caddforge-docs 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- caddforge_docs/__init__.py +1 -0
- caddforge_docs/cli.py +20 -0
- caddforge_docs/server.py +124 -0
- caddforge_docs/site/404.html +2118 -0
- caddforge_docs/site/assets/_mkdocstrings.css +237 -0
- caddforge_docs/site/assets/images/favicon.png +0 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
- caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
- caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
- caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
- caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
- caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
- caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
- caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
- caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
- caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
- caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
- caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
- caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
- caddforge_docs/site/core/cli/index.html +2446 -0
- caddforge_docs/site/core/concepts/index.html +2340 -0
- caddforge_docs/site/core/configuration/index.html +2300 -0
- caddforge_docs/site/core/index.html +2170 -0
- caddforge_docs/site/core/jobs-results/index.html +2315 -0
- caddforge_docs/site/core/plugins/index.html +2200 -0
- caddforge_docs/site/core/slurm/index.html +2562 -0
- caddforge_docs/site/development/ci-publishing/index.html +2345 -0
- caddforge_docs/site/development/contributing/index.html +2311 -0
- caddforge_docs/site/development/documentation/index.html +2380 -0
- caddforge_docs/site/development/index.html +2201 -0
- caddforge_docs/site/development/release-notes/index.html +2504 -0
- caddforge_docs/site/development/release-readiness/index.html +2333 -0
- caddforge_docs/site/development/security/index.html +2181 -0
- caddforge_docs/site/development/tool-authoring/index.html +2435 -0
- caddforge_docs/site/examples/index.html +2465 -0
- caddforge_docs/site/examples/manifest.json +158 -0
- caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
- caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
- caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
- caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
- caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
- caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
- caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
- caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
- caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
- caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
- caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
- caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
- caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
- caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
- caddforge_docs/site/examples/quickstart/index.html +2172 -0
- caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
- caddforge_docs/site/examples/quickstart/run.py +18 -0
- caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
- caddforge_docs/site/examples/quickstart/scores.csv +7 -0
- caddforge_docs/site/examples/quickstart/values.csv +31 -0
- caddforge_docs/site/examples/run_tool.py +40 -0
- caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
- caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
- caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
- caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
- caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
- caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
- caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
- caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
- caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
- caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
- caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
- caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
- caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
- caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
- caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
- caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
- caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
- caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
- caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
- caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
- caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
- caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
- caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
- caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
- caddforge_docs/site/explanation/references/index.html +2218 -0
- caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
- caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
- caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
- caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
- caddforge_docs/site/getting-started/index.html +2200 -0
- caddforge_docs/site/getting-started/installation/index.html +2541 -0
- caddforge_docs/site/gui/index.html +2267 -0
- caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
- caddforge_docs/site/gui/walkthrough/index.html +2181 -0
- caddforge_docs/site/how-to/jobs/index.html +2195 -0
- caddforge_docs/site/how-to/scatter/index.html +2193 -0
- caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
- caddforge_docs/site/index.html +2359 -0
- caddforge_docs/site/objects.inv +0 -0
- caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
- caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
- caddforge_docs/site/pipelines/examples/index.html +3186 -0
- caddforge_docs/site/pipelines/index.html +2164 -0
- caddforge_docs/site/pipelines/specification/index.html +2278 -0
- caddforge_docs/site/plugins/datascience/index.html +2405 -0
- caddforge_docs/site/plugins/descriptors/index.html +2609 -0
- caddforge_docs/site/plugins/docking/index.html +2480 -0
- caddforge_docs/site/plugins/fep/index.html +2508 -0
- caddforge_docs/site/plugins/index.html +2216 -0
- caddforge_docs/site/plugins/md/index.html +3795 -0
- caddforge_docs/site/plugins/ml/index.html +2815 -0
- caddforge_docs/site/plugins/qm/index.html +2309 -0
- caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
- caddforge_docs/site/reference/api/index.html +4414 -0
- caddforge_docs/site/reference/index.html +2166 -0
- caddforge_docs/site/search/search_index.json +1 -0
- caddforge_docs/site/sitemap.xml +191 -0
- caddforge_docs/site/sitemap.xml.gz +0 -0
- caddforge_docs-0.3.0.dist-info/METADATA +158 -0
- caddforge_docs-0.3.0.dist-info/RECORD +152 -0
- caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
- caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
- caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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464
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|
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465
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|
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466
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
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468
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+
|
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469
|
+
|
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470
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
|
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471
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|
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472
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|
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<span class="md-ellipsis">
|
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|
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|
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477
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How-to Guides
|
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478
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479
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480
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484
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<span class="md-nav__icon md-icon"></span>
|
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486
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</label>
|
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487
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|
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488
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
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489
|
+
<label class="md-nav__title" for="__nav_3">
|
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<span class="md-nav__icon md-icon"></span>
|
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491
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|
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492
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|
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How-to Guides
|
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494
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|
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495
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496
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</label>
|
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<ul class="md-nav__list" data-md-scrollfix>
|
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<li class="md-nav__item">
