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/getting-started/installation/index.html ADDED
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922
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923
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924
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925
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926
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927
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928
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929
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930
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931
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932
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933
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934
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935
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936
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937
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938
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939
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940
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941
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942
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943
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944
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945
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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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998
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999
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1000
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1001
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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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1010
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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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1027
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1028
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1029
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1030
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1031
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1032
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1033
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1034
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1035
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1036
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1037
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1038
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1039
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1040
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1041
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1042
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1044
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1045
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1047
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1048
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1049
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1050
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1051
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1052
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1053
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1054
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1055
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1056
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1057
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1058
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1059
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1060
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1061
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1062
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1063
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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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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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1104
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1105
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1106
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1107
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1108
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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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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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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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1150
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1151
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1153
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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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1162
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1163
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1164
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1165
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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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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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1267
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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
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1286
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1287
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1288
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1289
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1290
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1291
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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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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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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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1334
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1335
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1336
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1337
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1338
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1339
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1343
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1347
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1355
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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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1374
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1375
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1383
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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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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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1465
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1471
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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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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
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1543
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1544
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1545
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1546
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1547
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1548
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1549
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1550
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1551
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1552
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1553
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1554
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1555
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1556
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1557
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1558
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1559
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1560
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1561
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1562
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1563
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1564
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1565
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1566
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1567
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1568
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1569
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1570
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
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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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1589
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1592
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1595
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1596
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1597
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1598
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1600
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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
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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
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1666
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1667
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1668
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1669
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1670
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1671
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1672
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1673
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1674
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1675
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1676
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1677
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1678
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1679
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1680
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1681
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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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1689
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1690
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1691
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1692
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1693
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1694
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1695
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1696
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1697
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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
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1725
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1726
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1727
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1728
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1729
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1730
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1731
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1732
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1733
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1734
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1735
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1736
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1737
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1738
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1739
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1740
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1741
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1742
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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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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
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1761
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1762
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1763
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1764
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1765
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1766
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1770
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1771
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1772
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1773
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1774
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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
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
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1799
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1800
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1801
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1802
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1803
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1804
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1805
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1806
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1807
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+ Method References
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+ </span>
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+ Security Reporting
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+
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2135
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+ Release Readiness
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+ <a href="../../development/ci-publishing/" class="md-nav__link">
2159
+
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2161
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+ <span class="md-ellipsis">
2163
+
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+
2165
+ CI and Publishing
2166
+
2167
+
2168
+
2169
+ </span>
2170
+
2171
+
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+
2173
+ </a>
2174
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+
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+
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+ </ul>
2180
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2181
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+ </li>
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+
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+ </ul>
2187
+ </nav>
2188
+ </div>
2189
+ </div>
2190
+ </div>
2191
+
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+
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2194
+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2195
+ <div class="md-sidebar__scrollwrap">
2196
+ <div class="md-sidebar__inner">
2197
+
2198
+
2199
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2200
+
2201
+
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+
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+
2204
+
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+
2206
+ <label class="md-nav__title" for="__toc">
2207
+ <span class="md-nav__icon md-icon"></span>
2208
+ Table of contents
2209
+ </label>
2210
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2211
+
2212
+ <li class="md-nav__item">
2213
+ <a href="#choose-the-smallest-environment-for-your-task" class="md-nav__link">
