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/plugins/md/index.html ADDED
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+ <html lang="en" class="no-js">
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+
951
+
952
+
953
+ </span>
954
+
955
+
956
+
957
+ </a>
958
+ </li>
959
+
960
+
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
+ <li class="md-nav__item">
970
+ <a href="../../pipelines/built-ins/" class="md-nav__link">
971
+
972
+
973
+
974
+ <span class="md-ellipsis">
975
+
976
+
977
+ Built-in Stages
978
+
979
+
980
+
981
+ </span>
982
+
983
+
984
+
985
+ </a>
986
+ </li>
987
+
988
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989
+
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
+ <li class="md-nav__item">
998
+ <a href="../../pipelines/examples/" class="md-nav__link">
999
+
1000
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1001
+
1002
+ <span class="md-ellipsis">
1003
+
1004
+
1005
+ Examples
1006
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1007
+
1008
+
1009
+ </span>
1010
+
1011
+
1012
+
1013
+ </a>
1014
+ </li>
1015
+
1016
+
1017
+
1018
+
1019
+ </ul>
1020
+ </nav>
1021
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1022
+ </li>
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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1037
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1038
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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
+ <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
1063
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1064
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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
+
1073
+
1074
+ <span class="md-ellipsis">
1075
+
1076
+
1077
+ Plugins
1078
+
1079
+
1080
+
1081
+ </span>
1082
+
1083
+
1084
+
1085
+ </a>
1086
+
1087
+
1088
+ <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
1089
+ <span class="md-nav__icon md-icon"></span>
1090
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1091
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1092
+ </div>
1093
+
1094
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
1095
+ <label class="md-nav__title" for="__nav_6">
1096
+ <span class="md-nav__icon md-icon"></span>
1097
+
1098
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1099
+ Plugins
1100
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1101
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1102
+ </label>
1103
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1104
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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
+
1114
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1115
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1116
+ <span class="md-ellipsis">
1117
+
1118
+
1119
+ Version Matrix
1120
+
1121
+
1122
+
1123
+ </span>
1124
+
1125
+
1126
+
1127
+ </a>
1128
+ </li>
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
+ <span class="md-ellipsis">
1145
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1146
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1147
+ Docking
1148
+
1149
+
1150
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1151
+ </span>
1152
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1153
+
1154
+
1155
+ </a>
1156
+ </li>
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
+ <span class="md-ellipsis">
1173
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1174
+
1175
+ Descriptors
1176
+
1177
+
1178
+
1179
+ </span>
1180
+
1181
+
1182
+
1183
+ </a>
1184
+ </li>
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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1195
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1196
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1197
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1199
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1200
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1204
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1206
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1209
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1213
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1214
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1216
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1217
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1218
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1220
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1221
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1222
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1224
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1225
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1227
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1228
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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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1238
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1239
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1240
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1241
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1242
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
1243
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1245
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1246
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1247
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1248
+
1249
+ <label class="md-nav__title" for="__toc">
1250
+ <span class="md-nav__icon md-icon"></span>
1251
+ Table of contents
1252
+ </label>
1253
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
1254
+
1255
+ <li class="md-nav__item">
1256
+ <a href="#requirements-and-example-status" class="md-nav__link">
1257
+ <span class="md-ellipsis">
1258
+
1259
+ Requirements and example status
1260
+
1261
+ </span>
1262
+ </a>
1263
+
1264
+ </li>
1265
+
1266
+ <li class="md-nav__item">
1267
+ <a href="#fix-structure" class="md-nav__link">
1268
+ <span class="md-ellipsis">
1269
+
1270
+ fix-structure
1271
+
1272
+ </span>
1273
+ </a>
1274
+
1275
+ <nav class="md-nav" aria-label="fix-structure">
1276
+ <ul class="md-nav__list">
1277
+
1278
+ <li class="md-nav__item">
1279
+ <a href="#terminal-chemistry" class="md-nav__link">
1280
+ <span class="md-ellipsis">
1281
+
1282
+ Terminal chemistry
1283
+
1284
+ </span>
1285
+ </a>
1286
+
1287
+ </li>
1288
+
1289
+ <li class="md-nav__item">
1290
+ <a href="#pipeline-example" class="md-nav__link">
1291
+ <span class="md-ellipsis">
1292
+
1293
+ Pipeline example
1294
+
1295
+ </span>
1296
+ </a>
1297
+
1298
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1299
+
1300
+ </ul>
1301
+ </nav>
1302
+
1303
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1304
+
1305
+ <li class="md-nav__item">
1306
+ <a href="#center-and-align" class="md-nav__link">
1307
+ <span class="md-ellipsis">
1308
+
1309
+ center-and-align
1310
+
1311
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1312
+ </a>
1313
+
1314
+ </li>
1315
+
1316
+ <li class="md-nav__item">
1317
+ <a href="#extract-frames" class="md-nav__link">
1318
+ <span class="md-ellipsis">
1319
+
1320
+ extract-frames
1321
+
1322
+ </span>
1323
+ </a>
1324
+
1325
+ </li>
1326
+
1327
+ <li class="md-nav__item">
1328
+ <a href="#cluster-representative" class="md-nav__link">
1329
+ <span class="md-ellipsis">
1330
+
1331
+ cluster-representative
1332
+
1333
+ </span>
1334
+ </a>
1335
+
1336
+ </li>
1337
+
1338
+ <li class="md-nav__item">
1339
+ <a href="#plain-md" class="md-nav__link">
1340
+ <span class="md-ellipsis">
1341
+
1342
+ plain-md
1343
+
1344
+ </span>
1345
+ </a>
1346
+
1347
+ </li>
1348
+
1349
+ <li class="md-nav__item">
1350
+ <a href="#minimize" class="md-nav__link">
1351
+ <span class="md-ellipsis">
1352
+
1353
+ minimize
1354
+
1355
+ </span>
1356
+ </a>
1357
+
1358
+ <nav class="md-nav" aria-label="minimize">
1359
+ <ul class="md-nav__list">
1360
+
1361
+ <li class="md-nav__item">
1362
+ <a href="#minimize-installation-and-execution" class="md-nav__link">
1363
+ <span class="md-ellipsis">
1364
+
1365
+ Minimize installation and execution
1366
+
1367
+ </span>
1368
+ </a>
1369
+
1370
+ </li>
1371
+
1372
+ <li class="md-nav__item">
1373
+ <a href="#minimize-inputs-and-physical-model" class="md-nav__link">
1374
+ <span class="md-ellipsis">
1375
+
1376
+ Minimize inputs and physical model
1377
+
1378
+ </span>
1379
+ </a>
1380
+
1381
+ </li>
1382
+
1383
+ <li class="md-nav__item">
1384
+ <a href="#minimize-regions-and-modes" class="md-nav__link">
1385
+ <span class="md-ellipsis">
1386
+
1387
+ Minimize regions and modes
1388
+
1389
+ </span>
1390
+ </a>
1391
+
1392
+ </li>
1393
+
1394
+ <li class="md-nav__item">
1395
+ <a href="#minimize-convergence-diagnostics-and-quality" class="md-nav__link">
1396
+ <span class="md-ellipsis">
1397
+
1398
+ Minimize convergence, diagnostics, and quality
1399
+
1400
+ </span>
1401
+ </a>
1402
+
1403
+ </li>
1404
+
1405
+ <li class="md-nav__item">
1406
+ <a href="#minimize-artifacts-and-pipelines" class="md-nav__link">
1407
+ <span class="md-ellipsis">
1408
+
1409
+ Minimize artifacts and pipelines
1410
+
1411
+ </span>
1412
+ </a>
1413
+
1414
+ </li>
1415
+
1416
+ </ul>
1417
+ </nav>
1418
+
1419
+ </li>
1420
+
1421
+ <li class="md-nav__item">
1422
+ <a href="#openbpmd" class="md-nav__link">
1423
+ <span class="md-ellipsis">
1424
+
1425
+ openbpmd
1426
+
1427
+ </span>
1428
+ </a>
1429
+
1430
+ </li>
1431
+
1432
+ <li class="md-nav__item">
1433
+ <a href="#grand" class="md-nav__link">
1434
+ <span class="md-ellipsis">
1435
+
1436
+ grand
1437
+
1438
+ </span>
1439
+ </a>
1440
+
1441
+ <nav class="md-nav" aria-label="grand">
1442
+ <ul class="md-nav__list">
1443
+
1444
+ <li class="md-nav__item">
1445
+ <a href="#configuration-options" class="md-nav__link">
1446
+ <span class="md-ellipsis">
1447
+
1448
+ Configuration options
1449
+
1450
+ </span>
1451
+ </a>
1452
+
1453
+ </li>
1454
+
1455
+ <li class="md-nav__item">
1456
+ <a href="#slurm-scratch-execution" class="md-nav__link">
1457
+ <span class="md-ellipsis">
1458
+
1459
+ Slurm scratch execution
1460
+
1461
+ </span>
1462
+ </a>
1463
+
1464
+ </li>
1465
+
1466
+ <li class="md-nav__item">
1467
+ <a href="#log-syncing" class="md-nav__link">
1468
+ <span class="md-ellipsis">
1469
+
1470
+ Log syncing
1471
+
1472
+ </span>
1473
+ </a>
1474
+
1475
+ </li>
1476
+
1477
+ <li class="md-nav__item">
1478
+ <a href="#outputs" class="md-nav__link">
1479
+ <span class="md-ellipsis">
1480
+
1481
+ Outputs
1482
+
1483
+ </span>
1484
+ </a>
1485
+
1486
+ </li>
1487
+
1488
+ </ul>
1489
+ </nav>
1490
+
1491
+ </li>
1492
+
1493
+ <li class="md-nav__item">
1494
+ <a href="#compressed-inputs" class="md-nav__link">
1495
+ <span class="md-ellipsis">
1496
+
1497
+ Compressed inputs
1498
+
1499
+ </span>
1500
+ </a>
1501
+
1502
+ </li>
1503
+
1504
+ <li class="md-nav__item">
1505
+ <a href="#inducia" class="md-nav__link">
1506
+ <span class="md-ellipsis">
1507
+
1508
+ inducia
1509
+
1510
+ </span>
1511
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1512
+
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
+
1533
+
1534
+
1535
+ <span class="md-ellipsis">
1536
+
1537
+
1538
+ FEP
1539
+
1540
+
1541
+
1542
+ </span>
1543
+
1544
+
1545
+
1546
+ </a>
1547
+ </li>
1548
+
1549
+
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
+ <a href="../qm/" class="md-nav__link">
1560
+
1561
+
1562
+
1563
+ <span class="md-ellipsis">
1564
+
1565
+
1566
+ QM
1567
+
1568
+
1569
+
1570
+ </span>
1571
+
1572
+
1573
+
1574
+ </a>
1575
+ </li>
1576
+
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
+
1589
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1590
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1591
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1592
+
1593
+
1594
+ ML
1595
+
1596
+
1597
+
1598
+ </span>
1599
+
1600
+
1601
+
1602
+ </a>
1603
+ </li>
1604
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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
+
1621
+
1622
+ Data Science
1623
+
1624
+
1625
+
1626
+ </span>
1627
+
1628
+
1629
+
1630
+ </a>
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
+
1671
+
1672
+ <div class="md-nav__link md-nav__container">
1673
+ <a href="../../gui/" class="md-nav__link ">
1674
+
1675
+
1676
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1677
+ <span class="md-ellipsis">
1678
+
1679
+
1680
+ GUI
1681
+
1682
+
1683
+
1684
+ </span>
1685
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1686
+
1687
+
1688
+ </a>
1689
+
1690
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1691
+ <label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
1692
+ <span class="md-nav__icon md-icon"></span>
1693
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1694
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1695
+ </div>
1696
+
1697
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
1698
+ <label class="md-nav__title" for="__nav_7">
1699
+ <span class="md-nav__icon md-icon"></span>
1700
+
1701
+
1702
+ GUI
1703
+
1704
+
1705
+ </label>
1706
+ <ul class="md-nav__list" data-md-scrollfix>
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
+ <li class="md-nav__item">
1715
+ <a href="../../gui/walkthrough/" class="md-nav__link">
1716
+
1717
+
1718
+
1719
+ <span class="md-ellipsis">
1720
+
1721
+
1722
+ Walkthrough
1723
+
1724
+
1725
+
1726
+ </span>
1727
+
1728
+
1729
+
1730
+ </a>
1731
+ </li>
1732
+
1733
+
1734
+
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
+ <li class="md-nav__item">
1743
+ <a href="../../gui/plugin-authoring/" class="md-nav__link">
1744
+
1745
+
1746
+
1747
+ <span class="md-ellipsis">
1748
+
1749
+
1750
+ Plugin GUI Authoring
1751
+
1752
+
1753
+
1754
+ </span>
1755
+
1756
+
1757
+
1758
+ </a>
1759
+ </li>
1760
+
1761
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1762
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1763
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1764
+ </ul>
1765
+ </nav>
1766
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1767
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1768
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1769
+
1770
+
1771
+
1772
+
1773
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2170
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2174
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2178
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2198
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2200
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2202
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2206
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2207
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2250
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2254
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2255
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2260
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2262
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2263
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2264
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2276
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2279
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2280
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2281
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2282
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2283
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2284
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2285
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2286
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2287
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2288
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2289
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2290
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2291
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2292
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2293
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2301
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2302
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2303
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2304
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2305
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2306
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2307
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2308
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2309
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2310
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2311
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2312
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2313
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2314
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
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2324
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2325
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2326
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2327
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2328
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2329
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2330
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2331
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2332
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2333
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2334
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2335
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2336
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2337
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2338
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2339
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2340
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2341
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
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2353
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2354
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2355
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2356
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2357
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2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
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2366
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2367
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2368
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2369
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2370
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2371
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2372