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506
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<a href="../../how-to/jobs/" class="md-nav__link">
|
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508
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|
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509
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<span class="md-ellipsis">
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511
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512
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Jobs and Results
|
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</span>
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</a>
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532
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<li class="md-nav__item">
|
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534
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<a href="../../how-to/scatter/" class="md-nav__link">
|
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535
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|
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536
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|
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537
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|
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538
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<span class="md-ellipsis">
|
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539
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|
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540
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|
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541
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Scatter and Reduce
|
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542
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|
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543
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544
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|
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545
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</span>
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</a>
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</li>
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|
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|
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560
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561
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<li class="md-nav__item">
|
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562
|
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
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563
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|
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564
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+
|
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565
|
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|
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566
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<span class="md-ellipsis">
|
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567
|
+
|
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568
|
+
|
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569
|
+
Troubleshooting
|
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570
|
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|
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571
|
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|
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572
|
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|
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573
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</span>
|
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|
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|
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576
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|
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577
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</a>
|
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578
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</li>
|
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579
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|
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580
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|
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581
|
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|
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582
|
+
|
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583
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</ul>
|
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584
|
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</nav>
|
|
585
|
+
|
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586
|
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</li>
|
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587
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588
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|
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|
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619
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|
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
621
|
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|
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622
|
+
|
|
623
|
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|
|
624
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
|
|
625
|
+
|
|
626
|
+
|
|
627
|
+
<div class="md-nav__link md-nav__container">
|
|
628
|
+
<a href="../../core/" class="md-nav__link ">
|
|
629
|
+
|
|
630
|
+
|
|
631
|
+
|
|
632
|
+
<span class="md-ellipsis">
|
|
633
|
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|
|
634
|
+
|
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635
|
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Core
|
|
636
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|
|
637
|
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|
|
638
|
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|
|
639
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</span>
|
|
640
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|
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641
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|
|
642
|
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|
|
643
|
+
</a>
|
|
644
|
+
|
|
645
|
+
|
|
646
|
+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
647
|
+
<span class="md-nav__icon md-icon"></span>
|
|
648
|
+
</label>
|
|
649
|
+
|
|
650
|
+
</div>
|
|
651
|
+
|
|
652
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
|
|
653
|
+
<label class="md-nav__title" for="__nav_4">
|
|
654
|
+
<span class="md-nav__icon md-icon"></span>
|
|
655
|
+
|
|
656
|
+
|
|
657
|
+
Core
|
|
658
|
+
|
|
659
|
+
|
|
660
|
+
</label>
|
|
661
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
662
|
+
|
|
663
|
+
|
|
664
|
+
|
|
665
|
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|
|
666
|
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|
|
667
|
+
|
|
668
|
+
|
|
669
|
+
<li class="md-nav__item">
|
|
670
|
+
<a href="../../core/concepts/" class="md-nav__link">
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
<span class="md-ellipsis">
|
|
675
|
+
|
|
676
|
+
|
|
677
|
+
Concepts
|
|
678
|
+
|
|
679
|
+
|
|
680
|
+
|
|
681
|
+
</span>
|
|
682
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|
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683
|
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|
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684
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|
|
685
|
+
</a>
|
|
686
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</li>
|
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687
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|
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688
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|
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689
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694
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|
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695
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|
|
696
|
+
|
|
697
|
+
<li class="md-nav__item">
|
|
698
|
+
<a href="../../core/configuration/" class="md-nav__link">
|
|
699
|
+
|
|
700
|
+
|
|
701
|
+
|
|
702
|
+
<span class="md-ellipsis">
|
|
703
|
+
|
|
704
|
+
|
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705
|
+
Configuration
|
|
706
|
+
|
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707
|
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|
|
708
|
+
|
|
709
|
+
</span>
|
|
710
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|
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711
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|
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712
|
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|
|
713
|
+
</a>
|
|
714
|
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</li>
|
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715
|
+
|
|
716
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|
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717
