>
2385
+ <tr>
2386
+ <td>material-design-color</td>
2387
+ <td>2.3.2</td>
2388
+ <td><a href="https://github.com/mrmlnc/material-color">mrmlnc/material-color</a></td>
2389
+ <td><a href="../../assets/licenses/material-design-color-LICENSE.txt">MIT</a></td>
2390
+ </tr>
2391
+ <tr>
2392
+ <td>material-shadows</td>
2393
+ <td>3.0.1</td>
2394
+ <td><a href="https://github.com/mrmlnc/material-shadows">mrmlnc/material-shadows</a></td>
2395
+ <td><a href="../../assets/licenses/material-shadows-LICENSE.txt">MIT</a></td>
2396
+ </tr>
2397
+ </tbody>
2398
+ </table>
2399
+ <p>Copyrights include Martin Donath (theme), Zeno Rocha (clipboard and listener
2400
+ utilities), Scott Corgan (emitter), TJ Holowaychuk, Andreas Lubbe and Tiancheng Gu
2401
+ (escaping), WICG contributors (focus), Jean Christophe Roy and GitHub Inc.
2402
+ (fuzzy matching), Oliver Nightingale (search), Google, Netflix, Microsoft and
2403
+ contributors (RxJS), Jason Miller (Preact), and Denis Malinochkin (colours and
2404
+ shadows). The licence files preserve the individual notices.</p>
2405
+ <p>The fuzzaldrin-plus notice was checked against the redistributed original in
2406
+ <a href="https://industrial-assets.io/_licenses.html">IAH's licence inventory</a> and
2407
+ <a href="https://cache.industry.siemens.com/dl/files/030/109824030/att_1153706/v1/OSS_SINEC-NMS_99.pdf">Siemens' software notices</a>.
2408
+ The material-shadows copyright was checked against
2409
+ <a href="https://www.univerge.blue/pdf/emea/meet-open-source-notice-emea.pdf">UNIVERGE BLUE's software notices</a>
2410
+ and its upstream MIT declaration.</p>
2411
+ <p>The site provides English search. The build excludes unused language-search
2412
+ assets, including <code>lunr-languages</code>, TinySegmenter and Wordcut. English search
2413
+ uses Lunr inside the retained search worker. Adding another search language
2414
+ requires reviewing and shipping its licences and any corresponding source
2415
+ obligations before enabling it.</p>
2416
+ <h2 id="icons">Icons<a class="headerlink" href="#icons" title="Permanent link">&para;</a></h2>
2417
+ <p>Material embeds icons from these upstream collections; their original licences
2418
+ are preserved even when only a subset of icons is rendered.</p>
2419
+ <table>
2420
+ <thead>
2421
+ <tr>
2422
+ <th>Collection</th>
2423
+ <th>Upstream</th>
2424
+ <th>Licence text</th>
2425
+ </tr>
2426
+ </thead>
2427
+ <tbody>
2428
+ <tr>
2429
+ <td>Font Awesome Free</td>
2430
+ <td><a href="https://github.com/FortAwesome/Font-Awesome">FortAwesome/Font-Awesome</a></td>
2431
+ <td><a href="../../assets/licenses/fontawesome-LICENSE.txt">CC BY 4.0 icons, OFL fonts, MIT code</a></td>
2432
+ </tr>
2433
+ <tr>
2434
+ <td>Material Design Icons</td>
2435
+ <td><a href="https://github.com/Templarian/MaterialDesign">Templarian/MaterialDesign</a></td>
2436
+ <td><a href="../../assets/licenses/material-LICENSE.txt">Upstream terms</a></td>
2437
+ </tr>
2438
+ <tr>
2439
+ <td>Octicons</td>
2440
+ <td><a href="https://github.com/primer/octicons">primer/octicons</a></td>
2441
+ <td><a href="../../assets/licenses/octicons-LICENSE.txt">MIT</a></td>
2442
+ </tr>
2443
+ <tr>
2444
+ <td>Simple Icons</td>
2445
+ <td><a href="https://github.com/simple-icons/simple-icons">simple-icons/simple-icons</a></td>
2446
+ <td><a href="../../assets/licenses/simple-LICENSE.txt">CC0 and upstream notices</a></td>
2447
+ </tr>
2448
+ </tbody>
2449
+ </table>
2450
+ <h2 id="scientific-runtime-dependencies">Scientific runtime dependencies<a class="headerlink" href="#scientific-runtime-dependencies" title="Permanent link">&para;</a></h2>
2451
+ <p>PyOCL is installed separately as
2452
+ <a href="https://pypi.org/project/pyocl-idor/"><code>pyocl-idor</code></a> and imported as <code>pyocl</code>.