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2373
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2374
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2375
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2376
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2377
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2378
+ <label class="md-nav__title" for="__toc">
2379
+ <span class="md-nav__icon md-icon"></span>
2380
+ Table of contents
2381
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2382
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2383
+
2384
+ <li class="md-nav__item">
2385
+ <a href="#requirements-and-example-status" class="md-nav__link">
2386
+ <span class="md-ellipsis">
2387
+
2388
+ Requirements and example status
2389
+
2390
+ </span>
2391
+ </a>
2392
+
2393
+ </li>
2394
+
2395
+ <li class="md-nav__item">
2396
+ <a href="#fix-structure" class="md-nav__link">
2397
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2398
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2399
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2400
+
2401
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2402
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2403
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2404
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2405
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2406
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2407
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2408
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2409
+ <span class="md-ellipsis">
2410
+
2411
+ Terminal chemistry
2412
+
2413
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2414
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2415
+
2416
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2417
+
2418
+ <li class="md-nav__item">
2419
+ <a href="#pipeline-example" class="md-nav__link">
2420
+ <span class="md-ellipsis">
2421
+
2422
+ Pipeline example
2423
+
2424
+ </span>
2425
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2426
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2427
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2428
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2429
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2430
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2431
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2432
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2433
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2434
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2435
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2436
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2437
+
2438
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2439
+
2440
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2441
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2442
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2443
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2444
+
2445
+ <li class="md-nav__item">
2446
+ <a href="#extract-frames" class="md-nav__link">
2447
+ <span class="md-ellipsis">
2448
+
2449
+ extract-frames
2450
+
2451
+ </span>
2452
+ </a>
2453
+
2454
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2455
+
2456
+ <li class="md-nav__item">
2457
+ <a href="#cluster-representative" class="md-nav__link">
2458
+ <span class="md-ellipsis">
2459
+
2460
+ cluster-representative
2461
+
2462
+ </span>
2463
+ </a>
2464
+
2465
+ </li>
2466
+
2467
+ <li class="md-nav__item">
2468
+ <a href="#plain-md" class="md-nav__link">
2469
+ <span class="md-ellipsis">
2470
+
2471
+ plain-md
2472
+
2473
+ </span>
2474
+ </a>
2475
+
2476
+ </li>
2477
+
2478
+ <li class="md-nav__item">
2479
+ <a href="#minimize" class="md-nav__link">
2480
+ <span class="md-ellipsis">
2481
+
2482
+ minimize
2483
+
2484
+ </span>
2485
+ </a>
2486
+
2487
+ <nav class="md-nav" aria-label="minimize">
2488
+ <ul class="md-nav__list">
2489
+
2490
+ <li class="md-nav__item">
2491
+ <a href="#minimize-installation-and-execution" class="md-nav__link">
2492
+ <span class="md-ellipsis">
2493
+
2494
+ Minimize installation and execution
2495
+
2496
+ </span>
2497
+ </a>
2498
+
2499
+ </li>
2500
+
2501
+ <li class="md-nav__item">
2502
+ <a href="#minimize-inputs-and-physical-model" class="md-nav__link">
2503
+ <span class="md-ellipsis">
2504
+
2505
+ Minimize inputs and physical model
2506
+
2507
+ </span>
2508
+ </a>
2509
+
2510
+ </li>
2511
+
2512
+ <li class="md-nav__item">
2513
+ <a href="#minimize-regions-and-modes" class="md-nav__link">
2514
+ <span class="md-ellipsis">
2515
+
2516
+ Minimize regions and modes
2517
+
2518
+ </span>
2519
+ </a>
2520
+
2521
+ </li>
2522
+
2523
+ <li class="md-nav__item">
2524
+ <a href="#minimize-convergence-diagnostics-and-quality" class="md-nav__link">
2525
+ <span class="md-ellipsis">
2526
+
2527
+ Minimize convergence, diagnostics, and quality
2528
+
2529
+ </span>
2530
+ </a>
2531
+
2532
+ </li>
2533
+
2534
+ <li class="md-nav__item">
2535
+ <a href="#minimize-artifacts-and-pipelines" class="md-nav__link">
2536
+ <span class="md-ellipsis">
2537
+
2538
+ Minimize artifacts and pipelines
2539
+
2540
+ </span>
2541
+ </a>
2542
+
2543
+ </li>
2544
+
2545
+ </ul>
2546
+ </nav>
2547
+
2548
+ </li>
2549
+
2550
+ <li class="md-nav__item">
2551
+ <a href="#openbpmd" class="md-nav__link">
2552
+ <span class="md-ellipsis">
2553
+
2554
+ openbpmd
2555
+
2556
+ </span>
2557
+ </a>
2558
+
2559
+ </li>
2560
+
2561
+ <li class="md-nav__item">
2562
+ <a href="#grand" class="md-nav__link">
2563
+ <span class="md-ellipsis">
2564
+
2565
+ grand
2566
+
2567
+ </span>
2568
+ </a>
2569
+
2570
+ <nav class="md-nav" aria-label="grand">
2571
+ <ul class="md-nav__list">
2572
+
2573
+ <li class="md-nav__item">
2574
+ <a href="#configuration-options" class="md-nav__link">
2575
+ <span class="md-ellipsis">
2576
+
2577
+ Configuration options
2578
+
2579
+ </span>
2580
+ </a>
2581
+
2582
+ </li>
2583
+
2584
+ <li class="md-nav__item">
2585
+ <a href="#slurm-scratch-execution" class="md-nav__link">
2586
+ <span class="md-ellipsis">
2587
+
2588
+ Slurm scratch execution
2589
+
2590
+ </span>
2591
+ </a>
2592
+
2593
+ </li>
2594
+
2595
+ <li class="md-nav__item">
2596
+ <a href="#log-syncing" class="md-nav__link">
2597
+ <span class="md-ellipsis">
2598
+
2599
+ Log syncing
2600
+
2601
+ </span>
2602
+ </a>
2603
+
2604
+ </li>
2605
+
2606
+ <li class="md-nav__item">
2607
+ <a href="#outputs" class="md-nav__link">
2608
+ <span class="md-ellipsis">
2609
+
2610
+ Outputs
2611
+
2612
+ </span>
2613
+ </a>
2614
+
2615
+ </li>
2616
+
2617
+ </ul>
2618
+ </nav>
2619
+
2620
+ </li>
2621
+
2622
+ <li class="md-nav__item">
2623
+ <a href="#compressed-inputs" class="md-nav__link">
2624
+ <span class="md-ellipsis">
2625
+
2626
+ Compressed inputs
2627
+
2628
+ </span>
2629
+ </a>
2630
+
2631
+ </li>
2632
+
2633
+ <li class="md-nav__item">
2634
+ <a href="#inducia" class="md-nav__link">
2635
+ <span class="md-ellipsis">
2636
+
2637
+ inducia
2638
+
2639
+ </span>
2640
+ </a>
2641
+
2642
+ </li>
2643
+
2644
+ </ul>
2645
+
2646
+ </nav>
2647
+ </div>
2648
+ </div>
2649
+ </div>
2650
+
2651
+
2652
+
2653
+ <div class="md-content" data-md-component="content">
2654
+
2655
+ <article class="md-content__inner md-typeset">
2656
+
2657
+
2658
+
2659
+
2660
+
2661
+
2662
+
2663
+
2664
+ <h1 id="md-plugin">MD Plugin<a class="headerlink" href="#md-plugin" title="Permanent link">&para;</a></h1>
2665
+ <p>Package: <code>caddforge-md</code></p>
2666
+ <div class="admonition info">
2667
+ <p class="admonition-title">Public source tag</p>
2668
+ <p>This page describes <code>caddforge-md</code> <code>0.13.0</code>, tagged as <code>v0.13.0</code>.
2669
+ PyPI publication is pending; see the <a href="../version-matrix/">version matrix</a>.</p>
2670
+ </div>
2671
+ <p>The MD plugin provides molecular dynamics preparation, simulation, and analysis workflows.</p>
2672
+ <h2 id="requirements-and-example-status">Requirements and example status<a class="headerlink" href="#requirements-and-example-status" title="Permanent link">&para;</a></h2>
2673
+ <p>The <a href="../../examples/">example library</a> provides downloadable configuration
2674
+ templates for every workflow on this page, plus a shared Python runner. File paths
2675
+ refer to inputs you must prepare; these are not bundled research datasets. Schema
2676
+ validation does not establish scientific validity or engine availability. See the
2677
+ <a href="../version-matrix/">version matrix</a> for release tags and publication status.</p>
2678
+ <h2 id="fix-structure"><code>fix-structure</code><a class="headerlink" href="#fix-structure" title="Permanent link">&para;</a></h2>
2679
+ <p>Conservatively repairs protein hydrogens in a protein-only PDB, protein-ligand complex PDB, or existing POPC/POPE membrane system before OpenMM simulations. The tool preserves explicit protein protonation choices where possible, repairs configured membrane lipid hydrogens with OpenMM force-field templates, leaves ligands/cofactors untouched, and preserves ligand/cofactor <code>CONECT</code> records and PDB formal-charge fields by default.</p>
2680
+ <p>CLI:</p>
2681
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>fix-structure<span class="w"> </span>--config<span class="w"> </span>fix_structure.yaml
2682
+ </code></pre></div>
2683
+ <p>YAML:</p>
2684
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2685
+ <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nt">input_pdb</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/complex.pdb</span>
2686
+ <a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nt">forcefields</span><span class="p">:</span>
2687
+ <a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">amber14-all.xml</span>
2688
+ <a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">amber14/tip3p.xml</span>
2689
+ <a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nt">ph</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">7.0</span>
2690
+ <a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nt">protonation_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">preserve</span>
2691
+ <a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="nt">termini_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">charged</span>
2692
+ <a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="nt">fix_nonstandard_residues</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">auto</span>
2693
+ <a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a><span class="nt">strict_all</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
2694
+ <a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a><span class="nt">membrane_lipid_resnames</span><span class="p">:</span>
2695
+ <a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">POPC</span>
2696
+ <a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">POPE</span>
2697
+ <a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a><span class="nt">validate_openmm_system</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">auto</span>
2698
+ <a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a><span class="nt">sanitize_mixed_residues</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">auto</span>
2699
+ <a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a><span class="nt">preserve_conect</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
2700
+ <a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a><span class="nt">quiet</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
2701
+ <a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
2702
+ <a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a><span class="nt">output_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2703
+ </code></pre></div>
2704
+ <p><code>validate_openmm_system: auto</code> keeps normal non-membrane behavior unchanged and runs an OpenMM <code>ForceField.createSystem()</code> validation when configured membrane lipid residues are present. <code>sanitize_mixed_residues: auto</code> separates mixed PDB residue ids and reassembles split atom records before OpenMM parsing, for example POPC records interrupted by CL/T3P records that reuse the same residue number. POPC/POPE are detected from both standard and 4-character PDB residue-name layouts. For POPC/POPE Amber-style inputs, include force fields that cover protein, lipids, water, and ions; <code>amber14-all.xml</code> includes lipid templates and <code>amber14/tip3p.xml</code> covers TIP3P water and common ions. Unmatched ligands/cofactors left untouched by this repair tool are reported in <code>repair_metadata.openmm_system_validation.ignored_unmatched_residues</code> and must still be parameterized by the downstream MD workflow.</p>
2705
+ <p>Python:</p>
2706
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
2707
+ <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
2708
+ <a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
2709
+ <a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"fix-structure"</span><span class="p">)</span>
2710
+ <a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
2711
+ <a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a> <span class="n">input_pdb</span><span class="o">=</span><span class="s2">"data/complex.pdb"</span><span class="p">,</span>
2712
+ <a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a> <span class="n">forcefields</span><span class="o">=</span><span class="p">[</span><span class="s2">"amber14-all.xml"</span><span class="p">,</span> <span class="s2">"amber14/tip3p.xml"</span><span class="p">],</span>
2713
+ <a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
2714
+ <a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a><span class="p">)</span>
2715
+ <a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
2716
+ <a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
2717
+ <a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
2718
+ <a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
2719
+ <a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a><span class="p">)</span>
2720
+ <a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
2721
+ <a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
2722
+ <a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">[</span><span class="s2">"output_pdb"</span><span class="p">])</span>
2723
+ </code></pre></div>
2724
+ <p>Outputs to inspect: <code>results/output/&lt;input_stem&gt;_fixed.pdb</code>,
2725
+ <code>results/result_record.json</code>. In pipelines, bind input artifact <code>structure</code> and consume output
2726
+ artifact <code>repaired_structure</code>.</p>
2727
+ <h3 id="terminal-chemistry">Terminal chemistry<a class="headerlink" href="#terminal-chemistry" title="Permanent link">&para;</a></h3>
2728
+ <p><code>termini_policy</code> controls terminal chemistry separately from side-chain protonation:</p>
2729
+ <table>
2730
+ <thead>
2731
+ <tr>
2732
+ <th>Policy</th>
2733
+ <th>Behavior</th>
2734
+ </tr>
2735
+ </thead>
2736
+ <tbody>
2737
+ <tr>
2738
+ <td><code>charged</code> (default)</td>
2739
+ <td>Prepare free N-termini as positively charged and free C-termini as negatively charged, independently of pH. Repair missing terminal OXT when the backbone permits reconstruction.</td>
2740
+ </tr>
2741
+ <tr>
2742
+ <td><code>preserve</code></td>
2743
+ <td>Preserve the input terminal state and validate against the supplied force fields. Ambiguous or incomplete terminal groups fail with a residue-specific explanation.</td>
2744
+ </tr>
2745
+ <tr>
2746
+ <td><code>cap</code></td>
2747
+ <td>Add ACE/NME caps to eligible neutral or incomplete termini. Already charged or capped termini remain unchanged.</td>
2748
+ </tr>
2749
+ </tbody>
2750
+ </table>
2751
+ <p>A protonated, uncapped C-terminus (<code>–COOH</code>) is neutral. A deprotonated C-terminus
2752
+ (<code>–COO⁻</code>) is charged. A neutral NME cap (<code>–CONHCH₃</code>) is chemically different from
2753
+ an uncapped neutral acid. Capping can affect both N- and C-termini.</p>
2754
+ <p>Terminal policy takes precedence over <code>protonation_policy</code> <strong>only at terminal
2755
+ groups</strong>. Thus the default <code>charged</code> policy can remove HXT even when
2756
+ <code>protonation_policy: preserve</code>; unrelated residue substitutions remain forbidden.
2757
+ Missing terminal hydrogens can make preservation ambiguous (for example, only
2758
+ one H on an ordinary free N-terminus). Prepare the intended terminal state
2759
+ explicitly rather than relying on pH to select it in preserve mode. Hydrogen
2760
+ repair still fills unrelated missing hydrogens.</p>
2761
+ <p>Stock OpenMM <code>amber14-all.xml</code> supports standard charged termini and ACE/NME caps,
2762
+ but does not include a neutral uncapped <code>–COOH</code> template. To preserve that form,
2763
+ supply a compatible force field or additional, scientifically validated templates:</p>
2764
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nt">input_pdb</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/protein_with_explicit_terminal_states.pdb</span>
2765
+ <a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nt">forcefields</span><span class="p">:</span>
2766
+ <a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">amber14-all.xml</span>
2767
+ <a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/absolute/path/to/your_validated_terminal_templates.xml</span>
2768
+ <a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="nt">protonation_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">preserve</span>
2769
+ <a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a><span class="nt">termini_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">preserve</span>
2770
+ </code></pre></div>
2771
+ <p>The extra XML above is user-supplied, not bundled with CADDForge. Force-field
2772
+ compatibility is checked; preserve mode never silently converts an unsupported
2773
+ neutral terminus. Setting <code>validate_openmm_system: never</code> does not disable
2774
+ protein/cap template matching or terminal-state validation. This feature concerns
2775
+ terminal states of recognized protein residues, not arbitrary modified residues.</p>
2776
+ <p>For standard charged preparation, set <code>termini_policy: charged</code>. For explicitly
2777
+ requested caps, set <code>termini_policy: cap</code>; side-chain preservation can stay enabled.
2778
+ Approximate reconstructed atoms and caps should be minimized before production MD.</p>
2779
+ <p><strong>Migration:</strong> <code>cap_neutral_termini: true</code> is a deprecated alias for
2780
+ <code>termini_policy: cap</code>. Combining it with an explicit different policy fails.