2214
+ <span class="md-ellipsis">
2215
+
2216
+ Choose the smallest environment for your task
2217
+
2218
+ </span>
2219
+ </a>
2220
+
2221
+ </li>
2222
+
2223
+ <li class="md-nav__item">
2224
+ <a href="#install-conda-managed-scientific-stacks-first" class="md-nav__link">
2225
+ <span class="md-ellipsis">
2226
+
2227
+ Install conda-managed scientific stacks first
2228
+
2229
+ </span>
2230
+ </a>
2231
+
2232
+ </li>
2233
+
2234
+ <li class="md-nav__item">
2235
+ <a href="#install-caddforge-packages" class="md-nav__link">
2236
+ <span class="md-ellipsis">
2237
+
2238
+ Install CADDForge packages
2239
+
2240
+ </span>
2241
+ </a>
2242
+
2243
+ </li>
2244
+
2245
+ <li class="md-nav__item">
2246
+ <a href="#external-software" class="md-nav__link">
2247
+ <span class="md-ellipsis">
2248
+
2249
+ External software
2250
+
2251
+ </span>
2252
+ </a>
2253
+
2254
+ </li>
2255
+
2256
+ <li class="md-nav__item">
2257
+ <a href="#pyocl-and-java" class="md-nav__link">
2258
+ <span class="md-ellipsis">
2259
+
2260
+ PyOCL and Java
2261
+
2262
+ </span>
2263
+ </a>
2264
+
2265
+ </li>
2266
+
2267
+ <li class="md-nav__item">
2268
+ <a href="#documentation-package" class="md-nav__link">
2269
+ <span class="md-ellipsis">
2270
+
2271
+ Documentation package
2272
+
2273
+ </span>
2274
+ </a>
2275
+
2276
+ </li>
2277
+
2278
+ <li class="md-nav__item">
2279
+ <a href="#gui-extras" class="md-nav__link">
2280
+ <span class="md-ellipsis">
2281
+
2282
+ GUI extras
2283
+
2284
+ </span>
2285
+ </a>
2286
+
2287
+ </li>
2288
+
2289
+ <li class="md-nav__item">
2290
+ <a href="#migrating-an-existing-installation" class="md-nav__link">
2291
+ <span class="md-ellipsis">
2292
+
2293
+ Migrating an existing installation
2294
+
2295
+ </span>
2296
+ </a>
2297
+
2298
+ </li>
2299
+
2300
+ </ul>
2301
+
2302
+ </nav>
2303
+ </div>
2304
+ </div>
2305
+ </div>
2306
+
2307
+
2308
+
2309
+ <div class="md-content" data-md-component="content">
2310
+
2311
+ <article class="md-content__inner md-typeset">
2312
+
2313
+
2314
+
2315
+
2316
+
2317
+
2318
+
2319
+
2320
+ <h1 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">&para;</a></h1>
2321
+ <p>CADDForge packages require Python 3.10 or newer.</p>
2322
+ <h2 id="choose-the-smallest-environment-for-your-task">Choose the smallest environment for your task<a class="headerlink" href="#choose-the-smallest-environment-for-your-task" title="Permanent link">&para;</a></h2>
2323
+ <p>For the introductory table tutorial, core plus <code>caddforge-datascience</code> is sufficient;
2324
+ no molecular simulation environment is needed. For the generic pipeline tutorial,
2325
+ core alone is sufficient. Scientific plugin extras do not install every external
2326
+ engine, GPU driver, or prepared input dataset.</p>
2327
+ <table>
2328
+ <thead>
2329
+ <tr>
2330
+ <th>Component</th>
2331
+ <th>Declared Python support</th>
2332
+ <th>Validation / runtime scope</th>
2333
+ </tr>
2334
+ </thead>
2335
+ <tbody>
2336
+ <tr>
2337
+ <td>Core and docs</td>
2338
+ <td>Python 3.10+</td>
2339
+ <td>Package CI targets Linux/Python 3.10 and 3.12; local documentation checks also use 3.13</td>
2340
+ </tr>
2341
+ <tr>
2342
+ <td>Full bundle</td>
2343
+ <td>Check each pinned component</td>
2344
+ <td>Release CI targets Linux/Python 3.10 and 3.12; validation of the updated public pins remains pending</td>
2345
+ </tr>
2346
+ <tr>
2347
+ <td>Scientific tools</td>
2348
+ <td>Check plugin and engine requirements</td>
2349
+ <td>External binaries, platform/GPU support, and conda stacks vary; this is not a claim of universal support</td>
2350
+ </tr>
2351
+ </tbody>
2352
+ </table>
2353
+ <h2 id="install-conda-managed-scientific-stacks-first">Install conda-managed scientific stacks first<a class="headerlink" href="#install-conda-managed-scientific-stacks-first" title="Permanent link">&para;</a></h2>
2354
+ <p>If a plugin recommends installing scientific dependencies with conda, install those conda packages
2355
+ before installing any pip packages, including <code>caddforge</code>.</p>
2356
+ <p>Recommended order:</p>
2357
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>caddforge<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.10
2358
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>caddforge
2359
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>
2360
+ <a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="c1"># Install heavy scientific/runtime packages first.</span>
2361
+ <a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>conda<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>openfe<span class="w"> </span>openff-toolkit<span class="w"> </span>rdkit<span class="w"> </span>pdbfixer<span class="w"> </span>openmm
2362
+ <a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a>
2363
+ <a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a><span class="c1"># Install published CADDForge components after the conda environment is complete.</span>
2364
+ <a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-core<span class="o">==</span><span class="m">0</span>.22.0<span class="w"> </span>caddforge-fep<span class="o">==</span><span class="m">0</span>.7.0
2365
+ </code></pre></div>
2366
+ <p>Installing conda packages after pip packages have already populated the environment can replace or
2367
+ downgrade shared dependencies and leave the environment inconsistent. When in doubt, create a fresh
2368
+ environment and install the conda-managed stack first.</p>
2369
+ <p>For Slurm jobs, the compute node also needs access to this environment. See the
2370
+ <a href="../../core/slurm/">Slurm backend guide</a> for packed-environment and wheelhouse options.</p>
2371
+ <h2 id="install-caddforge-packages">Install CADDForge packages<a class="headerlink" href="#install-caddforge-packages" title="Permanent link">&para;</a></h2>
2372
+ <p>The updated public bundle is still awaiting its docs release, final component
2373
+ pins, and full installation validation. Install published components individually
2374
+ for now; the <a href="../../plugins/version-matrix/">version matrix</a> records availability.
2375
+ After that bundle release, this command installs the complete toolbox, including
2376
+ GUI integrations, MD minimization, ML UI dependencies, and installed documentation:</p>
2377
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge
2378
+ </code></pre></div>
2379
+ <p>The metadata-only <code>caddforge</code> bundle installs no modules or commands itself.
2380
+ Its copied metadata retains baseline <code>0.22.1</code> and pins core <code>0.21.0</code>, data science
2381
+ <code>0.4.0</code>, descriptors <code>0.10.1</code>, docking <code>0.6.1</code>, FEP <code>0.6.0</code>, GUI <code>0.5.0</code>, MD <code>0.12.1</code>,
2382
+ ML <code>0.3.0</code>, QM <code>0.2.1</code>, and docs <code>0.2.1</code> for local validation. These inherited pins
2383
+ do not identify releases of the edited public sources. New public component
2384
+ versions are tagged; the bundle pins must be updated and tested with the
2385
+ docs <code>0.3.0</code> before bundle publication.
2386
+ Documentation authoring and test extras are excluded from the runtime bundle.</p>
2387
+ <p>For core alone or selected plugins:</p>
2388
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-core<span class="o">==</span><span class="m">0</span>.22.0
2389
+ <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-qm<span class="o">==</span><span class="m">0</span>.3.0
2390
+ </code></pre></div>
2391
+ <p>Plugins depend directly on <code>caddforge-core</code> and install it automatically. Python imports
2392
+ remain <code>caddforge</code> and CLI commands remain <code>caddforge ...</code>.</p>
2393
+ <p>The versions in the selective-install examples above are published on PyPI.
2394
+ MD <code>0.13.0</code> is tagged and awaiting publication as of 2026-10-15; use its
2395
+ tagged source checkout until it is available on the index. Full-bundle release
2396
+ validation targets Linux on Python 3.10 and 3.12. Installing Python plugins
2397
+ does not install external scientific engines.</p>
2398
+ <p>The bundle's <code>0.x</code> series remains initial development: its public API and supported
2399
+ component set may change. Version <code>1.0.0</code> is reserved for a future stable API commitment.