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|
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718
|
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|
|
719
|
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|
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720
|
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|
|
721
|
+
|
|
722
|
+
|
|
723
|
+
|
|
724
|
+
|
|
725
|
+
<li class="md-nav__item">
|
|
726
|
+
<a href="../../core/cli/" class="md-nav__link">
|
|
727
|
+
|
|
728
|
+
|
|
729
|
+
|
|
730
|
+
<span class="md-ellipsis">
|
|
731
|
+
|
|
732
|
+
|
|
733
|
+
CLI
|
|
734
|
+
|
|
735
|
+
|
|
736
|
+
|
|
737
|
+
</span>
|
|
738
|
+
|
|
739
|
+
|
|
740
|
+
|
|
741
|
+
</a>
|
|
742
|
+
</li>
|
|
743
|
+
|
|
744
|
+
|
|
745
|
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|
|
746
|
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|
|
747
|
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|
|
748
|
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|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
|
|
752
|
+
|
|
753
|
+
<li class="md-nav__item">
|
|
754
|
+
<a href="../../core/jobs-results/" class="md-nav__link">
|
|
755
|
+
|
|
756
|
+
|
|
757
|
+
|
|
758
|
+
<span class="md-ellipsis">
|
|
759
|
+
|
|
760
|
+
|
|
761
|
+
Jobs and Results
|
|
762
|
+
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
</span>
|
|
766
|
+
|
|
767
|
+
|
|
768
|
+
|
|
769
|
+
</a>
|
|
770
|
+
</li>
|
|
771
|
+
|
|
772
|
+
|
|
773
|
+
|
|
774
|
+
|
|
775
|
+
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
<li class="md-nav__item">
|
|
782
|
+
<a href="../../core/slurm/" class="md-nav__link">
|
|
783
|
+
|
|
784
|
+
|
|
785
|
+
|
|
786
|
+
<span class="md-ellipsis">
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
Slurm Backend
|
|
790
|
+
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
</span>
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
|
|
797
|
+
</a>
|
|
798
|
+
</li>
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
<li class="md-nav__item">
|
|
810
|
+
<a href="../../core/plugins/" class="md-nav__link">
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
<span class="md-ellipsis">
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
Plugins
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
</span>
|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
</a>
|
|
826
|
+
</li>
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
</ul>
|
|
832
|
+
</nav>
|
|
833
|
+
|
|
834
|
+
</li>
|
|
835
|
+
|
|
836
|
+
|
|
837
|
+
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
|
|
864
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
<div class="md-nav__link md-nav__container">
|
|
872
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<span class="md-ellipsis">
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
Pipelines
|
|
880
|
+
|
|
881
|
+
|
|
882
|
+
|
|
883
|
+
</span>
|
|
884
|
+
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
</a>
|
|
888
|
+
|
|
889
|
+
|
|
890
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
891
|
+
<span class="md-nav__icon md-icon"></span>
|
|
892
|
+
</label>
|
|
893
|
+
|
|
894
|
+
</div>
|
|
895
|
+
|
|
896
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
|
897
|
+
<label class="md-nav__title" for="__nav_5">
|
|
898
|
+
<span class="md-nav__icon md-icon"></span>
|
|
899
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<div class="md-nav__link md-nav__container">
|
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<a href="../" class="md-nav__link ">
|
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Plugins
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
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|
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|
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|
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|
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Plugins
|
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1100
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1101
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|
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1102
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</label>
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1103
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<ul class="md-nav__list" data-md-scrollfix>
|
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<li class="md-nav__item">
|
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<a href="../version-matrix/" class="md-nav__link">
|
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<span class="md-ellipsis">
|
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Version Matrix
|
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1120
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|
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1121
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|
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1122
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|
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1123
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<a href="../docking/" class="md-nav__link">
|
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|
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|
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Descriptors
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|
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|
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<a href="./" class="md-nav__link md-nav__link--active">
|
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|
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1203
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</a>
|
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
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1215
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1217
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<label class="md-nav__title" for="__toc">
|
|
1222
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1223
|
+
Table of contents
|
|
1224
|
+
</label>
|
|
1225
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
1226
|
+
|
|
1227
|
+
<li class="md-nav__item">
|
|
1228
|
+
<a href="#requirements-and-example-status" class="md-nav__link">
|
|
1229
|
+
<span class="md-ellipsis">
|
|
1230
|
+
|
|
1231
|
+
Requirements and example status
|
|
1232
|
+
|
|
1233
|
+
</span>
|
|
1234
|
+
</a>
|
|
1235
|
+
|
|
1236
|
+
</li>
|
|
1237
|
+
|
|
1238
|
+
<li class="md-nav__item">
|
|
1239
|
+
<a href="#ani-psa" class="md-nav__link">
|
|
1240
|
+
<span class="md-ellipsis">
|
|
1241
|
+
|
|
1242
|
+
ani-psa
|
|
1243
|
+
|
|
1244
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+
</span>
|
|
1245
|
+
</a>
|
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1246
|
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|
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1247
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</li>
|
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1248
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1249
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<li class="md-nav__item">
|
|
1250
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<a href="#phesa" class="md-nav__link">
|
|
1251
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<span class="md-ellipsis">
|
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1252
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+
|
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1253
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phesa
|
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1254
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|
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1255
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|
|
1256
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</a>
|
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1257
|
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|
|
1258
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|
|
1259
|
+
|
|
1260
|
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<li class="md-nav__item">
|
|
1261
|
+
<a href="#ani-conformers" class="md-nav__link">
|
|
1262
|
+
<span class="md-ellipsis">
|
|
1263
|
+
|
|
1264
|
+
ani-conformers
|
|
1265
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+
|
|
1266
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+
</span>
|
|
1267
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+
</a>
|
|
1268
|
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|
|
1269
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|
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1270
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+
|
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1271
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<li class="md-nav__item">
|
|
1272
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+
<a href="#cluster-molecules" class="md-nav__link">
|
|
1273
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+
<span class="md-ellipsis">
|
|
1274
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+
|
|
1275
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cluster-molecules
|
|
1276
|
+
|
|
1277
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+
</span>
|
|
1278
|
+
</a>
|
|
1279
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|
|
1280
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</li>
|
|
1281
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+