2781
+ <code>false</code> does not override the new policy. <code>fix_nonstandard_residues</code> now controls
2782
+ modified-residue normalization only; setting it to <code>never</code> does not disable
2783
+ terminal treatment. Users who previously relied on <code>protonation_policy: preserve</code>
2784
+ to reject terminal conversions must now also set <code>termini_policy: preserve</code>.</p>
2785
+ <p>The report at <code>paths.normalization</code> records requested/effective policy, original
2786
+ terminal evidence, normalization edits or added caps, final decisions, and
2787
+ validation status under <code>normalization.terminal_treatment</code>. It is retained on
2788
+ failure. Successful results also expose <code>repair_metadata.terminal_treatment</code>.</p>
2789
+ <h3 id="pipeline-example">Pipeline example<a class="headerlink" href="#pipeline-example" title="Permanent link">&para;</a></h3>
2790
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nt">version</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
2791
+ <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">prepare-protein</span>
2792
+ <a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="nt">stages</span><span class="p">:</span>
2793
+ <a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">id</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">repair</span>
2794
+ <a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="w"> </span><span class="nt">tool</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">md/fix-structure</span>
2795
+ <a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="w"> </span><span class="nt">config</span><span class="p">:</span>
2796
+ <a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="w"> </span><span class="nt">input_pdb</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/protein.pdb</span>
2797
+ <a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a><span class="w"> </span><span class="nt">forcefields</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">amber14-all.xml</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">amber14/tip3p.xml</span><span class="p p-Indicator">]</span>
2798
+ <a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a><span class="w"> </span><span class="nt">protonation_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">preserve</span>
2799
+ <a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a><span class="w"> </span><span class="nt">termini_policy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">charged</span>
2800
+ <a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a><span class="w"> </span><span class="nt">outputs</span><span class="p">:</span>
2801
+ <a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a><span class="w"> </span><span class="nt">protein</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output_pdb</span>
2802
+ <a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">id</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">cleanup</span>
2803
+ <a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a><span class="w"> </span><span class="nt">tool</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">md/minimize</span>
2804
+ <a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a><span class="w"> </span><span class="nt">inputs</span><span class="p">:</span>
2805
+ <a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a><span class="w"> </span><span class="nt">protein</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">repair.protein</span>
2806
+ <a id="__codelineno-4-17" name="__codelineno-4-17" href="#__codelineno-4-17"></a><span class="w"> </span><span class="nt">config</span><span class="p">:</span>
2807
+ <a id="__codelineno-4-18" name="__codelineno-4-18" href="#__codelineno-4-18"></a><span class="w"> </span><span class="nt">ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligand.sdf</span>
2808
+ <a id="__codelineno-4-19" name="__codelineno-4-19" href="#__codelineno-4-19"></a><span class="w"> </span><span class="nt">mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ligand_only</span>
2809
+ </code></pre></div>
2810
+ <p>The input must be a protein-only receptor for this example; ligand chemistry is
2811
+ supplied separately to <code>minimize</code>. The repair tool's existing input port
2812
+ <code>structure</code> and output port <code>repaired_structure</code> are unchanged. The explicit
2813
+ <code>protein: output_pdb</code> output alias above binds the same PDB for the next stage.</p>
2814
+ <h2 id="center-and-align"><code>center-and-align</code><a class="headerlink" href="#center-and-align" title="Permanent link">&para;</a></h2>
2815
+ <p>Centers, wraps, optionally aligns, and writes a processed trajectory.</p>
2816
+ <p>CLI:</p>
2817
+ <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>run<span class="w"> </span>md<span class="w"> </span>center-and-align<span class="w"> </span>--config<span class="w"> </span>center_and_align.yaml
2818
+ </code></pre></div>
2819
+ <p>YAML:</p>
2820
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2821
+ <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nt">topology_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/system.pdb</span>
2822
+ <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="nt">trajectory_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/traj.xtc</span>
2823
+ <a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="nt">center_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein or resname MOL</span>
2824
+ <a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nt">keep_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein or resname MOL</span>
2825
+ <a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nt">align_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein and backbone</span>
2826
+ <a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nt">unwrap</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
2827
+ <a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="nt">center</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
2828
+ <a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="nt">wrap</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
2829
+ <a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nt">center_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">geometry</span>
2830
+ <a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="nt">wrap_compound</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">residues</span>
2831
+ <a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a><span class="nt">align_weights</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">mass</span>
2832
+ <a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
2833
+ <a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="nt">output_trajectory_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">traj-centered.xtc</span>
2834
+ <a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="nt">output_structure_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">traj-centered.pdb</span>
2835
+ </code></pre></div>
2836
+ <p>Python:</p>
2837
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
2838
+ <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
2839
+ <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
2840
+ <a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"center-and-align"</span><span class="p">)</span>
2841
+ <a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
2842
+ <a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a> <span class="n">topology_path</span><span class="o">=</span><span class="s2">"data/system.pdb"</span><span class="p">,</span>
2843
+ <a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a> <span class="n">trajectory_path</span><span class="o">=</span><span class="s2">"data/traj.xtc"</span><span class="p">,</span>
2844
+ <a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a> <span class="n">center_selection</span><span class="o">=</span><span class="s2">"protein or resname MOL"</span><span class="p">,</span>
2845
+ <a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a> <span class="n">keep_selection</span><span class="o">=</span><span class="s2">"protein or resname MOL"</span><span class="p">,</span>
2846
+ <a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a> <span class="n">align_selection</span><span class="o">=</span><span class="s2">"protein and backbone"</span><span class="p">,</span>
2847
+ <a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
2848
+ <a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a><span class="p">)</span>
2849
+ <a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
2850
+ <a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
2851
+ <a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
2852
+ <a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
2853
+ <a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a><span class="p">)</span>
2854
+ <a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
2855
+ <a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
2856
+ <a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">)</span>
2857
+ </code></pre></div>
2858
+ <p>Outputs to inspect: <code>results/output/&lt;trajectory&gt;</code>, <code>results/output/&lt;structure&gt;</code>,
2859
+ <code>results/result_record.json</code>.</p>
2860
+ <h2 id="extract-frames"><code>extract-frames</code><a class="headerlink" href="#extract-frames" title="Permanent link">&para;</a></h2>
2861
+ <p>Extracts one or more frames from a trajectory. For multi-frame selections it writes a sliced
2862
+ trajectory and a first selected-frame structure; for single-frame selections it writes only
2863
+ structure-style outputs.</p>
2864
+ <p>CLI:</p>
2865
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>extract-frames<span class="w"> </span>--config<span class="w"> </span>extract_frames.yaml
2866
+ </code></pre></div>
2867
+ <p>YAML:</p>
2868
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2869
+ <a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="nt">topology_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/traj-centered.pdb</span>
2870
+ <a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="nt">trajectory_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/traj-centered.xtc</span>
2871
+ <a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="nt">ligand_template_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/template.sdf</span>
2872
+ <a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a><span class="nt">ligand_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">UNK</span>
2873
+ <a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a><span class="nt">extract_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein or resname UNK</span>
2874
+ <a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a><span class="nt">frame_index</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2875
+ <a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a><span class="nt">last_ns</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10.0</span>
2876
+ <a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a><span class="nt">frame_slice</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2877
+ <a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a><span class="nt">write_per_frame_pdbs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
2878
+ <a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
2879
+ <a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a><span class="nt">output_trajectory_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">last-10ns.xtc</span>
2880
+ <a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a><span class="nt">output_structure_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">last-10ns_first_complex.pdb</span>
2881
+ <a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a><span class="nt">protein_trajectory_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">last-10ns_protein.xtc</span>
2882
+ <a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a><span class="nt">protein_structure_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">last-10ns_first_protein.pdb</span>
2883
+ <a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a><span class="nt">ligand_sdf_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">last-10ns_first_ligand.sdf</span>
2884
+ </code></pre></div>
2885
+ <p>Use exactly one frame-selection mode. A Python-style slice is written as:</p>
2886
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="nt">frame_index</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2887
+ <a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="nt">last_ns</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2888
+ <a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="nt">frame_slice</span><span class="p">:</span>
2889
+ <a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="w"> </span><span class="nt">start</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100</span>
2890
+ <a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="w"> </span><span class="nt">stop</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1000</span>
2891
+ <a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a><span class="w"> </span><span class="nt">step</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
2892
+ </code></pre></div>
2893
+ <p>Python:</p>
2894
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
2895
+ <a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
2896
+ <a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
2897
+ <a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"extract-frames"</span><span class="p">)</span>
2898
+ <a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
2899
+ <a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a> <span class="n">topology_path</span><span class="o">=</span><span class="s2">"data/traj-centered.pdb"</span><span class="p">,</span>
2900
+ <a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a> <span class="n">trajectory_path</span><span class="o">=</span><span class="s2">"data/traj-centered.xtc"</span><span class="p">,</span>
2901
+ <a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a> <span class="n">ligand_template_sdf</span><span class="o">=</span><span class="s2">"data/template.sdf"</span><span class="p">,</span>
2902
+ <a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a> <span class="n">ligand_resname</span><span class="o">=</span><span class="s2">"UNK"</span><span class="p">,</span>
2903
+ <a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a> <span class="n">extract_selection</span><span class="o">=</span><span class="s2">"protein or resname UNK"</span><span class="p">,</span>
2904
+ <a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></a> <span class="n">last_ns</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span>
2905
+ <a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
2906
+ <a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></a><span class="p">)</span>
2907
+ <a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
2908
+ <a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
2909
+ <a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
2910
+ <a id="__codelineno-11-17" name="__codelineno-11-17" href="#__codelineno-11-17"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
2911
+ <a id="__codelineno-11-18" name="__codelineno-11-18" href="#__codelineno-11-18"></a><span class="p">)</span>
2912
+ <a id="__codelineno-11-19" name="__codelineno-11-19" href="#__codelineno-11-19"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
2913
+ <a id="__codelineno-11-20" name="__codelineno-11-20" href="#__codelineno-11-20"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
2914
+ <a id="__codelineno-11-21" name="__codelineno-11-21" href="#__codelineno-11-21"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">)</span>
2915
+ </code></pre></div>
2916
+ <p>Outputs to inspect: <code>results/output/&lt;structure&gt;</code>, optional <code>results/output/&lt;trajectory&gt;</code> for
2917
+ multi-frame selections, optional protein-only outputs, optional corrected ligand SDF,
2918
+ <code>results/output/frame_manifest.json</code>, <code>results/result_record.json</code>.</p>
2919
+ <h2 id="cluster-representative"><code>cluster-representative</code><a class="headerlink" href="#cluster-representative" title="Permanent link">&para;</a></h2>
2920
+ <p>Clusters selected trajectory frames and writes the medoid of the largest cluster. By default,
2921
+ ligand systems cluster on ligand heavy atoms when <code>ligand_resname</code> is provided, while
2922
+ <code>extract_selection</code> controls the atoms written to the representative complex PDB.</p>
2923
+ <p>CLI:</p>
2924
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>cluster-representative<span class="w"> </span>--config<span class="w"> </span>cluster_representative.yaml
2925
+ </code></pre></div>
2926
+ <p>YAML:</p>
2927
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2928
+ <a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="nt">topology_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/traj-centered.pdb</span>
2929
+ <a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="nt">trajectory_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/traj-centered.xtc</span>
2930
+ <a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="nt">ligand_template_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/template.sdf</span>
2931
+ <a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="nt">ligand_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">UNK</span>
2932
+ <a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a><span class="nt">cluster_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2933
+ <a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a><span class="nt">extract_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein or resname UNK</span>
2934
+ <a id="__codelineno-13-8" name="__codelineno-13-8" href="#__codelineno-13-8"></a><span class="nt">last_ns</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10.0</span>
2935
+ <a id="__codelineno-13-9" name="__codelineno-13-9" href="#__codelineno-13-9"></a><span class="nt">frame_slice</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2936
+ <a id="__codelineno-13-10" name="__codelineno-13-10" href="#__codelineno-13-10"></a><span class="nt">distance_threshold_nm</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.2</span>
2937
+ <a id="__codelineno-13-11" name="__codelineno-13-11" href="#__codelineno-13-11"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
2938
+ <a id="__codelineno-13-12" name="__codelineno-13-12" href="#__codelineno-13-12"></a><span class="nt">output_complex_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">largest_cluster_representative_complex.pdb</span>
2939
+ <a id="__codelineno-13-13" name="__codelineno-13-13" href="#__codelineno-13-13"></a><span class="nt">output_protein_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">largest_cluster_representative_protein.pdb</span>
2940
+ <a id="__codelineno-13-14" name="__codelineno-13-14" href="#__codelineno-13-14"></a><span class="nt">output_ligand_sdf_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">largest_cluster_representative_ligand.sdf</span>
2941
+ <a id="__codelineno-13-15" name="__codelineno-13-15" href="#__codelineno-13-15"></a><span class="nt">clustering_summary_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">clustering_summary.json</span>
2942
+ </code></pre></div>
2943
+ <p>For slice-based clustering, replace <code>last_ns</code> with:</p>
2944
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="nt">last_ns</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2945
+ <a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="nt">frame_slice</span><span class="p">:</span>