2400
+ The <a href="../../plugins/version-matrix/">version matrix</a> records tags and publication status.</p>
2401
+ <p>The core package includes <code>conda-pack</code> as a dependency. This provides <code>caddforge pack-env</code>, which
2402
+ creates managed Slurm environment archives and checksum sidecars without a separate <code>conda-pack</code>
2403
+ installation step.</p>
2404
+ <p>For editable installs from checkouts containing the public tags, select the
2405
+ versions in the <a href="../../plugins/version-matrix/">version matrix</a> and install
2406
+ without version overrides:</p>
2407
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>git<span class="w"> </span>-C<span class="w"> </span>../caddforge-core<span class="w"> </span>switch<span class="w"> </span>--detach<span class="w"> </span>v0.22.0
2408
+ <a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>../caddforge-core
2409
+ <a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>git<span class="w"> </span>-C<span class="w"> </span>../caddforge-docking<span class="w"> </span>switch<span class="w"> </span>--detach<span class="w"> </span>v0.7.0
2410
+ <a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span><span class="s2">"../caddforge-docking[gui]"</span>
2411
+ </code></pre></div>
2412
+ <p>For MD before its index publication, use a checkout containing <code>v0.13.0</code>:</p>
2413
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>git<span class="w"> </span>-C<span class="w"> </span>../caddforge-md<span class="w"> </span>switch<span class="w"> </span>--detach<span class="w"> </span>v0.13.0
2414
+ <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>../caddforge-md
2415
+ </code></pre></div>
2416
+ <p>Published artifacts must use their actual public release versions. Temporary
2417
+ VCS version overrides are only for local validation, never for publishing.</p>
2418
+ <p>After installation, verify plugin discovery:</p>
2419
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>caddforge<span class="w"> </span>list-tools
2420
+ </code></pre></div>
2421
+ <h2 id="external-software">External software<a class="headerlink" href="#external-software" title="Permanent link">&para;</a></h2>
2422
+ <p>Some plugins call external scientific software that is not installed by the Python package. Examples
2423
+ include docking engines, QM programs, and MD engines. Check the plugin pages for
2424
+ tool-specific runtime requirements.</p>
2425
+ <h2 id="pyocl-and-java">PyOCL and Java<a class="headerlink" href="#pyocl-and-java" title="Permanent link">&para;</a></h2>
2426
+ <p>QM, descriptors, and docking install the public <code>pyocl-idor&gt;=0.8.3</code> distribution.
2427
+ MD can use it through those plugins, and the complete bundle includes it
2428
+ indirectly. The Python import package remains <code>pyocl</code>.</p>
2429
+ <p>Install Java 21 or newer and point <code>JAVA_HOME</code> to that installation. The affected
2430
+ GitHub workflows already provision Java 21. To check the Python package and JVM
2431
+ in the same environment:</p>
2432
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>show<span class="w"> </span>pyocl-idor
2433
+ <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>java<span class="w"> </span>-version
2434
+ <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import pyocl; print(pyocl.__version__)"</span>
2435
+ </code></pre></div>
2436
+ <p>A JVM lookup or class-version error indicates a missing, misconfigured, or older
2437
+ Java runtime; see <a href="../../how-to/troubleshooting/#pyocl-or-java-fails">troubleshooting</a>.</p>
2438
+ <h2 id="documentation-package">Documentation package<a class="headerlink" href="#documentation-package" title="Permanent link">&para;</a></h2>
2439
+ <p>The planned bundle includes docs automatically. Documentation <code>0.3.0</code> is tagged;
2440
+ its package-index publication is pending. Until then, install the source checkout with
2441
+ <code>python -m pip install ../caddforge-docs</code>. Once its public release is available,
2442
+ core-only and selective plugin installations can install it separately:</p>
2443
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-docs
2444
+ <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>caddforge<span class="w"> </span>docs
2445
+ </code></pre></div>
2446