|
|
1282
|
+
<li class="md-nav__item">
|
|
1283
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+
<a href="#compressed-inputs" class="md-nav__link">
|
|
1284
|
+
<span class="md-ellipsis">
|
|
1285
|
+
|
|
1286
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+
Compressed inputs
|
|
1287
|
+
|
|
1288
|
+
</span>
|
|
1289
|
+
</a>
|
|
1290
|
+
|
|
1291
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+
</li>
|
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1292
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|
|
1293
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</ul>
|
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1294
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|
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1295
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</nav>
|
|
1296
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|
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1297
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</li>
|
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1298
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1299
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1300
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|
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1301
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1304
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1306
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|
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1307
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|
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1308
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<li class="md-nav__item">
|
|
1309
|
+
<a href="../md/" class="md-nav__link">
|
|
1310
|
+
|
|
1311
|
+
|
|
1312
|
+
|
|
1313
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<span class="md-ellipsis">
|
|
1314
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|
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1315
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|
|
1316
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MD
|
|
1317
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|
|
1318
|
+
|
|
1319
|
+
|
|
1320
|
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</span>
|
|
1321
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|
|
1322
|
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|
|
1323
|
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|
|
1324
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</a>
|
|
1325
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</li>
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|
1326
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Security Reporting
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2089
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2090
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2109
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2110
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2111
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<span class="md-ellipsis">
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2113
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2114
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2115
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Release Readiness
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2116
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2117
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2118
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2119
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2139
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<span class="md-ellipsis">
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2141
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2142
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2143
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CI and Publishing
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2144
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2145
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</nav>
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2159
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2160
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2161
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2162
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2163
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2164
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</ul>
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2165
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</nav>
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2166
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</div>
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2167
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</div>
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2168
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</div>
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2169
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2170
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+
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2171
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+
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2172
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
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2173
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2174
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+
<div class="md-sidebar__inner">
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2175
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2176
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2177
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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2178
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2179
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2180
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<label class="md-nav__title" for="__toc">
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2185
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<span class="md-nav__icon md-icon"></span>
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2186
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Table of contents
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2187
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2188
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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2189
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2190
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2191
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2192
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<span class="md-ellipsis">
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2193
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|
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2194
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Requirements and example status
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|
2195
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2196
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</span>
|
|
2197
|
+
</a>
|
|
2198
|
+
|
|
2199
|
+
</li>
|
|
2200
|
+
|
|
2201
|
+
<li class="md-nav__item">
|
|
2202
|
+
<a href="#ani-psa" class="md-nav__link">
|
|
2203
|
+
<span class="md-ellipsis">
|
|
2204
|
+
|
|
2205
|
+
ani-psa
|
|
2206
|
+
|
|
2207
|
+
</span>
|
|
2208
|
+
</a>
|
|
2209
|
+
|
|
2210
|
+
</li>
|
|
2211
|
+
|
|
2212
|
+
<li class="md-nav__item">
|
|
2213
|
+
<a href="#phesa" class="md-nav__link">
|
|
2214
|
+
<span class="md-ellipsis">
|
|
2215
|
+
|
|
2216
|
+
phesa
|
|
2217
|
+
|
|
2218
|
+
</span>
|
|
2219
|
+
</a>
|
|
2220
|
+
|
|
2221
|
+
</li>
|
|
2222
|
+
|
|
2223
|
+
<li class="md-nav__item">
|
|
2224
|
+
<a href="#ani-conformers" class="md-nav__link">
|
|
2225
|
+
<span class="md-ellipsis">
|
|
2226
|
+
|
|
2227
|
+
ani-conformers
|
|
2228
|
+
|
|
2229
|
+
</span>
|
|
2230
|
+
</a>
|
|
2231
|
+
|
|
2232
|
+
</li>
|
|
2233
|
+
|
|
2234
|
+
<li class="md-nav__item">
|
|
2235
|
+
<a href="#cluster-molecules" class="md-nav__link">
|
|
2236
|
+
<span class="md-ellipsis">
|
|
2237
|
+
|
|
2238
|
+
cluster-molecules
|
|
2239
|
+
|
|
2240
|
+
</span>
|
|
2241
|
+
</a>
|
|
2242
|
+
|
|
2243
|
+
</li>
|
|
2244
|
+
|
|
2245
|
+
<li class="md-nav__item">
|
|
2246
|
+
<a href="#compressed-inputs" class="md-nav__link">
|
|
2247
|
+
<span class="md-ellipsis">
|
|
2248
|
+
|
|
2249
|
+
Compressed inputs
|
|
2250
|
+
|
|
2251
|
+
</span>
|
|
2252
|
+
</a>
|
|
2253
|
+
|
|
2254
|
+
</li>
|
|
2255
|
+
|
|
2256
|
+
</ul>
|
|
2257
|
+
|
|
2258
|
+
</nav>
|
|
2259
|
+
</div>
|
|
2260
|
+
</div>
|
|
2261
|
+
</div>
|
|
2262
|
+
|
|
2263
|
+
|
|
2264
|
+
|
|
2265
|
+
<div class="md-content" data-md-component="content">
|
|
2266
|
+
|
|
2267
|
+
<article class="md-content__inner md-typeset">
|
|
2268
|
+
|
|
2269
|
+
|
|
2270
|
+
|
|
2271
|
+
|
|
2272
|
+
|
|
2273
|
+
|
|
2274
|
+
|
|
2275
|
+
|
|
2276
|
+
<h1 id="descriptors-plugin">Descriptors Plugin<a class="headerlink" href="#descriptors-plugin" title="Permanent link">¶</a></h1>
|
|
2277
|
+
<p>Package: <code>caddforge-descriptors</code></p>
|
|
2278
|
+
<div class="admonition info">
|
|
2279
|
+
<p class="admonition-title">Public source tag</p>
|
|
2280
|
+
<p>This page describes <code>caddforge-descriptors</code> <code>0.11.0</code>, tagged as <code>v0.11.0</code>.