2946
+ <a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="w"> </span><span class="nt">start</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1000</span>
2947
+ <a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="w"> </span><span class="nt">stop</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
2948
+ <a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a><span class="w"> </span><span class="nt">step</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5</span>
2949
+ </code></pre></div>
2950
+ <p>Python:</p>
2951
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
2952
+ <a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
2953
+ <a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>
2954
+ <a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"cluster-representative"</span><span class="p">)</span>
2955
+ <a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
2956
+ <a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a> <span class="n">topology_path</span><span class="o">=</span><span class="s2">"data/traj-centered.pdb"</span><span class="p">,</span>
2957
+ <a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a> <span class="n">trajectory_path</span><span class="o">=</span><span class="s2">"data/traj-centered.xtc"</span><span class="p">,</span>
2958
+ <a id="__codelineno-15-8" name="__codelineno-15-8" href="#__codelineno-15-8"></a> <span class="n">ligand_template_sdf</span><span class="o">=</span><span class="s2">"data/template.sdf"</span><span class="p">,</span>
2959
+ <a id="__codelineno-15-9" name="__codelineno-15-9" href="#__codelineno-15-9"></a> <span class="n">ligand_resname</span><span class="o">=</span><span class="s2">"UNK"</span><span class="p">,</span>
2960
+ <a id="__codelineno-15-10" name="__codelineno-15-10" href="#__codelineno-15-10"></a> <span class="n">extract_selection</span><span class="o">=</span><span class="s2">"protein or resname UNK"</span><span class="p">,</span>
2961
+ <a id="__codelineno-15-11" name="__codelineno-15-11" href="#__codelineno-15-11"></a> <span class="n">last_ns</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span>
2962
+ <a id="__codelineno-15-12" name="__codelineno-15-12" href="#__codelineno-15-12"></a> <span class="n">distance_threshold_nm</span><span class="o">=</span><span class="mf">0.2</span><span class="p">,</span>
2963
+ <a id="__codelineno-15-13" name="__codelineno-15-13" href="#__codelineno-15-13"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
2964
+ <a id="__codelineno-15-14" name="__codelineno-15-14" href="#__codelineno-15-14"></a><span class="p">)</span>
2965
+ <a id="__codelineno-15-15" name="__codelineno-15-15" href="#__codelineno-15-15"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
2966
+ <a id="__codelineno-15-16" name="__codelineno-15-16" href="#__codelineno-15-16"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
2967
+ <a id="__codelineno-15-17" name="__codelineno-15-17" href="#__codelineno-15-17"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
2968
+ <a id="__codelineno-15-18" name="__codelineno-15-18" href="#__codelineno-15-18"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
2969
+ <a id="__codelineno-15-19" name="__codelineno-15-19" href="#__codelineno-15-19"></a><span class="p">)</span>
2970
+ <a id="__codelineno-15-20" name="__codelineno-15-20" href="#__codelineno-15-20"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
2971
+ <a id="__codelineno-15-21" name="__codelineno-15-21" href="#__codelineno-15-21"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
2972
+ <a id="__codelineno-15-22" name="__codelineno-15-22" href="#__codelineno-15-22"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
2973
+ </code></pre></div>
2974
+ <p>Outputs to inspect: <code>results/output/largest_cluster_representative_complex.pdb</code>, optional
2975
+ <code>results/output/largest_cluster_representative_protein.pdb</code>, optional corrected ligand SDF,
2976
+ <code>results/output/clustering_summary.json</code>, <code>results/result_record.json</code>.</p>
2977
+ <h2 id="plain-md"><code>plain-md</code><a class="headerlink" href="#plain-md" title="Permanent link">&para;</a></h2>
2978
+ <p>Runs a standard OpenMM simulation, with optional OpenFF/SMIRNOFF parameterization for non-standard
2979
+ molecules. For already complete systems, <code>system_preparation_mode: prepared</code> skips hydrogen,
2980
+ solvent, and ion addition and builds a snug periodic box around the provided atoms. Membrane
2981
+ systems can use OpenMM's membrane-specific barostat with <code>barostat: membrane</code>.</p>
2982
+ <p>CLI:</p>
2983
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>plain-md<span class="w"> </span>--config<span class="w"> </span>plain_md.yaml
2984
+ <a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>plain-md<span class="w"> </span>--config<span class="w"> </span>plain_md.yaml<span class="w"> </span>--backend<span class="w"> </span>slurm<span class="w"> </span>--slurm-time<span class="w"> </span><span class="m">24</span>:00:00
2985
+ </code></pre></div>
2986
+ <p>YAML:</p>
2987
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2988
+ <a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="nt">system_pdb_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/system.pdb</span>
2989
+ <a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="nt">molecule_sdf_paths</span><span class="p">:</span>
2990
+ <a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligand.sdf</span>
2991
+ <a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="nt">ph</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">7.4</span>
2992
+ <a id="__codelineno-17-6" name="__codelineno-17-6" href="#__codelineno-17-6"></a><span class="nt">system_preparation_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">solvate</span>
2993
+ <a id="__codelineno-17-7" name="__codelineno-17-7" href="#__codelineno-17-7"></a><span class="nt">padding</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
2994
+ <a id="__codelineno-17-8" name="__codelineno-17-8" href="#__codelineno-17-8"></a><span class="nt">ionic_strength</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.15</span>
2995
+ <a id="__codelineno-17-9" name="__codelineno-17-9" href="#__codelineno-17-9"></a><span class="nt">prepared_box_margin</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
2996
+ <a id="__codelineno-17-10" name="__codelineno-17-10" href="#__codelineno-17-10"></a><span class="nt">nonbonded_cutoff</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
2997
+ <a id="__codelineno-17-11" name="__codelineno-17-11" href="#__codelineno-17-11"></a><span class="nt">barostat</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">isotropic</span>
2998
+ <a id="__codelineno-17-12" name="__codelineno-17-12" href="#__codelineno-17-12"></a><span class="nt">pressure</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
2999
+ <a id="__codelineno-17-13" name="__codelineno-17-13" href="#__codelineno-17-13"></a><span class="nt">membrane_surface_tension</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
3000
+ <a id="__codelineno-17-14" name="__codelineno-17-14" href="#__codelineno-17-14"></a><span class="nt">membrane_xy_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">isotropic</span>
3001
+ <a id="__codelineno-17-15" name="__codelineno-17-15" href="#__codelineno-17-15"></a><span class="nt">membrane_z_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">free</span>
3002
+ <a id="__codelineno-17-16" name="__codelineno-17-16" href="#__codelineno-17-16"></a><span class="nt">barostat_frequency</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">25</span>
3003
+ <a id="__codelineno-17-17" name="__codelineno-17-17" href="#__codelineno-17-17"></a><span class="nt">temperature</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">300.0</span>
3004
+ <a id="__codelineno-17-18" name="__codelineno-17-18" href="#__codelineno-17-18"></a><span class="nt">step_size_fs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">4</span>
3005
+ <a id="__codelineno-17-19" name="__codelineno-17-19" href="#__codelineno-17-19"></a><span class="nt">simulation_time_ns</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
3006
+ <a id="__codelineno-17-20" name="__codelineno-17-20" href="#__codelineno-17-20"></a><span class="nt">trajectory_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">traj.xtc</span>
3007
+ <a id="__codelineno-17-21" name="__codelineno-17-21" href="#__codelineno-17-21"></a><span class="nt">report_interval</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10000</span>
3008
+ <a id="__codelineno-17-22" name="__codelineno-17-22" href="#__codelineno-17-22"></a><span class="nt">checkpoint_interval</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5000</span>
3009
+ <a id="__codelineno-17-23" name="__codelineno-17-23" href="#__codelineno-17-23"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
3010
+ <a id="__codelineno-17-24" name="__codelineno-17-24" href="#__codelineno-17-24"></a><span class="nt">seed</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
3011
+ <a id="__codelineno-17-25" name="__codelineno-17-25" href="#__codelineno-17-25"></a><span class="nt">repeats</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
3012
+ <a id="__codelineno-17-26" name="__codelineno-17-26" href="#__codelineno-17-26"></a><span class="nt">checkpoint_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
3013
+ <a id="__codelineno-17-27" name="__codelineno-17-27" href="#__codelineno-17-27"></a><span class="nt">max_restarts</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
3014
+ </code></pre></div>
3015
+ <p>Python:</p>
3016
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
3017
+ <a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
3018
+ <a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a>
3019
+ <a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"plain-md"</span><span class="p">)</span>
3020
+ <a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
3021
+ <a id="__codelineno-18-6" name="__codelineno-18-6" href="#__codelineno-18-6"></a> <span class="n">system_pdb_path</span><span class="o">=</span><span class="s2">"data/system.pdb"</span><span class="p">,</span>
3022
+ <a id="__codelineno-18-7" name="__codelineno-18-7" href="#__codelineno-18-7"></a> <span class="n">molecule_sdf_paths</span><span class="o">=</span><span class="p">[</span><span class="s2">"data/ligand.sdf"</span><span class="p">],</span>
3023
+ <a id="__codelineno-18-8" name="__codelineno-18-8" href="#__codelineno-18-8"></a> <span class="n">simulation_time_ns</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
3024
+ <a id="__codelineno-18-9" name="__codelineno-18-9" href="#__codelineno-18-9"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
3025
+ <a id="__codelineno-18-10" name="__codelineno-18-10" href="#__codelineno-18-10"></a><span class="p">)</span>
3026
+ <a id="__codelineno-18-11" name="__codelineno-18-11" href="#__codelineno-18-11"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
3027
+ <a id="__codelineno-18-12" name="__codelineno-18-12" href="#__codelineno-18-12"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
3028
+ <a id="__codelineno-18-13" name="__codelineno-18-13" href="#__codelineno-18-13"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
3029
+ <a id="__codelineno-18-14" name="__codelineno-18-14" href="#__codelineno-18-14"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
3030
+ <a id="__codelineno-18-15" name="__codelineno-18-15" href="#__codelineno-18-15"></a><span class="p">)</span>
3031
+ <a id="__codelineno-18-16" name="__codelineno-18-16" href="#__codelineno-18-16"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
3032
+ <a id="__codelineno-18-17" name="__codelineno-18-17" href="#__codelineno-18-17"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
3033
+ <a id="__codelineno-18-18" name="__codelineno-18-18" href="#__codelineno-18-18"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
3034
+ </code></pre></div>
3035
+ <p>Outputs to inspect: <code>results/output/*_prepared.pdb</code>, <code>results/output/*_minimized.pdb</code>,
3036
+ <code>results/output/traj.xtc</code>, <code>results/output/checkpoint.chk</code>, <code>results/result_record.json</code>.
3037
+ The standardized result exposes <code>prepared_structure</code>, <code>minimized_structure</code>, <code>trajectory</code>,
3038
+ <code>checkpoint</code>, and <code>output_dir</code> as pipeline-ready result paths.</p>
3039
+ <p>Set <code>repeats</code> above one to submit independent simulations with distinct reproducible seeds. The
3040
+ parent records child IDs and publishes <code>replicas_manifest.json</code> with aggregate completion metrics
3041
+ when every child reaches a terminal state. Slurm repeat children are submitted before the parent
3042
+ waits for results.</p>
3043
+ <p>For an already prepared system, use:</p>
3044
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="nt">system_preparation_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">prepared</span>
3045
+ <a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a><span class="nt">prepared_box_margin</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
3046
+ </code></pre></div>
3047
+ <p>In this mode, <code>padding</code> and <code>ionic_strength</code> are ignored. The workflow derives an
3048
+ orthorhombic box from the existing coordinates plus <code>prepared_box_margin</code> and fails if the
3049
+ resulting box is too small for the configured nonbonded cutoff.</p>
3050
+ <p>For membrane systems oriented in the XY plane with the membrane normal along Z, use:</p>
3051
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a><span class="nt">barostat</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">membrane</span>
3052
+ <a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a><span class="nt">membrane_surface_tension</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
3053
+ <a id="__codelineno-20-3" name="__codelineno-20-3" href="#__codelineno-20-3"></a><span class="nt">membrane_xy_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">isotropic</span>
3054
+ <a id="__codelineno-20-4" name="__codelineno-20-4" href="#__codelineno-20-4"></a><span class="nt">membrane_z_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">free</span>
3055
+ <a id="__codelineno-20-5" name="__codelineno-20-5" href="#__codelineno-20-5"></a><span class="nt">barostat_frequency</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">25</span>
3056
+ </code></pre></div>
3057
+ <h2 id="minimize"><code>minimize</code><a class="headerlink" href="#minimize" title="Permanent link">&para;</a></h2>
3058
+ <p>Minimize one protein–ligand complex with OpenMM L-BFGS. This is local pose
3059
+ cleanup: the reported physical-model energy includes implicit solvation and is
3060
+ <strong>not a binding affinity or a score for comparing different chemical systems</strong>.
3061
+ The tool emits finite poses with quality flags by default; strict mode can reject
3062
+ flagged jobs while retaining their structures and diagnostics.</p>
3063
+ <h3 id="minimize-installation-and-execution">Minimize installation and execution<a class="headerlink" href="#minimize-installation-and-execution" title="Permanent link">&para;</a></h3>
3064
+ <p>Use an environment containing AmberTools (<code>pdb4amber</code>, <code>antechamber</code>, <code>parmchk2</code>,
3065
+ <code>tleap</code>), OpenMM &gt;=8.2, ParmEd, RDKit, NumPy, SciPy, and this plugin. For example:</p>
3066
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>caddforge-minimize<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.13<span class="w"> </span>ambertools<span class="w"> </span><span class="nv">openmm</span><span class="o">=</span><span class="m">8</span>.2<span class="w"> </span>parmed<span class="w"> </span>rdkit<span class="w"> </span>numpy<span class="w"> </span>scipy
3067
+ <a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>caddforge-minimize
3068
+ <a id="__codelineno-21-3" name="__codelineno-21-3" href="#__codelineno-21-3"></a><span class="c1"># Use the reviewed public checkout, which includes the Amber validation fixes.</span>
3069
+ <a id="__codelineno-21-4" name="__codelineno-21-4" href="#__codelineno-21-4"></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="s1">'/path/to/caddforge-md[minimize]'</span>
3070
+ <a id="__codelineno-21-5" name="__codelineno-21-5" href="#__codelineno-21-5"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>md<span class="w"> </span>minimize
3071
+ <a id="__codelineno-21-6" name="__codelineno-21-6" href="#__codelineno-21-6"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>minimize<span class="w"> </span>--config<span class="w"> </span>minimize.yaml
3072
+ </code></pre></div>
3073
+ <p>Save this configuration as <code>minimize.yaml</code>, replacing the input paths:</p>
3074
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a><span class="nt">complex_pdb_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/complex.pdb</span>
3075
+ <a id="__codelineno-22-2" name="__codelineno-22-2" href="#__codelineno-22-2"></a><span class="nt">ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligand.sdf</span>
3076
+ <a id="__codelineno-22-3" name="__codelineno-22-3" href="#__codelineno-22-3"></a><span class="nt">lig_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">LIG</span>
3077
+ <a id="__codelineno-22-4" name="__codelineno-22-4" href="#__codelineno-22-4"></a><span class="nt">mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ligand_only</span>
3078
+ <a id="__codelineno-22-5" name="__codelineno-22-5" href="#__codelineno-22-5"></a><span class="nt">pocket_radius_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5.0</span>
3079
+ <a id="__codelineno-22-6" name="__codelineno-22-6" href="#__codelineno-22-6"></a><span class="nt">shell_radius_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5.0</span>
3080
+ <a id="__codelineno-22-7" name="__codelineno-22-7" href="#__codelineno-22-7"></a><span class="nt">backbone_restraint_strength</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">moderate</span>
3081
+ <a id="__codelineno-22-8" name="__codelineno-22-8" href="#__codelineno-22-8"></a><span class="nt">shell_restraint_strength</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">very_strong</span>
3082
+ <a id="__codelineno-22-9" name="__codelineno-22-9" href="#__codelineno-22-9"></a><span class="nt">tolerance_kj_mol_nm</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10.0</span>
3083
+ <a id="__codelineno-22-10" name="__codelineno-22-10" href="#__codelineno-22-10"></a><span class="nt">max_iterations</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1000</span>
3084
+ <a id="__codelineno-22-11" name="__codelineno-22-11" href="#__codelineno-22-11"></a><span class="nt">platform</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">CPU</span>
3085
+ <a id="__codelineno-22-12" name="__codelineno-22-12" href="#__codelineno-22-12"></a><span class="nt">run_directory</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">runs/minimize-one-complex</span>
3086
+ </code></pre></div>
3087
+ <p>For separate inputs, replace <code>complex_pdb_path</code> with <code>protein_pdb_path</code>; retain
3088
+ <code>ligand_path</code> in the same coordinate frame. To submit through Slurm, use
3089
+ <code>caddforge run md minimize --config minimize.yaml --backend slurm</code> with your
3090
+ site's <a href="../../core/slurm/">backend/environment settings</a>. There is no dedicated
3091
+ minimize GUI in this revision.</p>
3092
+ <p>AmberTools is installed separately from the Python extra. A prepared Amber input
3093
+ does not run AmberTools. Scientific imports are deferred until execution.