+ <p>After installing a bundle that includes docs, run <code>caddforge docs</code> directly.</p>
2447
+ <p>Installing this package enables the optional <code>docs</code> command on core 0.21.0 or later. It opens
2448
+ the documentation shipped with the installed docs release and serves until Ctrl+C. The built site
2449
+ works without internet access or documentation build tools. Use <code>--host</code> and <code>--port</code> to choose
2450
+ the listening address, or <code>--no-browser</code> to open the printed URL manually. See the
2451
+ <a href="../../core/cli/#open-documentation">CLI reference</a>.</p>
2452
+ <h2 id="gui-extras">GUI extras<a class="headerlink" href="#gui-extras" title="Permanent link">&para;</a></h2>
2453
+ <p>The planned complete bundle includes GUI extras. For selective installations,
2454
+ install the plugin's GUI extra. Docking and FEP are published; the MD command
2455
+ requires its tagged release to be available on the index:</p>
2456
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span><span class="s2">"caddforge-docking[gui]"</span>
2457
+ <a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span><span class="s2">"caddforge-md[gui]"</span>
2458
+ <a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span><span class="s2">"caddforge-fep[gui]"</span>
2459
+ </code></pre></div>
2460
+ <h2 id="migrating-an-existing-installation">Migrating an existing installation<a class="headerlink" href="#migrating-an-existing-installation" title="Permanent link">&para;</a></h2>
2461
+ <p>Prefer a fresh environment. To migrate the former core distribution in place,
2462
+ install the renamed core and upgrade every retained plugin to its public release.
2463
+ The example below retains docking and QM; adapt that list to your environment:</p>
2464
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>uninstall<span class="w"> </span>caddforge
2465
+ <a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>--upgrade<span class="w"> </span>caddforge-core<span class="w"> </span>caddforge-docking<span class="w"> </span>caddforge-qm
2466
+ <a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>check
2467
+ <a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>caddforge<span class="w"> </span>list-tools
2468
+ </code></pre></div>
2469
+ <p>For a minimal installation, install <code>caddforge-core</code> instead and upgrade every retained
2470
+ plugin to its migrated release. Keep older plugin releases in their original
2471
+ environments: they depend on the legacy
2472
+ <code>caddforge</code> core distribution. Do not install both old and renamed core distributions,
2473
+ because they own the same Python files. If both were installed, remove the old
2474
+ <code>caddforge</code> distribution and force-reinstall <code>caddforge-core</code> afterwards.</p>
2475
+ <p><code>importlib.metadata.version("caddforge-core")</code> reports the runtime version;
2476
+ <code>version("caddforge")</code> reports the optional bundle version. MD provenance distinguishes
2477
+ both. Historical configuration, registry, result, and provenance records remain readable.
2478
+ Uninstalling the new bundle does not uninstall its dependencies.</p>
2479
+
2480
+
2481
+
2482
+
2483
+
2484
+
2485
+
2486
+
2487
+
2488
+
2489
+
2490
+
2491
+
2492
+ </article>
2493
+ </div>
2494
+
2495
+
2496
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
2497
+ </div>
2498
+
2499
+ <button type="button" class="md-top md-icon" data-md-component="top" hidden>
2500
+
2501
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
2502
+ Back to top
2503
+ </button>
2504
+
2505
+ </main>
2506
+
2507
+ <footer class="md-footer">
2508
+
2509
+ <div class="md-footer-meta md-typeset">
2510
+ <div class="md-footer-meta__inner md-grid">
2511
+ <div class="md-copyright">
2512
+
2513
+
2514
+ Made with
2515
+ <a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
2516
+ Material for MkDocs
2517
+ </a>
2518
+
2519
+ </div>
2520
+
2521
+ </div>
2522
+ </div>
2523
+ </footer>
2524
+
2525
+ </div>
2526
+ <div class="md-dialog" data-md-component="dialog">
2527
+ <div class="md-dialog__inner md-typeset"></div>
2528
+ </div>
2529
+
2530
+
2531
+
2532
+
2533
+
2534
+ <script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
2535
+
2536
+
2537
+ <script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
2538
+
2539
+
2540
+ </body>
2541
+ </html>