|
|
2281
|
+
Published on PyPI; see the <a href="../version-matrix/">version matrix</a>.</p>
|
|
2282
|
+
</div>
|
|
2283
|
+
<p>The descriptors plugin provides molecular descriptor, conformer, shape/pharmacophore similarity,
|
|
2284
|
+
and clustering workflows.</p>
|
|
2285
|
+
<h2 id="requirements-and-example-status">Requirements and example status<a class="headerlink" href="#requirements-and-example-status" title="Permanent link">¶</a></h2>
|
|
2286
|
+
<p>PheSA imports <code>pyocl</code>, supplied by <code>pyocl-idor>=0.8.3</code>. Its OpenChemLib runtime
|
|
2287
|
+
requires Java 21 or newer and a configured <code>JAVA_HOME</code>.</p>
|
|
2288
|
+
<p>The <a href="../../examples/">example library</a> provides downloadable configuration
|
|
2289
|
+
templates for every workflow on this page, plus a shared Python runner. File paths
|
|
2290
|
+
refer to inputs you must prepare; these are not bundled research datasets. Schema
|
|
2291
|
+
validation does not establish scientific validity or engine availability. See the
|
|
2292
|
+
<a href="../version-matrix/">version matrix</a> for release tags and publication status.</p>
|
|
2293
|
+
<h2 id="ani-psa"><code>ani-psa</code><a class="headerlink" href="#ani-psa" title="Permanent link">¶</a></h2>
|
|
2294
|
+
<p>Computes ANI-weighted 3D polar surface area values from one molecule or a batch.</p>
|
|
2295
|
+
<p>CLI:</p>
|
|
2296
|
+
<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>descriptors<span class="w"> </span>ani-psa<span class="w"> </span>--config<span class="w"> </span>ani_psa.yaml
|
|
2297
|
+
</code></pre></div>
|
|
2298
|
+
<p>YAML:</p>
|
|
2299
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nt">smiles</span><span class="p">:</span><span class="w"> </span><span class="s">"CC(=O)Oc1ccccc1C(=O)O"</span>
|
|
2300
|
+
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nt">num_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100</span>
|
|
2301
|
+
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nt">top_n</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
|
|
2302
|
+
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="nt">rmsd_cluster_thresh</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2303
|
+
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="nt">max_mmff_iters</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
|
|
2304
|
+
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nt">temperature</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">298.15</span>
|
|
2305
|
+
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nt">model_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ANI2x</span>
|
|
2306
|
+
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="nt">device</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">cpu</span>
|
|
2307
|
+
</code></pre></div>
|
|
2308
|
+
<p>Python:</p>
|
|
2309
|
+
<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>
|
|
2310
|
+
<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>
|
|
2311
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
|
|
2312
|
+
<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">"descriptors"</span><span class="p">,</span> <span class="s2">"ani-psa"</span><span class="p">)</span>
|
|
2313
|
+
<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><span class="n">smiles</span><span class="o">=</span><span class="s2">"CCO"</span><span class="p">,</span> <span class="n">top_n</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">)</span>
|
|
2314
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></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>
|
|
2315
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2316
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></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>
|
|
2317
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></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>
|
|
2318
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="p">)</span>
|
|
2319
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></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>
|
|
2320
|
+
<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></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>
|
|
2321
|
+
<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></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>
|
|
2322
|
+
</code></pre></div>
|
|
2323
|
+
<p>Outputs to inspect: <code>results/results.json</code>, <code>results/results.csv</code>, <code>results/result_record.json</code>.</p>
|
|
2324
|
+
<h2 id="phesa"><code>phesa</code><a class="headerlink" href="#phesa" title="Permanent link">¶</a></h2>
|
|
2325
|
+
<p>Computes OpenChemLib PheSA shape/pharmacophore similarities between one reference molecule and one
|
|
2326
|
+
or more candidate molecules. The reference can be provided as SMILES, SDF, or an encoded
|
|
2327
|
+
PheSA descriptor file; candidates can be
|
|
2328
|
+
provided as SMILES strings or single-/multi-compound SDF files.</p>
|
|
2329
|
+
<div class="admonition note">
|
|
2330
|
+
<p class="admonition-title">Reference mode</p>
|
|
2331
|
+
<p>When <code>reference_smiles</code> is used, the reference descriptor is generated with
|
|
2332
|
+
<code>DescriptorHandlerShape</code> and the configured <code>max_confs</code> and <code>pp_weight</code>. When <code>reference_sdf</code>
|
|
2333
|
+
is used, the reference descriptor is generated with OpenChemLib's one-conformation handler.
|
|
2334
|
+
Candidate descriptors always use <code>DescriptorHandlerShape</code> with the configured <code>max_confs</code> and
|
|
2335
|
+
<code>pp_weight</code>.</p>
|
|
2336
|
+
</div>
|
|
2337
|
+
<p>Only SDF-reference mode restores aligned coordinates into the original SDF coordinate frame.
|
|
2338
|
+
SMILES and encoded-reference modes retain the generated PheSA alignment frame.
|
|
2339
|
+
Do not combine those coordinates with a receptor's coordinates without a validated transformation.</p>
|
|
2340
|
+
<p>Choose exactly one of <code>reference_smiles</code>, <code>reference_sdf</code>, and <code>reference_phesa_file</code>:</p>
|
|
2341
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Template: supply one encoded descriptor generated by a compatible public runtime.</span>
|
|
2342
|
+
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nt">reference_phesa_file</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/reference_phesa.txt</span>
|
|
2343
|
+
<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nt">candidate_smiles</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="s">"CCCO"</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="s">"CCCCO"</span><span class="p p-Indicator">]</span>
|
|
2344
|
+
<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="nt">max_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
|
|
2345
|
+
<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="nt">pp_weight</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2346
|
+
</code></pre></div>
|
|
2347
|
+
<p>The whole UTF-8 file contains one encoded descriptor; surrounding whitespace is
|
|
2348
|
+
stripped before decoding. This mode reuses its stored reference representation.