3094
+ CLI and pipeline execution use core input staging, including transparent gzip
3095
+ for declared input files. Checksums in chemistry/mapping records refer to the
3096
+ decompressed bytes. Nested cofactor chemistry paths are ordinary uncompressed
3097
+ configuration inputs and must be available on the execution node.</p>
3098
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">cadd_md.minimize</span><span class="w"> </span><span class="kn">import</span> <span class="n">MinimizeConfig</span><span class="p">,</span> <span class="n">MinimizeWorkflow</span>
3099
+ <a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a>
3100
+ <a id="__codelineno-23-3" name="__codelineno-23-3" href="#__codelineno-23-3"></a><span class="n">config</span> <span class="o">=</span> <span class="n">MinimizeConfig</span><span class="p">(</span>
3101
+ <a id="__codelineno-23-4" name="__codelineno-23-4" href="#__codelineno-23-4"></a> <span class="n">complex_pdb_path</span><span class="o">=</span><span class="s2">"complex.pdb"</span><span class="p">,</span>
3102
+ <a id="__codelineno-23-5" name="__codelineno-23-5" href="#__codelineno-23-5"></a> <span class="n">ligand_path</span><span class="o">=</span><span class="s2">"ligand.sdf"</span><span class="p">,</span>
3103
+ <a id="__codelineno-23-6" name="__codelineno-23-6" href="#__codelineno-23-6"></a> <span class="n">lig_resname</span><span class="o">=</span><span class="s2">"LIG"</span><span class="p">,</span>
3104
+ <a id="__codelineno-23-7" name="__codelineno-23-7" href="#__codelineno-23-7"></a> <span class="n">mode</span><span class="o">=</span><span class="s2">"pocket_restrained"</span><span class="p">,</span>
3105
+ <a id="__codelineno-23-8" name="__codelineno-23-8" href="#__codelineno-23-8"></a> <span class="n">run_directory</span><span class="o">=</span><span class="s2">"runs/cleanup"</span><span class="p">,</span>
3106
+ <a id="__codelineno-23-9" name="__codelineno-23-9" href="#__codelineno-23-9"></a> <span class="n">registry_path</span><span class="o">=</span><span class="s2">"runs/job_registry.sqlite"</span><span class="p">,</span>
3107
+ <a id="__codelineno-23-10" name="__codelineno-23-10" href="#__codelineno-23-10"></a><span class="p">)</span>
3108
+ <a id="__codelineno-23-11" name="__codelineno-23-11" href="#__codelineno-23-11"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">MinimizeWorkflow</span><span class="p">(</span><span class="n">config</span><span class="p">)</span>
3109
+ <a id="__codelineno-23-12" name="__codelineno-23-12" href="#__codelineno-23-12"></a><span class="n">result</span> <span class="o">=</span> <span class="n">workflow</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">workflow</span><span class="o">.</span><span class="n">prepare_job</span><span class="p">())</span>
3110
+ <a id="__codelineno-23-13" name="__codelineno-23-13" href="#__codelineno-23-13"></a><span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">status</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
3111
+ <a id="__codelineno-23-14" name="__codelineno-23-14" href="#__codelineno-23-14"></a><span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">[</span><span class="s2">"minimized_complex"</span><span class="p">])</span>
3112
+ </code></pre></div>
3113
+ <p>Paths follow the existing config convention: relative paths resolve from the
3114
+ submission working directory. Use the core CLI/backend for Slurm submission;
3115
+ the scientific workflow contains no scheduler-specific execution logic.
3116
+ Choose a fresh <code>run_directory</code> for each run; existing minimization outputs are
3117
+ preserved and cannot be overwritten by a new job.</p>
3118
+ <h3 id="minimize-inputs-and-physical-model">Minimize inputs and physical model<a class="headerlink" href="#minimize-inputs-and-physical-model" title="Permanent link">&para;</a></h3>
3119
+ <p>Supply either <code>complex_pdb_path</code>, or <code>protein_pdb_path</code> plus a ligand pose in the
3120
+ same coordinate frame. <code>ligand_path</code> is always required and supplies authoritative
3121
+ SDF/MOL/MOL2 chemistry. For a complex PDB, coordinates come from that complex;
3122
+ template coordinates are not used to align or move the pose. For separate inputs,
3123
+ the ligand file must contain one explicitly hydrogenated 3D molecule. The target
3124
+ residue is selected by <code>lig_resname</code>, which must occur exactly once.</p>
3125
+ <p>Preparation preserves supplied atoms, protonation, ligand stereochemistry, and
3126
+ disulfides, adds only missing hydrogens, and rejects missing protein heavy atoms.
3127
+ Repair missing protein heavy atoms upstream before submitting the complex; this tool only adds missing hydrogens. Bare histidines need
3128
+ unambiguous hydrogen evidence or an explicit <code>residue_states</code> entry. Optional
3129
+ <code>protein_states_path</code> and <code>protein_links_path</code> must be provided together and match
3130
+ the input structure checksum. Covalent target ligands are rejected.</p>
3131
+ <p>Automatic preparation uses ff14SB, GAFF2/AM1-BCC, TIP3P retained waters, and OBC2
3132
+ with <code>mbondi2</code> radii, ACE surface area, solute dielectric 1, solvent dielectric
3133
+ 78.5, and zero salt screening. It is nonperiodic with <code>NoCutoff</code>; no solvent box
3134
+ or neutralizing ions are added. Retained waters are explicit solute particles in
3135
+ the GB model, a hybrid approximation requiring application-specific validation.
3136
+ All force-field choices, parameterization commands, checksums, and available
3137
+ software versions are retained.
3138
+ Both atom typing and missing-parameter lookup explicitly select GAFF2. Unresolved
3139
+ <code>parmchk2</code> parameter warnings fail preparation and require reviewed parameters.</p>
3140
+ <p>Generated GAFF2/AM1-BCC charges are checked and, when necessary, normalized
3141
+ independently for each organic component. Minimize and OpenBPMD apply a uniform
3142
+ per-atom offset only when the total correction is at most <strong>0.005 e</strong> and each
3143
+ atom changes by at most <strong>0.0001 e</strong>. These are conservative engineering limits,
3144
+ not universal scientific guarantees. Final component charges must sum to the
3145
+ authoritative formal charge within <strong>1e-8 e</strong>, and mapped charges are verified
3146
+ again after Amber topology construction. Invalid chemistry or larger residuals
3147
+ fail preparation; supplied Amber charges are never normalized.</p>
3148
+ <p>Preparation retains the original <code>*.raw.mol2</code>, the final MOL2, and a
3149
+ <code>*.charge_validation.json</code> report with raw/final sums, correction, policy limits,
3150
+ checksums, and the decision. <code>charge_validation</code> in the preparation summary links
3151
+ the reports, including rejected corrections. Applied corrections also produce a
3152
+ log warning. A residual within the charge-token rounding bound is distinguished
3153
+ from a larger generation residual; the latter is not assumed to be rounding.
3154
+ Changing <code>ligand_net_charge</code> or disabling quality checks is not a remedy for this
3155
+ error. These rules also apply to pipeline and scatter jobs without new YAML
3156
+ options.</p>
3157
+ <p>Automatic preparation also retains Antechamber's <code>ANTECHAMBER_AC.AC</code> bond
3158
+ evidence. The shared validator checks mapped atoms, coordinates, atom types,
3159
+ connectivity (including hydrogen attachments), and total formal charge against
3160
+ the authoritative ligand. A missing or inconsistent AC file fails preparation.</p>
3161
+ <p>Amber MOL2 bond tokens are not always literal chemical bond orders: for example,
3162
+ carboxylate C–O bonds can both be written as single bonds. Validation accepts
3163
+ supported Amber encodings only in their permitted chemical environments and
3164
+ requires one complete authoritative or RDKit resonance form to explain every
3165
+ bond. Aromatic/Kekulé alternatives are supported; arbitrary bond-order changes,
3166
+ tautomers, and changed protonation are not accepted. At most 1,000 candidate
3167
+ forms are examined. An inconclusive capped search fails explicitly.</p>
3168
+ <p>The charge report contains a <code>graph_validation</code> record with source checksums,
3169
+ atom mapping, candidate count, interpreted bonds, and the acceptance or rejection
3170
+ reason. The validators never rewrite bond records, atom types, coordinates, or
3171
+ the authoritative ligand. Charge normalization runs only after graph validation.
3172
+ These rules apply equally to minimize, OpenBPMD, organic cofactors, and pipeline
3173
+ jobs; no configuration override is needed for supported representations.</p>
3174
+ <p>Noncovalent organic cofactors require <code>cofactors</code> entries with <code>residue_index</code>
3175
+ and <code>chemistry_path</code>; optional <code>atom_map_path</code> uses the shared explicit atom-map
3176
+ schema against the original complex. Residue and atom indices are zero-based
3177
+ indices in <code>preparation/inputs/input_identity.json</code>, not PDB serial numbers.
3178
+ Automatic isolated ions are restricted to Na+, K+, and Cl- and require explicit
3179
+ <code>isolated_ion_residue_indices</code>. These declarations must not be used to stand in
3180
+ for a coordinated metal-site model.</p>
3181
+ <p>Coordinated metals, metall cofactors, and other supported supplied components
3182
+ use all three fields: <code>amber_topology_path</code>, <code>amber_coordinates_path</code>, and
3183
+ <code>amber_mapping_path</code>, alongside the complete input complex. The topology must
3184
+ be nonperiodic, contain all bonded/nonbonded parameters and positive GB
3185
+ radii/screening factors, and have finite charges and positive masses. Unsupported
3186
+ force forms and virtual sites fail explicitly. The supplied radii and charges
3187
+ are used without substituting automatic values. Every non-isolated metal needs
3188
+ a <code>metal_sites</code> entry containing <code>atom_index</code>, <code>oxidation_state</code>,
3189
+ <code>coordinating_atom_indices</code>, and a descriptive <code>parameter_source</code>.</p>
3190
+ <p>The prepared Amber mapping is JSON:</p>
3191
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a><span class="p">{</span>
3192
+ <a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a><span class="w"> </span><span class="nt">"schema_version"</span><span class="p">:</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span>
3193
+ <a id="__codelineno-24-3" name="__codelineno-24-3" href="#__codelineno-24-3"></a><span class="w"> </span><span class="nt">"input_sha256"</span><span class="p">:</span><span class="w"> </span><span class="s2">"SHA256 of the complex PDB"</span><span class="p">,</span>
3194
+ <a id="__codelineno-24-4" name="__codelineno-24-4" href="#__codelineno-24-4"></a><span class="w"> </span><span class="nt">"topology_sha256"</span><span class="p">:</span><span class="w"> </span><span class="s2">"SHA256 of the Amber topology"</span><span class="p">,</span>
3195
+ <a id="__codelineno-24-5" name="__codelineno-24-5" href="#__codelineno-24-5"></a><span class="w"> </span><span class="nt">"coordinates_sha256"</span><span class="p">:</span><span class="w"> </span><span class="s2">"SHA256 of the Amber coordinates"</span><span class="p">,</span>
3196
+ <a id="__codelineno-24-6" name="__codelineno-24-6" href="#__codelineno-24-6"></a><span class="w"> </span><span class="nt">"input_atom_indices"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="mi">2</span><span class="p">,</span><span class="w"> </span><span class="kc">null</span><span class="p">],</span>
3197
+ <a id="__codelineno-24-7" name="__codelineno-24-7" href="#__codelineno-24-7"></a><span class="w"> </span><span class="nt">"input_residue_indices"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
3198
+ <a id="__codelineno-24-8" name="__codelineno-24-8" href="#__codelineno-24-8"></a><span class="p">}</span>
3199
+ </code></pre></div>
3200
+ <p>The arrays follow Amber topology order and must cover every input atom/residue
3201
+ exactly once. <code>null</code> is allowed only for an added hydrogen. Array lengths must
3202
+ match the actual topology; the short arrays above illustrate the schema only.
3203
+ Parameter sources and oxidation states are declarations, not an automatic
3204
+ validation of a metal model's physical accuracy.</p>
3205
+ <h3 id="minimize-regions-and-modes">Minimize regions and modes<a class="headerlink" href="#minimize-regions-and-modes" title="Permanent link">&para;</a></h3>
3206
+ <p>Pocket residues have any heavy atom within <code>pocket_radius_angstrom: 5.0</code> of any
3207
+ ligand heavy atom. The shell contains other protein residues with any heavy atom
3208
+ within <code>shell_radius_angstrom: 5.0</code> of <strong>any pocket heavy atom</strong>. Both selections
3209
+ expand to whole residues and stay fixed during minimization. An explicit
3210
+ <code>pocket_residues: ["A:42", "A:43:B"]</code> replaces automatic pocket selection;
3211
+ <code>_</code> denotes a blank chain. Unknown, duplicate, ambiguous, or empty selections fail.</p>
3212
+ <table>
3213
+ <thead>
3214
+ <tr>
3215
+ <th><code>mode</code></th>
3216
+ <th>Pocket side chains</th>
3217
+ <th>Pocket backbone</th>
3218
+ <th>Shell</th>
3219
+ </tr>
3220
+ </thead>
3221
+ <tbody>
3222
+ <tr>
3223
+ <td><code>ligand_only</code> (default)</td>
3224
+ <td>Fixed</td>
3225
+ <td>Fixed</td>
3226
+ <td>Fixed</td>
3227
+ </tr>
3228
+ <tr>
3229
+ <td><code>sidechains_free_backbone_fixed</code></td>
3230
+ <td>Free</td>
3231
+ <td>Fixed</td>
3232
+ <td>Fixed</td>
3233
+ </tr>
3234
+ <tr>
3235
+ <td><code>sidechains_free_backbone_restrained</code></td>
3236
+ <td>Free</td>
3237
+ <td>Restrained</td>
3238
+ <td>Fixed</td>
3239
+ </tr>
3240
+ <tr>
3241
+ <td><code>pocket_restrained</code></td>
3242
+ <td>Free</td>
3243
+ <td>Restrained</td>
3244
+ <td>Strongly restrained</td>
3245
+ </tr>
3246
+ <tr>
3247
+ <td><code>pocket_free_shell_restrained</code></td>
3248
+ <td>Free</td>
3249
+ <td>Free</td>
3250
+ <td>Strongly restrained</td>
3251
+ </tr>
3252
+ </tbody>
3253
+ </table>
3254
+ <p>The target ligand is free and distant protein is fixed in every mode. Backbone
3255
+ atoms are N/CA/C/O/OXT; terminal caps count as backbone. Hydrogens inherit their
3256
+ bonded parent's region. Waters, ions, metals, and cofactors are fixed by default;
3257
+ <code>component_mobility</code> permits explicit whole-residue <code>fixed</code>, <code>free</code>, or
3258
+ <code>restrained</code> overrides keyed by input residue index.</p>
3259
+ <p>Positional restraints use <strong>E = ½ k |r − r₀|²</strong>, with <strong>k in kJ mol⁻¹ nm⁻²</strong>.
