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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Examples
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</nav>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
|
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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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1078
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|
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1080
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
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<span class="md-nav__icon md-icon"></span>
|
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1090
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
|
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+
<label class="md-nav__title" for="__nav_6">
|
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<span class="md-nav__icon md-icon"></span>
|
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1097
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1098
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|
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1099
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Plugins
|
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1100
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|
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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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1111
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<li class="md-nav__item">
|
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|
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<a href="../version-matrix/" class="md-nav__link">
|
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1115
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<span class="md-ellipsis">
|
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|
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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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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
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|
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Docking
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1158
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1159
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|
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1177
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
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1187
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1189
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1190
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<label class="md-nav__title" for="__toc">
|
|
1194
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+
<span class="md-nav__icon md-icon"></span>
|
|
1195
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+
Table of contents
|
|
1196
|
+
</label>
|
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1197
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
1198
|
+
|
|
1199
|
+
<li class="md-nav__item">
|
|
1200
|
+
<a href="#requirements-and-example-status" class="md-nav__link">
|
|
1201
|
+
<span class="md-ellipsis">
|
|
1202
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+
|
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1203
|
+
Requirements and example status
|
|
1204
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+
|
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1205
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+
</span>
|
|
1206
|
+
</a>
|
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1207
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+
|
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1208
|
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</li>
|
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1209
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+
|
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1210
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<li class="md-nav__item">
|
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1211
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<a href="#unidock" class="md-nav__link">
|
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1212
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<span class="md-ellipsis">
|
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1213
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+
|
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1214
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unidock
|
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1215
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|
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1216
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</span>
|
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1217
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</a>
|
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1218
|
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|
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1219
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</li>
|
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1220
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|
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1221
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<li class="md-nav__item">
|
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1222
|
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<a href="#idockya" class="md-nav__link">
|
|
1223
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+
<span class="md-ellipsis">
|
|
1224
|
+
|
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1225
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+
idockya
|
|
1226
|
+
|
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1227
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+
</span>
|
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1228
|
+
</a>
|
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1229
|
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|
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1230
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|
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1231
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|
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1232
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<li class="md-nav__item">
|
|
1233
|
+
<a href="#gnina" class="md-nav__link">
|
|
1234
|
+
<span class="md-ellipsis">
|
|
1235
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+
|
|
1236
|
+
gnina
|
|
1237
|
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|
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1238
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</span>
|
|
1239
|
+
</a>
|
|
1240
|
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|
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1241
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|
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1242
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+
|
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1243
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<li class="md-nav__item">
|
|
1244
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+
<a href="#compressed-inputs" class="md-nav__link">
|
|
1245
|
+
<span class="md-ellipsis">
|
|
1246
|
+
|
|
1247
|
+
Compressed inputs
|
|
1248
|
+
|
|
1249
|
+
</span>
|
|
1250
|
+
</a>
|
|
1251
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|
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1252
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</li>
|
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1253
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|
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1254
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</ul>
|
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1255
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1256
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</nav>
|
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1257
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1258
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|
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<li class="md-nav__item">
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1270
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<a href="../descriptors/" class="md-nav__link">
|
|
1271
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+
|
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1272
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|
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1273
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1274
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<span class="md-ellipsis">
|
|
1275
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+
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1276
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1277
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Descriptors
|
|
1278
|
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|
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1279
|
+
|
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1280
|
+
|
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1281
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</span>
|
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1282
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1283
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1284
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|
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1285
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</a>
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1286
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1296
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|
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1297
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<li class="md-nav__item">
|
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1298
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+
<a href="../md/" class="md-nav__link">
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
|
|
1302
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+
<span class="md-ellipsis">
|
|
1303
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|
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1304
|
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|
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1305
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MD
|
|
1306
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|
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1307
|
+
|
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1308
|
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|
|
1309
|
+
</span>
|
|
1310
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+
|
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1311
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+
|
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1312
|
+
|
|
1313