|
|
2349
|
+
<code>max_confs</code> and <code>pp_weight</code> configure generated candidate descriptors. The aligned
|
|
2350
|
+
reference and candidate SDFs, including any merged candidate SDF, remain in the
|
|
2351
|
+
PheSA frame because an original SDF-coordinate transformation is unavailable.</p>
|
|
2352
|
+
<p>CLI:</p>
|
|
2353
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>descriptors<span class="w"> </span>phesa<span class="w"> </span>--config<span class="w"> </span>phesa.yaml
|
|
2354
|
+
</code></pre></div>
|
|
2355
|
+
<p>YAML:</p>
|
|
2356
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="nt">reference_smiles</span><span class="p">:</span><span class="w"> </span><span class="s">"CCO"</span>
|
|
2357
|
+
<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="nt">candidate_smiles</span><span class="p">:</span>
|
|
2358
|
+
<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="s">"CCCO"</span>
|
|
2359
|
+
<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="s">"CCCCO"</span>
|
|
2360
|
+
<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="nt">max_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
|
|
2361
|
+
<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a><span class="nt">pp_weight</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2362
|
+
</code></pre></div>
|
|
2363
|
+
<p>SDF reference and candidate files:</p>
|
|
2364
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="nt">reference_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/reference.sdf</span>
|
|
2365
|
+
<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="nt">candidate_sdf_files</span><span class="p">:</span>
|
|
2366
|
+
<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/candidates.sdf</span>
|
|
2367
|
+
<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/extra_candidate.sdf</span>
|
|
2368
|
+
<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="nt">max_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
|
|
2369
|
+
<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="nt">pp_weight</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2370
|
+
<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="nt">write_merged_aligned_candidates_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2371
|
+
</code></pre></div>
|
|
2372
|
+
<p>Each valid molecule record in <code>candidate_sdf_files</code> is scored as one candidate. PHESA uses SDF
|
|
2373
|
+
record names as <code>candidate_id</code> values when present, falling back to the source file stem plus the
|
|
2374
|
+
record index.</p>
|
|
2375
|
+
<p>Set <code>write_merged_aligned_candidates_sdf: true</code> to additionally write a merged SDF containing all
|
|
2376
|
+
successfully aligned candidate molecules. The default filename is
|
|
2377
|
+
<code>results/aligned/aligned_candidates.sdf</code> and can be changed with
|
|
2378
|
+
<code>merged_aligned_candidates_sdf_name</code>.</p>
|
|
2379
|
+
<p>Python:</p>
|
|
2380
|
+
<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>
|
|
2381
|
+
<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>
|
|
2382
|
+
<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
|
|
2383
|
+
<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">"descriptors"</span><span class="p">,</span> <span class="s2">"phesa"</span><span class="p">)</span>
|
|
2384
|
+
<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>
|
|
2385
|
+
<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a> <span class="n">reference_smiles</span><span class="o">=</span><span class="s2">"CCO"</span><span class="p">,</span>
|
|
2386
|
+
<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a> <span class="n">candidate_smiles</span><span class="o">=</span><span class="p">[</span><span class="s2">"CCCO"</span><span class="p">,</span> <span class="s2">"CCCCO"</span><span class="p">],</span>
|
|
2387
|
+
<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a> <span class="n">max_confs</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span>
|
|
2388
|
+
<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a> <span class="n">pp_weight</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
|
|
2389
|
+
<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2390
|
+
<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a><span class="p">)</span>
|
|
2391
|
+
<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></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>
|
|
2392
|
+
<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2393
|
+
<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></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>
|
|
2394
|
+
<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></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>
|
|
2395
|
+
<a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a><span class="p">)</span>
|
|
2396
|
+
<a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></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>
|
|
2397
|
+
<a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></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>
|
|
2398
|
+
<a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></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>
|
|
2399
|
+
</code></pre></div>
|
|
2400
|
+
<p>Pipeline stage:</p>
|
|
2401
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="nt">stages</span><span class="p">:</span>
|
|
2402
|
+
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></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">phesa_similarity</span>
|
|
2403
|
+
<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></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">descriptors/phesa</span>
|
|
2404
|
+
<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w"> </span><span class="nt">config</span><span class="p">:</span>
|
|
2405
|
+
<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w"> </span><span class="nt">reference_sdf</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/reference.sdf</span>
|
|
2406
|
+
<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></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>
|
|
2407
|
+
<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w"> </span><span class="nt">pp_weight</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2408
|
+
<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="w"> </span><span class="nt">inputs</span><span class="p">:</span>
|
|
2409
|
+
<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="w"> </span><span class="nt">candidates</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">upstream_stage.poses</span>
|
|
2410
|
+
</code></pre></div>
|
|
2411
|
+
<p>Pipeline ports:</p>
|
|
2412
|
+
<table>
|
|
2413
|
+
<thead>
|
|
2414
|
+
<tr>
|