3260
+ Named strengths are <code>weak: 100</code>, <code>moderate: 1000</code>, and <code>very_strong: 10000</code>;
3261
+ positive numeric strengths are accepted. <code>backbone_restraint_strength</code> defaults
3262
+ to <code>moderate</code>, and <code>shell_restraint_strength</code> to <code>very_strong</code>. They are starting
3263
+ regimes, not universally validated settings. Only heavy atoms are restrained
3264
+ unless <code>restrain_hydrogens: true</code>. Fixed regions include their hydrogens.</p>
3265
+ <p>Fixed particles have zero mass in a private minimization-system copy. The
3266
+ exported physical system retains original masses. Bonds and water geometry are
3267
+ flexible by default. <code>constraints: mobile_hbonds</code> constrains bonds involving
3268
+ hydrogen only when both endpoints are mobile, using their force-field equilibrium
3269
+ lengths and retaining the physical bonded terms. Constraints involving fixed
3270
+ atoms are rejected. Disulfide connectivity is preserved across region boundaries.</p>
3271
+ <h3 id="minimize-convergence-diagnostics-and-quality">Minimize convergence, diagnostics, and quality<a class="headerlink" href="#minimize-convergence-diagnostics-and-quality" title="Permanent link">&para;</a></h3>
3272
+ <p>Defaults are <code>tolerance_kj_mol_nm: 10.0</code>, <code>max_iterations: 1000</code>,
3273
+ <code>constraint_tolerance: 0.00001</code>, <code>platform: CPU</code>, and <code>cpu_threads: 1</code>.
3274
+ GPU platforms accept <code>precision: single|mixed|double</code> where supported. Explicitly
3275
+ requested unavailable platforms or precision settings fail instead of falling back.</p>
3276
+ <p>The iteration budget spans OpenMM constraint restarts. The trace distinguishes
3277
+ the physical-plus-positional objective from OpenMM's temporary bond-constraint
3278
+ penalty. Final convergence is independently checked using RMS force components
3279
+ over mobile atoms, projected onto the allowed constraint tangent space when
3280
+ needed, plus maximum relative constraint error. A normal OpenMM return alone
3281
+ does not establish convergence. Status is <code>verified_converged</code>, <code>iteration_limit</code>,
3282
+ <code>not_verified</code>, or <code>failed</code>; the record also reports a reached budget even if the
3283
+ last iterate independently satisfies the convergence tests.
3284
+ The implementation targets the <a href="https://github.com/openmm/openmm/blob/8.2.0/openmmapi/src/LocalEnergyMinimizer.cpp">OpenMM 8.2 minimizer and reporter behavior</a>.</p>
3285
+ <p>Diagnostics include initial/final molecular-mechanics, GB, physical, positional,
3286
+ and total objective energies; physical/total RMS and maximum forces for all,
3287
+ mobile, and fixed atoms; iteration counts; constraint errors; heavy-atom ligand,
3288
+ pocket, backbone, shell, receptor, and component RMSDs without alignment; and
3289
+ maximum displacements with atom indices. Preparation displacement is separate.
3290
+ Ordinary nonbonded clashes, 1–4 overlaps, and declared metal coordination are
3291
+ reported separately. Bonded and angle-connected contacts are excluded.</p>
3292
+ <p>Default review triggers under <code>quality_thresholds</code> are:</p>
3293
+ <table>
3294
+ <thead>
3295
+ <tr>
3296
+ <th>Field</th>
3297
+ <th>Default</th>
3298
+ </tr>
3299
+ </thead>
3300
+ <tbody>
3301
+ <tr>
3302
+ <td><code>ligand_rmsd_angstrom</code></td>
3303
+ <td>1.0</td>
3304
+ </tr>
3305
+ <tr>
3306
+ <td><code>ligand_max_displacement_angstrom</code></td>
3307
+ <td>2.0</td>
3308
+ </tr>
3309
+ <tr>
3310
+ <td><code>pocket_backbone_rmsd_angstrom</code></td>
3311
+ <td>0.5</td>
3312
+ </tr>
3313
+ <tr>
3314
+ <td><code>receptor_max_displacement_angstrom</code></td>
3315
+ <td>2.0</td>
3316
+ </tr>
3317
+ <tr>
3318
+ <td><code>absolute_energy_per_atom_kj_mol</code></td>
3319
+ <td>10000</td>
3320
+ </tr>
3321
+ <tr>
3322
+ <td><code>maximum_force_kj_mol_nm</code></td>
3323
+ <td>100000</td>
3324
+ </tr>
3325
+ <tr>
3326
+ <td><code>allowed_vdw_overlap_angstrom</code></td>
3327
+ <td>0.6</td>
3328
+ </tr>
3329
+ <tr>
3330
+ <td><code>coordination_distance_change_angstrom</code></td>
3331
+ <td>0.3</td>
3332
+ </tr>
3333
+ <tr>
3334
+ <td><code>objective_increase_absolute_kj_mol</code></td>
3335
+ <td>0.01</td>
3336
+ </tr>
3337
+ <tr>
3338
+ <td><code>objective_increase_relative</code></td>
3339
+ <td>1e-8</td>
3340
+ </tr>
3341
+ </tbody>
3342
+ </table>
3343
+ <p>These are review triggers, not universal validity bounds; geometric overlaps,
3344
+ especially 1–4 contacts, need chemical interpretation. Nonfinite states, invalid
3345
+ chemistry, or any fixed-atom movement always fail. Other findings produce
3346
+ machine-readable <code>quality_flags</code>. Set <code>strict_quality: true</code> to fail on every
3347
+ flag, or combine <code>strict_quality: true</code> with <code>strict_quality_flags</code> to fail only on selected codes such as
3348
+ <code>convergence_unverified</code>, <code>large_ligand_displacement</code>, or
3349
+ <code>residual_nonbonded_clashes</code>. Finite strict-failure poses remain available.</p>
3350
+ <h3 id="minimize-artifacts-and-pipelines">Minimize artifacts and pipelines<a class="headerlink" href="#minimize-artifacts-and-pipelines" title="Permanent link">&para;</a></h3>
3351
+ <p>Canonical results are saved in <code>results/result_record.json</code>. Scientific artifacts
3352
+ are under <code>results/minimize/</code>: <code>structures/</code> contains minimized PDB/SDF files and
3353
+ fresh handoff records; <code>preparation/</code> contains the physical system, initial
3354
+ coordinates, atom mapping, and provenance; <code>minimization/</code> contains diagnostics,
3355
+ full-precision final coordinates, and the iteration trace. Exact region membership
3356
+ is in <code>results/minimize/regions.json</code>.</p>
3357
+ <p>Pipeline input names differ from config fields:</p>
3358
+ <table>
3359
+ <thead>
3360
+ <tr>
3361
+ <th>Input port</th>
3362
+ <th>Config field</th>
3363
+ </tr>
3364
+ </thead>
3365
+ <tbody>
3366
+ <tr>
3367
+ <td><code>complex</code></td>
3368
+ <td><code>complex_pdb_path</code></td>
3369
+ </tr>
3370
+ <tr>
3371
+ <td><code>protein</code></td>
3372
+ <td><code>protein_pdb_path</code></td>
3373
+ </tr>
3374
+ <tr>
3375
+ <td><code>ligand</code></td>
3376
+ <td><code>ligand_path</code></td>
3377
+ </tr>
3378
+ <tr>
3379
+ <td><code>ligand_atom_map</code></td>
3380
+ <td><code>ligand_atom_map_path</code></td>
3381
+ </tr>
3382
+ <tr>
3383
+ <td><code>protein_states</code>, <code>protein_links</code></td>
3384
+ <td><code>protein_states_path</code>, <code>protein_links_path</code></td>
3385
+ </tr>
3386
+ <tr>
3387
+ <td><code>amber_topology</code>, <code>amber_coordinates</code>, <code>amber_mapping</code></td>
3388
+ <td><code>amber_topology_path</code>, <code>amber_coordinates_path</code>, <code>amber_mapping_path</code></td>
3389
+ </tr>
3390
+ </tbody>
3391
+ </table>
3392
+ <p>Supply exactly one structure input and a ligand chemistry file. The paired
3393
+ protein-state/link inputs and the three prepared-Amber inputs must be complete
3394
+ when provided.</p>
3395
+ <table>
3396
+ <thead>
3397
+ <tr>
3398
+ <th>Output port</th>
3399
+ <th><code>Result.paths</code> key</th>
3400
+ </tr>
3401
+ </thead>
3402
+ <tbody>
3403
+ <tr>
3404
+ <td><code>complex</code></td>
3405
+ <td><code>minimized_complex</code></td>
3406
+ </tr>
3407
+ <tr>
3408
+ <td><code>protein</code></td>
3409
+ <td><code>minimized_protein</code></td>
3410
+ </tr>
3411
+ <tr>
3412
+ <td><code>ligand</code></td>
3413
+ <td><code>minimized_ligand</code></td>
3414
+ </tr>
3415
+ <tr>
3416
+ <td><code>result_record</code></td>
3417
+ <td><code>result_record</code></td>
3418
+ </tr>
3419
+ <tr>
3420
+ <td><code>diagnostics</code></td>
3421
+ <td><code>diagnostics</code></td>
3422
+ </tr>
3423
+ </tbody>
3424
+ </table>
3425
+ <p>All other output ports below use the same name as their result-path key. Output ports expose
3426
+ <code>complex</code>, <code>protein</code>, <code>ligand</code>, <code>diagnostics</code>, <code>regions</code>, <code>atom_mapping</code>,
3427
+ <code>output_mapping</code>, <code>preparation_summary</code>, <code>physical_system</code>, <code>prepared_positions</code>,
3428
+ <code>minimized_positions</code>, <code>amber_topology</code>, <code>amber_coordinates</code>, <code>structure_manifest</code>,
3429
+ <code>protein_states</code>, <code>protein_links</code>, <code>receptor_protein_states</code>,
3430
+ <code>receptor_protein_links</code>, optional <code>iteration_trace</code>, <code>result_record</code>, and <code>output_dir</code>.
3431
+ The complex handoff records match the complex checksum; <code>receptor_*</code> records
3432
+ match the protein output. A covalently connected environment component is retained
3433
+ in the receptor export to avoid cutting chemical bonds, and this is recorded.</p>
3434
+ <p>The ligand SDF preserves chemistry, title, and user properties. PDB coordinates
3435
+ are rounded to 0.001 Å and SDF coordinates to 0.0001 Å; NumPy coordinate artifacts
3436
+ retain full precision in <strong>nanometers</strong>, in physical-system particle order. The
3437
+ Amber coordinate artifact is the prepared starting configuration. Use the
3438
+ separate minimized coordinate artifact for the final pose. The exported physical
3439
+ system contains no zero-mass freezes or positional restraints and still needs an
3440
+ appropriate MD protocol before dynamics.</p>
3441
+ <p>Download example configurations for
3442
+ <a href="../../examples/minimize/ligand_only.yaml">ligand only</a>,
3443
+ <a href="../../examples/minimize/sidechains_free_backbone_fixed.yaml">free side chains/fixed backbone</a>,
3444
+ <a href="../../examples/minimize/sidechains_free_backbone_restrained.yaml">free side chains/restrained backbone</a>,
3445
+ <a href="../../examples/minimize/pocket_restrained.yaml">restrained pocket</a>,
3446
+ <a href="../../examples/minimize/pocket_free_shell_restrained.yaml">free pocket/restrained shell</a>,
3447
+ <a href="../../examples/minimize/component_overrides.yaml">component overrides</a>, and
3448
+ <a href="../../examples/minimize/prepared_metal.yaml">supplied metal parameters</a>.