2453
+ Its distribution supplies the Java helper classes and OpenChemLib runtime; these
2454
+ files are not copied into CADDForge wheels or documentation assets. The dependency
2455
+ retains its own licence and upstream notices. Refer to its published distribution
2456
+ and <a href="https://github.com/Actelion/openchemlib">OpenChemLib upstream</a> for attribution
2457
+ and redistribution terms.</p>
2458
+ <p>The <code>third-party/</code> workspace maintains two independent distributions published
2459
+ on PyPI. They are not vendored into CADDForge runtime wheels. Their upstream
2460
+ Python code and parameter data are unchanged; Uni-Dock Tools
2461
+ ships a rebuilt AutoGrid executable with its complete corresponding source.</p>
2462
+ <table>
2463
+ <thead>
2464
+ <tr>
2465
+ <th>Distribution</th>
2466
+ <th>Pinned upstream</th>
2467
+ <th>Terms and licence texts</th>
2468
+ </tr>
2469
+ </thead>
2470
+ <tbody>
2471
+ <tr>
2472
+ <td><a href="https://pypi.org/project/caddforge-opencosmors/0.0.1/"><code>caddforge-opencosmors</code> <code>0.0.1</code></a></td>
2473
+ <td><a href="https://github.com/TUHH-TVT/openCOSMO-RS_py/tree/64e42bbfa1d9eda93714d7a346d5cbfdeb8dc5d1">openCOSMO-RS_py commit 64e42bb</a></td>
2474
+ <td><a href="../../assets/licenses/caddforge-opencosmors-LICENSE.txt">LGPLv3</a>, incorporating <a href="../../assets/licenses/caddforge-opencosmors-COPYING.txt">GPLv3</a></td>
2475
+ </tr>
2476
+ <tr>
2477
+ <td><a href="https://pypi.org/project/caddforge-unidock-tools/1.1.3/"><code>caddforge-unidock-tools</code> <code>1.1.3</code></a></td>
2478
+ <td><a href="https://github.com/dptech-corp/Uni-Dock/tree/caf3161b28f7ceb5aa3b13bc98a505cb76a39db3/unidock_tools">Uni-Dock tag 1.1.3, commit caf3161</a></td>
2479
+ <td>Python code: <a href="../../assets/licenses/caddforge-unidock-tools-LICENSE.txt">Apache-2.0</a>; AutoGrid executable and parameter data: <a href="../../assets/licenses/autogrid-COPYING-GPL-2.txt">GPLv2 or later</a></td>
2480
+ </tr>
2481
+ </tbody>
2482
+ </table>
2483
+ <p>The import names remain <code>opencosmorspy</code> and <code>unidock_tools</code>; the Uni-Dock Tools
2484
+ command remains <code>unidocktools</code>. The openCOSMO-RS licence follows the newer
2485
+ upstream <code>LICENSE</code> and confirmed licence-change commit; its historical README
2486
+ and setup metadata have an outdated GPLv2 statement. Its wheel must be supplied
2487
+ with its matching complete source archive and LGPL/GPL texts.</p>
2488
+ <p>The maintained Uni-Dock Tools distribution replaces its original prebuilt AutoGrid
2489
+ executable with a validated Linux x86-64 build reported as <code>4.2.9+caddforge.1</code>.