|
2415
|
+
<th>Direction</th>
|
|
2416
|
+
<th>Name</th>
|
|
2417
|
+
<th>Kind</th>
|
|
2418
|
+
<th>Config/result key</th>
|
|
2419
|
+
</tr>
|
|
2420
|
+
</thead>
|
|
2421
|
+
<tbody>
|
|
2422
|
+
<tr>
|
|
2423
|
+
<td>Input</td>
|
|
2424
|
+
<td><code>reference_sdf</code></td>
|
|
2425
|
+
<td>file</td>
|
|
2426
|
+
<td><code>reference_sdf</code></td>
|
|
2427
|
+
</tr>
|
|
2428
|
+
<tr>
|
|
2429
|
+
<td>Input</td>
|
|
2430
|
+
<td><code>reference_phesa_file</code></td>
|
|
2431
|
+
<td>file</td>
|
|
2432
|
+
<td><code>reference_phesa_file</code></td>
|
|
2433
|
+
</tr>
|
|
2434
|
+
<tr>
|
|
2435
|
+
<td>Input</td>
|
|
2436
|
+
<td><code>candidates</code></td>
|
|
2437
|
+
<td>molecule collection</td>
|
|
2438
|
+
<td><code>candidate_sdf_files</code></td>
|
|
2439
|
+
</tr>
|
|
2440
|
+
<tr>
|
|
2441
|
+
<td>Output</td>
|
|
2442
|
+
<td><code>scores</code></td>
|
|
2443
|
+
<td>tabular scores</td>
|
|
2444
|
+
<td><code>scores_csv</code></td>
|
|
2445
|
+
</tr>
|
|
2446
|
+
<tr>
|
|
2447
|
+
<td>Output</td>
|
|
2448
|
+
<td><code>aligned_reference</code></td>
|
|
2449
|
+
<td>file</td>
|
|
2450
|
+
<td><code>aligned_reference_sdf</code></td>
|
|
2451
|
+
</tr>
|
|
2452
|
+
<tr>
|
|
2453
|
+
<td>Output</td>
|
|
2454
|
+
<td><code>aligned_candidates</code></td>
|
|
2455
|
+
<td>molecule collection</td>
|
|
2456
|
+
<td><code>aligned_manifest_csv</code>, column <code>aligned_candidate_sdf</code></td>
|
|
2457
|
+
</tr>
|
|
2458
|
+
<tr>
|
|
2459
|
+
<td>Output</td>
|
|
2460
|
+
<td><code>merged_aligned_candidates</code></td>
|
|
2461
|
+
<td>molecule collection</td>
|
|
2462
|
+
<td><code>merged_aligned_candidates_sdf</code></td>
|
|
2463
|
+
</tr>
|
|
2464
|
+
</tbody>
|
|
2465
|
+
</table>
|
|
2466
|
+
<p>Outputs to inspect: <code>results/results.json</code>, <code>results/scores.csv</code>,
|
|
2467
|
+
<code>results/aligned/reference.sdf</code>, <code>results/aligned/candidates/</code>,
|
|
2468
|
+
<code>results/aligned/manifest.csv</code>, optional <code>results/aligned/aligned_candidates.sdf</code>,
|
|
2469
|
+
<code>results/result_record.json</code>.</p>
|
|
2470
|
+
<h2 id="ani-conformers"><code>ani-conformers</code><a class="headerlink" href="#ani-conformers" title="Permanent link">¶</a></h2>
|
|
2471
|
+
<p>Generates RDKit conformers, re-ranks representatives with ANI, and writes selected conformers to
|
|
2472
|
+
SDF.</p>
|
|
2473
|
+
<p>CLI:</p>
|
|
2474
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>descriptors<span class="w"> </span>ani-conformers<span class="w"> </span>--config<span class="w"> </span>ani_conformers.yaml
|
|
2475
|
+
</code></pre></div>
|
|
2476
|
+
<p>YAML:</p>
|
|
2477
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="nt">smiles</span><span class="p">:</span><span class="w"> </span><span class="s">"CCO"</span>
|
|
2478
|
+
<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="nt">num_confs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100</span>
|
|
2479
|
+
<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="nt">top_n</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
|
|
2480
|
+
<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="nt">rmsd_cluster_thresh</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
|
2481
|
+
<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="nt">max_mmff_iters</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">200</span>
|
|
2482
|
+
<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a><span class="nt">model_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ANI2x</span>
|
|
2483
|
+
<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></a><span class="nt">device</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">cpu</span>
|
|
2484
|
+
<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a><span class="nt">output_sdf_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ranked_conformers.sdf</span>
|
|
2485
|
+
</code></pre></div>
|
|
2486
|
+
<p>Python:</p>
|
|
2487
|
+
<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>
|
|
2488
|
+
<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>
|
|
2489
|
+
<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
|
|
2490
|
+
<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">"descriptors"</span><span class="p">,</span> <span class="s2">"ani-conformers"</span><span class="p">)</span>
|
|
2491
|
+
<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><span class="n">smiles</span><span class="o">=</span><span class="s2">"CCO"</span><span class="p">,</span> <span class="n">top_n</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">num_confs</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">)</span>
|
|
2492
|
+
<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></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>
|
|
2493
|
+
<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2494
|
+
<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></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>
|
|
2495
|
+
<a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></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>
|
|
2496
|
+
<a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="p">)</span>
|
|
2497
|
+
<a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></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>
|
|
2498
|
+
<a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></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>
|
|
2499
|
+
<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></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">"ranked_conformers_sdf"</span><span class="p">])</span>
|
|
2500
|
+
</code></pre></div>
|
|
2501
|
+
<p>Outputs to inspect: <code>results/results.json</code>, <code>results/ranked_conformers.sdf</code>,
|
|
2502
|
+
<code>results/result_record.json</code>.</p>
|
|
2503
|
+
<h2 id="cluster-molecules"><code>cluster-molecules</code><a class="headerlink" href="#cluster-molecules" title="Permanent link">¶</a></h2>
|
|
2504
|
+
<p>Clusters molecules from SMILES/SDF/CSV/TSV input using fingerprint or scaffold algorithms.</p>
|
|
2505
|
+
<p>CLI:</p>
|
|
2506
|
+
<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>descriptors<span class="w"> </span>cluster-molecules<span class="w"> </span>--config<span class="w"> </span>cluster_molecules.yaml
|
|
2507
|
+
</code></pre></div>
|
|
2508
|
+
<p>YAML:</p>
|
|
2509
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="nt">input_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/molecules.csv</span>
|
|
2510
|
+
<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="nt">smiles_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">smiles</span>
|
|
2511
|
+
<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="nt">id_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">compound_id</span>