3449
+ See the <a href="../../pipelines/examples/#minimize-a-multi-pose-sdf">minimize pipeline examples</a>
3450
+ for complete YAML and artifact flow. The pipeline uses existing
3451
+ scatter/collect/filter stages and preserves per-pose provenance. Filtering quality
3452
+ flags does not establish pose accuracy; do not rank unrelated ligands by total
3453
+ minimization energy.</p>
3454
+ <p>Validation in the <code>caddforge-md</code> checkout: <code>python -m pytest tests/test_minimize_*.py</code>. Scientific fixtures use
3455
+ generated peptides/ligands and are marked <code>external</code>; optional GPU comparison
3456
+ tests skip with an explicit reason when no usable GPU platform exists.</p>
3457
+ <h2 id="openbpmd"><code>openbpmd</code><a class="headerlink" href="#openbpmd" title="Permanent link">&para;</a></h2>
3458
+ <p>Runs OpenBPMD preprocessing, simulations, and averaged multi-replica analysis.</p>
3459
+ <p>CLI:</p>
3460
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>openbpmd<span class="w"> </span>--config<span class="w"> </span>openbpmd.yaml
3461
+ </code></pre></div>
3462
+ <p>YAML:</p>
3463
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
3464
+ <a id="__codelineno-26-2" name="__codelineno-26-2" href="#__codelineno-26-2"></a><span class="nt">complex_pdb_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/complex.pdb</span>
3465
+ <a id="__codelineno-26-3" name="__codelineno-26-3" href="#__codelineno-26-3"></a><span class="nt">lig_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">MOL</span>
3466
+ <a id="__codelineno-26-4" name="__codelineno-26-4" href="#__codelineno-26-4"></a><span class="nt">ligand_net_charge</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
3467
+ <a id="__codelineno-26-5" name="__codelineno-26-5" href="#__codelineno-26-5"></a><span class="nt">nreps</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
3468
+ <a id="__codelineno-26-6" name="__codelineno-26-6" href="#__codelineno-26-6"></a><span class="nt">hill_height</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.05</span>
3469
+ <a id="__codelineno-26-7" name="__codelineno-26-7" href="#__codelineno-26-7"></a><span class="nt">deposit_interval_ps</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
3470
+ <a id="__codelineno-26-8" name="__codelineno-26-8" href="#__codelineno-26-8"></a><span class="nt">log_sync_interval_seconds</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">30</span>
3471
+ <a id="__codelineno-26-9" name="__codelineno-26-9" href="#__codelineno-26-9"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
3472
+ <a id="__codelineno-26-10" name="__codelineno-26-10" href="#__codelineno-26-10"></a><span class="nt">analysis_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">analysis</span>
3473
+ </code></pre></div>
3474
+ <p>Python:</p>
3475
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
3476
+ <a id="__codelineno-27-2" name="__codelineno-27-2" href="#__codelineno-27-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
3477
+ <a id="__codelineno-27-3" name="__codelineno-27-3" href="#__codelineno-27-3"></a>
3478
+ <a id="__codelineno-27-4" name="__codelineno-27-4" href="#__codelineno-27-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"openbpmd"</span><span class="p">)</span>
3479
+ <a id="__codelineno-27-5" name="__codelineno-27-5" href="#__codelineno-27-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
3480
+ <a id="__codelineno-27-6" name="__codelineno-27-6" href="#__codelineno-27-6"></a> <span class="n">complex_pdb_path</span><span class="o">=</span><span class="s2">"data/complex.pdb"</span><span class="p">,</span>
3481
+ <a id="__codelineno-27-7" name="__codelineno-27-7" href="#__codelineno-27-7"></a> <span class="n">lig_resname</span><span class="o">=</span><span class="s2">"MOL"</span><span class="p">,</span>
3482
+ <a id="__codelineno-27-8" name="__codelineno-27-8" href="#__codelineno-27-8"></a> <span class="n">nreps</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
3483
+ <a id="__codelineno-27-9" name="__codelineno-27-9" href="#__codelineno-27-9"></a> <span class="n">hill_height</span><span class="o">=</span><span class="mf">0.05</span><span class="p">,</span>
3484
+ <a id="__codelineno-27-10" name="__codelineno-27-10" href="#__codelineno-27-10"></a> <span class="n">deposit_interval_ps</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
3485
+ <a id="__codelineno-27-11" name="__codelineno-27-11" href="#__codelineno-27-11"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
3486
+ <a id="__codelineno-27-12" name="__codelineno-27-12" href="#__codelineno-27-12"></a><span class="p">)</span>
3487
+ <a id="__codelineno-27-13" name="__codelineno-27-13" href="#__codelineno-27-13"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
3488
+ <a id="__codelineno-27-14" name="__codelineno-27-14" href="#__codelineno-27-14"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
3489
+ <a id="__codelineno-27-15" name="__codelineno-27-15" href="#__codelineno-27-15"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
3490
+ <a id="__codelineno-27-16" name="__codelineno-27-16" href="#__codelineno-27-16"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
3491
+ <a id="__codelineno-27-17" name="__codelineno-27-17" href="#__codelineno-27-17"></a><span class="p">)</span>
3492
+ <a id="__codelineno-27-18" name="__codelineno-27-18" href="#__codelineno-27-18"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
3493
+ <a id="__codelineno-27-19" name="__codelineno-27-19" href="#__codelineno-27-19"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
3494
+ <a id="__codelineno-27-20" name="__codelineno-27-20" href="#__codelineno-27-20"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">)</span>
3495
+ </code></pre></div>
3496
+ <p>Outputs to inspect: <code>prep/</code>, <code>results/output/</code>, <code>results/analysis/results.csv</code>,
3497
+ <code>results/analysis/multi_rep_timeseries.csv</code>, <code>results/progress.json</code>,
3498
+ <code>results/result_record.json</code>.</p>
3499
+ <p>OpenBPMD streams subprocess output to scratch-first logs and publishes best-effort replica progress
3500
+ from the per-replica simulation logs. <code>log_sync_interval_seconds</code> controls publication frequency;
3501
+ temporary shared-filesystem failures are retried without changing the scientific outcome.</p>
3502
+ <h2 id="grand"><code>grand</code><a class="headerlink" href="#grand" title="Permanent link">&para;</a></h2>
3503
+ <p>Runs Grand Canonical Monte Carlo (GCMC) water sampling in a ligand-centred pocket region and then
3504
+ selects a single representative protein-ligand-water structure from the resulting trajectory, all
3505
+ within one job. The tool combines two stages so you obtain a usable representative hydration state
3506
+ without a separate manual step.</p>
3507
+ <p><strong>GCMC sampling stage.</strong> The first stage prepares the input protein-ligand complex (adds hydrogens
3508
+ at the configured pH, optionally solvates with padding and ionic strength, restrains solute heavy
3509
+ atoms, and adds ghost waters) and then performs GCMC insertion and deletion sampling inside a
3510
+ ligand-centred spherical region defined by <code>sphere_radius_angstrom</code>. It uses the configured
3511
+ initialization passes and maximum production passes with a running water-count convergence check.
3512
+ The stage writes the final-state checkpoint before any trajectory readback, then produces a
3513
+ trajectory, a per-frame ghost-water state file (one row per frame listing the inactive ghost-water
3514
+ residue indices for that frame), and a hydrated-complex structure. Post-processing is non-strict: if
3515
+ it fails, the error is recorded in the stage summary while the completed checkpoint and trajectory
3516
+ are preserved so the run can continue.</p>
3517
+ <p><strong>Representative-selection stage.</strong> The second stage runs on the produced trajectory and uses the
3518
+ per-frame ghost-water state file to exclude, for each analysed frame, that frame's ghost waters from
3519
+ all downstream selection and output. It deterministically selects exactly one representative frame
3520
+ from within the configured frame analysis interval (repeated runs on the same trajectory and
3521
+ configuration select the same frame) and writes a representative complex structure containing the
3522
+ ligand residue, the protein atoms, and the active non-ghost water residues present at the selected
3523
+ frame. When a ligand template SDF and <code>ligand_resname</code> are configured, it also writes a
3524
+ template-corrected ligand SDF whose bond orders and chemistry come from the template and whose
3525
+ coordinates come from the selected frame, plus an optional protein-only structure. Template ligand
3526
+ export is non-strict: on failure the error is recorded in the selection summary and the
3527
+ representative complex is still written.</p>
3528
+ <p>CLI:</p>
3529
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>grand<span class="w"> </span>--config<span class="w"> </span>grand.yaml
3530
+ <a id="__codelineno-28-2" name="__codelineno-28-2" href="#__codelineno-28-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>grand<span class="w"> </span>--config<span class="w"> </span>grand.yaml<span class="w"> </span>--backend<span class="w"> </span>slurm<span class="w"> </span>--slurm-time<span class="w"> </span><span class="m">24</span>:00:00
3531
+ </code></pre></div>
3532
+ <p>YAML:</p>
3533
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-29-1" name="__codelineno-29-1" href="#__codelineno-29-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
3534
+ <a id="__codelineno-29-2" name="__codelineno-29-2" href="#__codelineno-29-2"></a><span class="nt">complex_pdb_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/complex.pdb</span>
3535
+ <a id="__codelineno-29-3" name="__codelineno-29-3" href="#__codelineno-29-3"></a><span class="nt">ligand_template_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligand_template.sdf</span>
3536
+ <a id="__codelineno-29-4" name="__codelineno-29-4" href="#__codelineno-29-4"></a><span class="nt">ligand_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">LIG</span>
3537
+ <a id="__codelineno-29-5" name="__codelineno-29-5" href="#__codelineno-29-5"></a><span class="nt">sphere_radius_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10.0</span>
3538
+ <a id="__codelineno-29-6" name="__codelineno-29-6" href="#__codelineno-29-6"></a><span class="nt">n_ghost_waters</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">150</span>
3539
+ <a id="__codelineno-29-7" name="__codelineno-29-7" href="#__codelineno-29-7"></a><span class="nt">nonbonded_cutoff_nm</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.9</span>
3540
+ <a id="__codelineno-29-8" name="__codelineno-29-8" href="#__codelineno-29-8"></a><span class="nt">temperature_kelvin</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">300.0</span>
3541
+ <a id="__codelineno-29-9" name="__codelineno-29-9" href="#__codelineno-29-9"></a><span class="nt">initialization_passes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">7500</span>
3542
+ <a id="__codelineno-29-10" name="__codelineno-29-10" href="#__codelineno-29-10"></a><span class="nt">max_production_passes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100000</span>
3543
+ <a id="__codelineno-29-11" name="__codelineno-29-11" href="#__codelineno-29-11"></a><span class="nt">ph</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">7.4</span>
3544
+ <a id="__codelineno-29-12" name="__codelineno-29-12" href="#__codelineno-29-12"></a><span class="nt">padding_nm</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.2</span>
3545
+ <a id="__codelineno-29-13" name="__codelineno-29-13" href="#__codelineno-29-13"></a><span class="nt">ionic_strength_molar</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.15</span>
3546
+ <a id="__codelineno-29-14" name="__codelineno-29-14" href="#__codelineno-29-14"></a><span class="nt">ligand_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
3547
+ <a id="__codelineno-29-15" name="__codelineno-29-15" href="#__codelineno-29-15"></a><span class="nt">align_selection</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
3548
+ <a id="__codelineno-29-16" name="__codelineno-29-16" href="#__codelineno-29-16"></a><span class="nt">frame_analysis_interval</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
3549
+ <a id="__codelineno-29-17" name="__codelineno-29-17" href="#__codelineno-29-17"></a><span class="nt">log_sync_interval_seconds</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">30</span>
3550
+ <a id="__codelineno-29-18" name="__codelineno-29-18" href="#__codelineno-29-18"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">output</span>
3551
+ <a id="__codelineno-29-19" name="__codelineno-29-19" href="#__codelineno-29-19"></a><span class="nt">trajectory_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gcmc_trajectory.dcd</span>
3552
+ <a id="__codelineno-29-20" name="__codelineno-29-20" href="#__codelineno-29-20"></a><span class="nt">ghost_water_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ghost_water_state.txt</span>
3553
+ <a id="__codelineno-29-21" name="__codelineno-29-21" href="#__codelineno-29-21"></a><span class="nt">checkpoint_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gcmc_checkpoint.chk</span>
3554
+ <a id="__codelineno-29-22" name="__codelineno-29-22" href="#__codelineno-29-22"></a><span class="nt">hydrated_complex_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">hydrated_complex.pdb</span>
3555
+ <a id="__codelineno-29-23" name="__codelineno-29-23" href="#__codelineno-29-23"></a><span class="nt">gcmc_summary_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gcmc_summary.json</span>
3556
+ <a id="__codelineno-29-24" name="__codelineno-29-24" href="#__codelineno-29-24"></a><span class="nt">representative_complex_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">representative_complex.pdb</span>
3557
+ <a id="__codelineno-29-25" name="__codelineno-29-25" href="#__codelineno-29-25"></a><span class="nt">representative_protein_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">representative_protein.pdb</span>
3558
+ <a id="__codelineno-29-26" name="__codelineno-29-26" href="#__codelineno-29-26"></a><span class="nt">representative_ligand_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">representative_ligand.sdf</span>
3559
+ <a id="__codelineno-29-27" name="__codelineno-29-27" href="#__codelineno-29-27"></a><span class="nt">selection_summary_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">selection_summary.json</span>
3560
+ </code></pre></div>
3561
+ <p>Python:</p>
3562
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
3563
+ <a id="__codelineno-30-2" name="__codelineno-30-2" href="#__codelineno-30-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
3564
+ <a id="__codelineno-30-3" name="__codelineno-30-3" href="#__codelineno-30-3"></a>
3565
+ <a id="__codelineno-30-4" name="__codelineno-30-4" href="#__codelineno-30-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"md"</span><span class="p">,</span> <span class="s2">"grand"</span><span class="p">)</span>
3566
+ <a id="__codelineno-30-5" name="__codelineno-30-5" href="#__codelineno-30-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
3567
+ <a id="__codelineno-30-6" name="__codelineno-30-6" href="#__codelineno-30-6"></a> <span class="n">complex_pdb_path</span><span class="o">=</span><span class="s2">"data/complex.pdb"</span><span class="p">,</span>
3568
+ <a id="__codelineno-30-7" name="__codelineno-30-7" href="#__codelineno-30-7"></a> <span class="n">ligand_template_sdf</span><span class="o">=</span><span class="s2">"data/ligand_template.sdf"</span><span class="p">,</span>
3569
+ <a id="__codelineno-30-8" name="__codelineno-30-8" href="#__codelineno-30-8"></a> <span class="n">ligand_resname</span><span class="o">=</span><span class="s2">"LIG"</span><span class="p">,</span>
3570
+ <a id="__codelineno-30-9" name="__codelineno-30-9" href="#__codelineno-30-9"></a> <span class="n">sphere_radius_angstrom</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span>
3571
+ <a id="__codelineno-30-10" name="__codelineno-30-10" href="#__codelineno-30-10"></a> <span class="n">frame_analysis_interval</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
3572
+ <a id="__codelineno-30-11" name="__codelineno-30-11" href="#__codelineno-30-11"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
3573
+ <a id="__codelineno-30-12" name="__codelineno-30-12" href="#__codelineno-30-12"></a><span class="p">)</span>
3574
+ <a id="__codelineno-30-13" name="__codelineno-30-13" href="#__codelineno-30-13"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
3575
+ <a id="__codelineno-30-14" name="__codelineno-30-14" href="#__codelineno-30-14"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
3576
+ <a id="__codelineno-30-15" name="__codelineno-30-15" href="#__codelineno-30-15"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
3577
+ <a id="__codelineno-30-16" name="__codelineno-30-16" href="#__codelineno-30-16"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
3578