2490
+ Its source is <a href="https://github.com/ccsb-scripps/AutoGrid/tree/6d2847beaeac8ff43ca99094707fd74e3ca1ff37">AutoGrid v4.2.9</a>
2491
+ with a documented compatibility patch, including the GPL-licensed directional
2492
+ hydrogen-bond vector loop from
2493
+ <a href="https://github.com/ccsb-scripps/AutoGrid/blob/c3d5eafe08e53c59d4479f9338b6e769e8ccdbb2/main.cpp">commit c3d5eafe</a>.
2494
+ The source, original GPL text, patch, offline build helper, and provenance are
2495
+ included in both its wheel and source archive. Wheel installation places these
2496
+ under <code>share/caddforge-unidock-tools/autogrid/</code> in the Python environment.
2497
+ The matching GCC 11.4.0 OpenMP runtime is statically linked under GPLv3-or-later
2498
+ with the GCC Runtime Library Exception 3.1. Its
2499
+ <a href="../../assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt">GPL text</a>,
2500
+ <a href="../../assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt">exception</a>, and
2501
+ <a href="../../assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt">original notice</a> are included.
2502
+ The exception permits this GCC-compiled combination without changing the
2503
+ licences of the independent AutoGrid and Uni-Dock Tools code. The
2504
+ <code>manylinux_2_28_x86_64</code> wheel needs Linux x86-64 with glibc 2.28 or newer; users
2505
+ need no separate <code>libgomp</code> installation.
2506
+ The old ADFR Suite executable was identified exactly, but its complete source
2507
+ could not be verified; that binary is excluded. Optional BH-tree source files
2508
+ with conflicting MSMS-specific notices are neither distributed nor compiled.</p>
2509
+ <p>The original <code>AD4.1_bound.dat</code> retains the copyright of Garrett M. Morris,
2510
+ David S. Goodsell, Ruth Huey, and Arthur J. Olson. AutoGrid source retains The
2511
+ Scripps Research Institute notices. These components retain GPLv2-or-later terms;
2512
+ the complete distribution is not solely Apache-2.0. All 87 AD4 maps in the three
2513
+ public regression boxes match the original executable exactly. The direct atom
2514
+ scan is slower for AD4 grid generation; current default CADDForge receptor
2515
+ preparation does not generate those grids. GPU docking is not covered by those
2516
+ checks; see the release's <a href="https://github.com/idorsia/caddforge-unidock-tools/blob/v1.1.3/VALIDATION.md">validation report</a>
2517
+ and source README for practical limits.</p>
2518
+ <p>Each distribution preserves upstream authors, original notices and licence files,
2519
+ and records the exact revision and runtime hashes in <code>UPSTREAM.json</code>. CADDForge
2520
+ itself remains MIT licensed; renaming these dependencies does not relicense them.
2521
+ Both published distributions were installed together from public PyPI in a
2522
+ fresh Python 3.12 Linux x86-64 environment. Imports, command help, the bundled
2523
+ AutoGrid executable and source hashes, and a water/ethanol COSMO-RS numerical
2524
+ regression passed. The edited QM and docking sources now require
2525
+ <code>caddforge-opencosmors==0.0.1</code> and <code>caddforge-unidock-tools==1.1.3</code>,
2526
+ respectively. Release updated components and test new bundle pins before
2527
+ claiming a complete public CADDForge installation.</p>
2528
+ <h2 id="other-caddforge-packages">Other CADDForge packages<a class="headerlink" href="#other-caddforge-packages" title="Permanent link">&para;</a></h2>
2529
+ <p>The GUI ships React's full MIT text and copyright notice in
2530
+ <code>caddforge_gui/static/THIRD_PARTY_LICENSES</code>. Its Mol* helper loads the upstream
2531
+ viewer at runtime. The MD package preserves the vendored OpenBPMD notice and MIT
2532
+ licence in its source and wheel. Scientific method citations are listed
2533
+ separately in <a href="../references/">Method References</a>.</p>
2534
+ <p>When changing the theme, frontend dependencies, or embedded assets, review and
2535
+ update these notices and full texts against the actual generated distribution.
2536
+ Preserve embedded upstream comments when rebuilding JavaScript and CSS.</p>
2537
+
2538
+
2539
+
2540
+
2541
+
2542
+
2543
+
2544
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2546
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+ </article>
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