|
|
2512
|
+
<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="nt">algorithm</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">kmedoids</span>
|
|
2513
|
+
<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="nt">fingerprint_radius</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">2</span>
|
|
2514
|
+
<a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a><span class="nt">fingerprint_bits</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">2048</span>
|
|
2515
|
+
<a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a><span class="nt">kmedoids_n_clusters</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100</span>
|
|
2516
|
+
<a id="__codelineno-13-8" name="__codelineno-13-8" href="#__codelineno-13-8"></a><span class="nt">kmedoids_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">auto</span>
|
|
2517
|
+
<a id="__codelineno-13-9" name="__codelineno-13-9" href="#__codelineno-13-9"></a><span class="nt">kmedoids_max_exact_n</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5000</span>
|
|
2518
|
+
<a id="__codelineno-13-10" name="__codelineno-13-10" href="#__codelineno-13-10"></a><span class="nt">kmedoids_max_exact_pairs</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">25000000</span>
|
|
2519
|
+
</code></pre></div>
|
|
2520
|
+
<p>Python:</p>
|
|
2521
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></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>
|
|
2522
|
+
<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></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>
|
|
2523
|
+
<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>
|
|
2524
|
+
<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"descriptors"</span><span class="p">,</span> <span class="s2">"cluster-molecules"</span><span class="p">)</span>
|
|
2525
|
+
<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></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>
|
|
2526
|
+
<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a> <span class="n">input_path</span><span class="o">=</span><span class="s2">"data/molecules.csv"</span><span class="p">,</span>
|
|
2527
|
+
<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a> <span class="n">smiles_column</span><span class="o">=</span><span class="s2">"smiles"</span><span class="p">,</span>
|
|
2528
|
+
<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a> <span class="n">algorithm</span><span class="o">=</span><span class="s2">"kmedoids"</span><span class="p">,</span>
|
|
2529
|
+
<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a> <span class="n">kmedoids_n_clusters</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
|
|
2530
|
+
<a id="__codelineno-14-10" name="__codelineno-14-10" href="#__codelineno-14-10"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2531
|
+
<a id="__codelineno-14-11" name="__codelineno-14-11" href="#__codelineno-14-11"></a><span class="p">)</span>
|
|
2532
|
+
<a id="__codelineno-14-12" name="__codelineno-14-12" href="#__codelineno-14-12"></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>
|
|
2533
|
+
<a id="__codelineno-14-13" name="__codelineno-14-13" href="#__codelineno-14-13"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2534
|
+
<a id="__codelineno-14-14" name="__codelineno-14-14" href="#__codelineno-14-14"></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>
|
|
2535
|
+
<a id="__codelineno-14-15" name="__codelineno-14-15" href="#__codelineno-14-15"></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>
|
|
2536
|
+
<a id="__codelineno-14-16" name="__codelineno-14-16" href="#__codelineno-14-16"></a><span class="p">)</span>
|
|
2537
|
+
<a id="__codelineno-14-17" name="__codelineno-14-17" href="#__codelineno-14-17"></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>
|
|
2538
|
+
<a id="__codelineno-14-18" name="__codelineno-14-18" href="#__codelineno-14-18"></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>
|
|
2539
|
+
<a id="__codelineno-14-19" name="__codelineno-14-19" href="#__codelineno-14-19"></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>
|
|
2540
|
+
</code></pre></div>
|
|
2541
|
+
<p>Outputs to inspect: <code>results/assignments.csv</code>, <code>results/centroids.csv</code>,
|
|
2542
|
+
<code>results/summary.json</code>, <code>results/result_record.json</code>.</p>
|
|
2543
|
+
<h2 id="compressed-inputs">Compressed inputs<a class="headerlink" href="#compressed-inputs" title="Permanent link">¶</a></h2>
|
|
2544
|
+
<p>File-based SMILES, SDF, CSV, and TSV inputs may use a trailing <code>.gz</code>. This includes nested
|
|
2545
|
+
cluster-molecule inputs. CADDForge expands wrappers in runtime scratch; plain inputs and native tool
|
|
2546
|
+
formats remain unchanged.</p>
|
|
2547
|
+
|
|
2548
|
+
|
|
2549
|
+
|
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2550
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+
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2553
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</article>
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</div>
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<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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</div>
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<button type="button" class="md-top md-icon" data-md-component="top" hidden>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
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Back to top
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</button>
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</main>
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2575
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<footer class="md-footer">
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2576
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2577
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<div class="md-footer-meta md-typeset">
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<div class="md-footer-meta__inner md-grid">
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<div class="md-copyright">
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Made with
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<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
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Material for MkDocs
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</a>
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<script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
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<script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
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