+ <a id="__codelineno-30-17" name="__codelineno-30-17" href="#__codelineno-30-17"></a><span class="p">)</span>
3579
+ <a id="__codelineno-30-18" name="__codelineno-30-18" href="#__codelineno-30-18"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
3580
+ <a id="__codelineno-30-19" name="__codelineno-30-19" href="#__codelineno-30-19"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
3581
+ <a id="__codelineno-30-20" name="__codelineno-30-20" href="#__codelineno-30-20"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
3582
+ </code></pre></div>
3583
+ <h3 id="configuration-options">Configuration options<a class="headerlink" href="#configuration-options" title="Permanent link">&para;</a></h3>
3584
+ <p>GCMC sampling:</p>
3585
+ <ul>
3586
+ <li><code>complex_pdb_path</code>: input protein-ligand complex PDB (required, must exist, <code>.pdb</code>).</li>
3587
+ <li><code>ligand_template_sdf</code>: ligand template SDF providing bond orders and chemistry for ligand export
3588
+ (required, must exist, <code>.sdf</code>/<code>.sd</code>).</li>
3589
+ <li><code>ligand_resname</code>: residue name identifying the ligand in the complex (required, 1-4 characters, no
3590
+ whitespace or path separators). Used by both stages.</li>
3591
+ <li><code>sphere_radius_angstrom</code>: radius of the ligand-centred sampling region (default <code>10.0</code>, <code>&gt; 0</code>).</li>
3592
+ <li><code>n_ghost_waters</code>: number of ghost waters added for insertion/deletion (default <code>150</code>, <code>&gt;= 1</code>).</li>
3593
+ <li><code>nonbonded_cutoff_nm</code>: nonbonded interaction cutoff in nanometres (default <code>0.9</code>, <code>&gt; 0</code>).</li>
3594
+ <li><code>temperature_kelvin</code>: simulation temperature in kelvin (default <code>300.0</code>, <code>&gt; 0</code>).</li>
3595
+ <li><code>initialization_passes</code>: equilibration passes before production sampling (default <code>7500</code>, <code>&gt;= 1</code>).</li>
3596
+ <li><code>max_production_passes</code>: maximum production passes (default <code>100000</code>, <code>&gt;= 1</code>).</li>
3597
+ <li><code>ph</code>: pH used when adding hydrogens during preparation (default <code>7.4</code>).</li>
3598
+ <li><code>padding_nm</code>: solvent box padding in nanometres (default <code>1.2</code>, <code>&gt; 0</code>).</li>
3599
+ <li><code>ionic_strength_molar</code>: ionic strength in molar used when solvating (default <code>0.15</code>, <code>&gt;= 0</code>).</li>
3600
+ </ul>
3601
+ <p>Representative selection:</p>
3602
+ <ul>
3603
+ <li><code>ligand_selection</code>: atom selection for the ligand. Derived from <code>ligand_resname</code>
3604
+ (<code>resname &lt;ligand_resname&gt;</code>) when left unset.</li>
3605
+ <li><code>align_selection</code>: optional atom selection used to align frames; blank is normalized to none.</li>
3606
+ <li><code>frame_analysis_interval</code>: analyse every Nth trajectory frame (default <code>1</code>, positive integer).</li>
3607
+ </ul>
3608
+ <p>Log syncing and output:</p>
3609
+ <ul>
3610
+ <li><code>log_sync_interval_seconds</code>: interval between periodic log-sync copies (default <code>30</code>, <code>1</code>-<code>3600</code>
3611
+ inclusive).</li>
3612
+ <li><code>output_dir_name</code>: directory under <code>results/</code> that holds stage outputs (default <code>output</code>, no path
3613
+ separators).</li>
3614
+ <li>Output filename fields (<code>trajectory_filename</code>, <code>ghost_water_filename</code>, <code>checkpoint_filename</code>,
3615
+ <code>hydrated_complex_filename</code>, <code>gcmc_summary_filename</code>, <code>representative_complex_filename</code>,
3616
+ <code>representative_protein_filename</code>, <code>representative_ligand_filename</code>, <code>selection_summary_filename</code>):
3617
+ plain filenames only, each with a documented default.</li>
3618
+ </ul>
3619
+ <p>All input file paths are validated and normalized to absolute paths at configuration time, so
3620
+ invalid inputs are reported before any compute job is submitted and inputs resolve correctly when
3621
+ the run executes from a scratch directory.</p>
3622
+ <h3 id="slurm-scratch-execution">Slurm scratch execution<a class="headerlink" href="#slurm-scratch-execution" title="Permanent link">&para;</a></h3>
3623
+ <p>On the Slurm backend under an allocated runtime, the workflow executes both stages inside a
3624
+ node-local scratch working directory (rooted at <code>SLURM_TMPDIR</code>) rather than on shared storage, so
3625
+ intermediate I/O does not stress the shared filesystem. When both stages finish successfully, the
3626
+ complete produced output directory is copied back from scratch to the job directory results output
3627
+ directory, preserving its relative structure, and a completeness check verifies every produced file
3628
+ was reproduced. If a stage fails after producing some outputs, those partial outputs are copied back
3629
+ on a best-effort basis and the result records whether the partial copy succeeded. The scratch
3630
+ working directory is removed after the copy-back attempt. When not running under an allocated
3631
+ runtime (for example on the local backend), both stages execute directly in the job directory
3632
+ results output directory and no copy-back is needed.</p>
3633
+ <h3 id="log-syncing">Log syncing<a class="headerlink" href="#log-syncing" title="Permanent link">&para;</a></h3>
3634
+ <p>During long runs under an allocated runtime, the stdout and stderr logs are written in the scratch
3635
+ working directory and periodically copied back to the job directory once per
3636
+ <code>log_sync_interval_seconds</code>, so you can monitor progress while the job is still running. Log-sync
3637
+ copying is resilient: a temporary copy failure is logged as a warning and never crashes the job or
3638
+ changes its status, and the next copy is attempted at the following interval. When a stage finishes,
3639
+ whether it succeeds or fails, a final copy is performed so the job directory logs reflect the final
3640
+ state of the run.</p>
3641
+ <h3 id="outputs">Outputs<a class="headerlink" href="#outputs" title="Permanent link">&para;</a></h3>
3642
+ <p>Stage outputs are written under <code>results/&lt;output_dir_name&gt;/</code>:</p>
3643
+ <ul>
3644
+ <li><code>gcmc_trajectory.dcd</code>: the GCMC sampling trajectory.</li>
3645
+ <li><code>ghost_water_state.txt</code>: per-frame ghost-water state file (one row per trajectory frame).</li>
3646
+ <li><code>gcmc_checkpoint.chk</code>: final-state checkpoint written before trajectory readback.</li>
3647
+ <li><code>hydrated_complex.pdb</code>: the hydrated-complex structure.</li>
3648
+ <li><code>gcmc_summary.json</code>: GCMC stage summary (produced paths, frame count, success/failure).</li>
3649
+ <li><code>representative_complex.pdb</code>: the selected representative protein-ligand-water complex.</li>
3650
+ <li><code>representative_protein.pdb</code>: optional protein-only representative structure.</li>
3651
+ <li><code>representative_ligand.sdf</code>: optional template-corrected representative ligand.</li>
3652
+ <li><code>selection_summary.json</code>: selection stage summary (selected frame index, success/failure).</li>
3653
+ <li><code>results/result_record.json</code> and <code>results/results.json</code>: the standardized result and a
3654
+ human-readable summary.</li>
3655
+ <li><code>results/progress.json</code>: best-effort stage, pass-count, acceptance-rate, water-count, and ETA
3656
+ snapshot.</li>
3657
+ </ul>
3658
+ <p>The standardized result exposes <code>representative_complex</code>, <code>representative_protein</code>,
3659
+ <code>representative_ligand</code>, <code>trajectory</code>, <code>checkpoint</code>, and <code>output_dir</code> as pipeline-ready result
3660
+ paths, and its <code>metrics</code> include <code>n_frames_sampled</code> and <code>representative_frame_index</code>.</p>
3661
+ <h2 id="compressed-inputs">Compressed inputs<a class="headerlink" href="#compressed-inputs" title="Permanent link">&para;</a></h2>
3662
+ <p>Declared MD structure, molecule, topology, trajectory, checkpoint, and restart inputs may use a
3663
+ trailing <code>.gz</code>. CADDForge expands transparent wrappers at runtime while preserving the original
3664
+ paths. Plain inputs retain their existing behavior.</p>
3665
+ <h2 id="inducia"><code>inducia</code><a class="headerlink" href="#inducia" title="Permanent link">&para;</a></h2>
3666
+ <p>Inducia is a composite induced-fit docking and pose-stability workflow built from PheSA, GNINA,
3667
+ GRAND, and OpenBPMD. One job accepts one three-dimensional query ligand; use pipeline scatter for a
3668
+ multi-record query library.</p>
3669
+ <p>The modes are:</p>
3670
+ <ul>
3671
+ <li><code>template</code>: run PheSA at the fixed pharmacophore-point weights 0.00 through 1.00 in steps of
3672
+ 0.05, cluster the resulting poses by direct heavy-atom RMSD in the binding coordinate frame,
3673
+ identify clashing protein residues, and minimize each representative with those residues flexible
3674
+ in GNINA.</li>
3675
+ <li><code>independent</code>: run full flexible GNINA docking in an explicit box or autobox. The flexible-residue
3676
+ radius and maximum residue count are configurable.</li>
3677
+ </ul>
3678
+ <p>Every surviving GNINA pose is hydrated by GRAND. Hydrated poses with finite GNINA CNNscores are
3679
+ ordered from highest to lowest, and <code>openbpmd.max_input_complexes</code> limits how many continue to
3680
+ OpenBPMD. Final structures are ranked by ascending OpenBPMD CompScore.</p>
3681
+ <p>CLI:</p>
3682
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>md<span class="w"> </span>inducia
3683
+ <a id="__codelineno-31-2" name="__codelineno-31-2" href="#__codelineno-31-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>inducia<span class="w"> </span>--config<span class="w"> </span>inducia.yaml
3684
+ </code></pre></div>
3685
+ <p>Template-mode configuration shape:</p>
3686
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a><span class="nt">mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">template</span>
3687
+ <a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
3688
+ <a id="__codelineno-32-3" name="__codelineno-32-3" href="#__codelineno-32-3"></a><span class="nt">receptor_pdb_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/receptor.pdb</span>
3689
+ <a id="__codelineno-32-4" name="__codelineno-32-4" href="#__codelineno-32-4"></a><span class="nt">query_ligand_sdf_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/query.sdf</span>
3690
+ <a id="__codelineno-32-5" name="__codelineno-32-5" href="#__codelineno-32-5"></a><span class="nt">template_ligand_sdf_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/known_binder.sdf</span>
3691
+ <a id="__codelineno-32-6" name="__codelineno-32-6" href="#__codelineno-32-6"></a><span class="nt">ligand_resname</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">LIG</span>
3692
+ <a id="__codelineno-32-7" name="__codelineno-32-7" href="#__codelineno-32-7"></a><span class="nt">max_local_workers</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
3693
+ <a id="__codelineno-32-8" name="__codelineno-32-8" href="#__codelineno-32-8"></a><span class="nt">phesa</span><span class="p">:</span>
3694
+ <a id="__codelineno-32-9" name="__codelineno-32-9" href="#__codelineno-32-9"></a><span class="w"> </span><span class="nt">max_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
3695
+ <a id="__codelineno-32-10" name="__codelineno-32-10" href="#__codelineno-32-10"></a><span class="nt">clustering</span><span class="p">:</span>
3696
+ <a id="__codelineno-32-11" name="__codelineno-32-11" href="#__codelineno-32-11"></a><span class="w"> </span><span class="nt">rmsd_cutoff_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
3697
+ <a id="__codelineno-32-12" name="__codelineno-32-12" href="#__codelineno-32-12"></a><span class="nt">clash_detection</span><span class="p">:</span>
3698
+ <a id="__codelineno-32-13" name="__codelineno-32-13" href="#__codelineno-32-13"></a><span class="w"> </span><span class="nt">allowed_vdw_overlap_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.4</span>
3699
+ <a id="__codelineno-32-14" name="__codelineno-32-14" href="#__codelineno-32-14"></a><span class="nt">gnina</span><span class="p">:</span>
3700
+ <a id="__codelineno-32-15" name="__codelineno-32-15" href="#__codelineno-32-15"></a><span class="w"> </span><span class="nt">cnn_scoring</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">rescore</span>
3701
+ <a id="__codelineno-32-16" name="__codelineno-32-16" href="#__codelineno-32-16"></a><span class="w"> </span><span class="nt">pose_sort_order</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">CNNscore</span>
3702
+ <a id="__codelineno-32-17" name="__codelineno-32-17" href="#__codelineno-32-17"></a><span class="nt">grand</span><span class="p">:</span>
3703
+ <a id="__codelineno-32-18" name="__codelineno-32-18" href="#__codelineno-32-18"></a><span class="w"> </span><span class="nt">sphere_radius_angstrom</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10.0</span>
3704
+ <a id="__codelineno-32-19" name="__codelineno-32-19" href="#__codelineno-32-19"></a><span class="w"> </span><span class="nt">n_ghost_waters</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">150</span>
3705
+ <a id="__codelineno-32-20" name="__codelineno-32-20" href="#__codelineno-32-20"></a><span class="w"> </span><span class="nt">initialization_passes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">7500</span>
3706
+ <a id="__codelineno-32-21" name="__codelineno-32-21" href="#__codelineno-32-21"></a><span class="w"> </span><span class="nt">max_production_passes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100000</span>
3707
+ <a id="__codelineno-32-22" name="__codelineno-32-22" href="#__codelineno-32-22"></a><span class="nt">openbpmd</span><span class="p">:</span>
3708
+ <a id="__codelineno-32-23" name="__codelineno-32-23" href="#__codelineno-32-23"></a><span class="w"> </span><span class="nt">max_input_complexes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
3709
+ <a id="__codelineno-32-24" name="__codelineno-32-24" href="#__codelineno-32-24"></a><span class="w"> </span><span class="nt">nreps</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
3710
+ <a id="__codelineno-32-25" name="__codelineno-32-25" href="#__codelineno-32-25"></a><span class="w"> </span><span class="nt">hill_height</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.05</span>
3711
+ <a id="__codelineno-32-26" name="__codelineno-32-26" href="#__codelineno-32-26"></a><span class="w"> </span><span class="nt">deposit_interval_ps</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1.0</span>
3712
+ <a id="__codelineno-32-27" name="__codelineno-32-27" href="#__codelineno-32-27"></a><span class="nt">progress</span><span class="p">:</span>
3713
+ <a id="__codelineno-32-28" name="__codelineno-32-28" href="#__codelineno-32-28"></a><span class="w"> </span><span class="nt">interval_seconds</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">30</span>
3714
+ </code></pre></div>
3715
+ <p>Independent mode replaces <code>template_ligand_sdf_path</code> with either <code>autobox_ligand_path</code> or both
3716
+ <code>box_center</code> and <code>box_size</code>. Its GNINA settings include
3717
+ <code>independent_flex_radius_angstrom</code> (default <code>3.5</code>) and
3718
+ <code>independent_max_flexible_residues</code> (default <code>12</code>).</p>
3719
+ <p>Child phases use at most <code>max_local_workers</code> locally. With Slurm, all siblings in a phase are
3720
+ submitted before monitoring begins. Parent stdout records phase lifecycle, child IDs and statuses,
3721
+ heartbeats, concise child progress, completion, and failure information. Follow it with
3722
+ <code>caddforge logs &lt;job-id&gt; --follow</code>; detailed command logs remain in the child directories.</p>
3723
+ <p>Structured events are written to <code>results/inducia_progress.jsonl</code>. Temporary registry or shared
3724
+ filesystem failures are treated as monitoring outages and retried. Allocated-runtime publication
3725
+ copies file content without filesystem metadata for CIFS compatibility and verifies it by SHA-256.</p>
3726
+ <p>Primary outputs are <code>best_complex</code>, <code>best_protein</code>, <code>best_ligand</code>, <code>ranking_table</code>,
3727
+ <code>pose_manifest</code>, ranked complex/protein/ligand path collections, and <code>output_dir</code>. The complete pose
3728
+ manifest retains PheSA scores, cluster membership, flexible residues, all child jobs and statuses,
3729
+ CNNscore shortlist rank, GRAND/OpenBPMD artifacts, CompScore, and failure provenance.</p>
3730
+ <p>Inducia requires <code>caddforge-core&gt;=0.21.0</code>, <code>caddforge-descriptors&gt;=0.8.0</code>, and
3731
+ <code>caddforge-docking&gt;=0.3.0</code>, plus the external scientific runtimes required by PheSA, GNINA, GRAND,
3732
+ OpenMM, AmberTools, and OpenBPMD.</p>
3733
+
3734
+
3735
+
3736
+
3737
+
3738
+
3739
+
3740
+
3741
+
3742
+
3743
+
3744
+
3745
+
3746
+ </article>
3747
+ </div>
3748
+
3749
+
3750
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
3751
+ </div>
3752
+
3753
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