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+
</a>
|
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1314
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</li>
|
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1315
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1320
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1321
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1322
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|
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1323
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|
|
1324
|
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|
|
1325
|
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<li class="md-nav__item">
|
|
1326
|
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<a href="../fep/" class="md-nav__link">
|
|
1327
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+
|
|
1328
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+
|
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Public Python API
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1751
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|
|
1753
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|
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1754
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<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
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<span class="md-ellipsis">
|
|
1760
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|
|
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|
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Explanation
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|
1763
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1764
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|
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Documentation
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2022
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Security Reporting
|
|
2077
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|
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2078
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|
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2079
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|
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2080
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<a href="../../development/release-readiness/" class="md-nav__link">
|
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2098
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2099
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|
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2100
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<span class="md-ellipsis">
|
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2102
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2103
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2104
|
+
Release Readiness
|
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2105
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|
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2106
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|
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2107
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|
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2108
|
+
</span>
|
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2109
|
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|
|
2110
|
+
|
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2111
|
+
|
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2112
|
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|
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2113
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|
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|
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<a href="../../development/ci-publishing/" class="md-nav__link">
|
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2126
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2127
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+
|
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2128
|
+
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2129
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<span class="md-ellipsis">
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2130
|
+
|
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2131
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|
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2132
|
+
CI and Publishing
|
|
2133
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2134
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2135
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2136
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2144
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2146
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|
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2147
|
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</nav>
|
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2148
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2149
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2150
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2151
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2153
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</ul>
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2154
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</nav>
|
|
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</div>
|
|
2156
|
+
</div>
|
|
2157
|
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</div>
|
|
2158
|
+
|
|
2159
|
+
|
|
2160
|
+
|
|
2161
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2162
|
+
<div class="md-sidebar__scrollwrap">
|
|
2163
|
+
<div class="md-sidebar__inner">
|
|
2164
|
+
|
|
2165
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+
|
|
2166
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+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
2167
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+
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2168
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2169
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2170
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2171
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2172
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|
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2173
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<label class="md-nav__title" for="__toc">
|
|
2174
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+
<span class="md-nav__icon md-icon"></span>
|
|
2175
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+
Table of contents
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|
2176
|
+
</label>
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|
2177
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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2178
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+
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2179
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+
<li class="md-nav__item">
|
|
2180
|
+
<a href="#requirements-and-example-status" class="md-nav__link">
|
|
2181
|
+
<span class="md-ellipsis">
|
|
2182
|
+
|
|
2183
|
+
Requirements and example status
|
|
2184
|
+
|
|
2185
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+
</span>
|
|
2186
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+
</a>
|
|
2187
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+
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2188
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</li>
|
|
2189
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+
|
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2190
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+
<li class="md-nav__item">
|
|
2191
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+
<a href="#unidock" class="md-nav__link">
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|
2192
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+
<span class="md-ellipsis">
|
|
2193
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+
|
|
2194
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+
unidock
|
|
2195
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+
|
|
2196
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+
</span>
|
|
2197
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</a>
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2198
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2199
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</li>
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2200
|
+
|
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2201
|
+
<li class="md-nav__item">
|
|
2202
|
+
<a href="#idockya" class="md-nav__link">
|
|
2203
|
+
<span class="md-ellipsis">
|
|
2204
|
+
|
|
2205
|
+
idockya
|
|
2206
|
+
|
|
2207
|
+
</span>
|
|
2208
|
+
</a>
|
|
2209
|
+
|
|
2210
|
+
</li>
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2211
|
+
|
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2212
|
+
<li class="md-nav__item">
|
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2213
|
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<a href="#gnina" class="md-nav__link">
|
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2214
|
+
<span class="md-ellipsis">
|
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2215
|
+
|
|
2216
|
+
gnina
|
|
2217
|
+
|
|
2218
|
+
</span>
|
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2219
|
+
</a>
|
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2220
|
+
|
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2221
|
+
</li>
|
|
2222
|
+
|
|
2223
|
+
<li class="md-nav__item">
|
|
2224
|
+
<a href="#compressed-inputs" class="md-nav__link">
|
|
2225
|
+
<span class="md-ellipsis">
|
|
2226
|
+
|
|
2227
|
+
Compressed inputs
|
|
2228
|
+
|
|
2229
|
+
</span>
|
|
2230
|
+
</a>
|
|
2231
|
+
|
|
2232
|
+
</li>
|
|
2233
|
+
|
|
2234
|
+
</ul>
|
|
2235
|
+
|
|
2236
|
+
</nav>
|
|
2237
|
+
</div>
|
|
2238
|
+
</div>
|
|
2239
|
+
</div>
|
|
2240
|
+
|
|
2241
|
+
|
|
2242
|
+
|
|
2243
|
+
<div class="md-content" data-md-component="content">
|
|
2244
|
+
|
|
2245
|
+
<article class="md-content__inner md-typeset">
|
|
2246
|
+
|
|
2247
|
+
|
|
2248
|
+
|
|
2249
|
+
|
|
2250
|
+
|
|
2251
|
+
|
|
2252
|
+
|
|
2253
|
+
|
|
2254
|
+
<h1 id="docking-plugin">Docking Plugin<a class="headerlink" href="#docking-plugin" title="Permanent link">¶</a></h1>
|
|
2255
|
+
<p>Package: <code>caddforge-docking</code></p>
|
|
2256
|
+
<div class="admonition info">
|
|
2257
|
+
<p class="admonition-title">Public source tag</p>
|
|
2258
|
+
<p>This page describes <code>caddforge-docking</code> <code>0.7.0</code>, tagged as <code>v0.7.0</code>.
|
|
2259
|
+
Published on PyPI; see the <a href="../version-matrix/">version matrix</a>.</p>
|
|
2260
|
+
</div>
|
|
2261
|
+
<p>The docking plugin provides docking and rescoring workflows through the standard CADDForge
|
|
2262
|
+
workflow/job interface.</p>
|
|
2263
|
+
<p>Install optional GUI support with:</p>
|
|
2264
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span><span class="s2">"caddforge-docking[gui]"</span>
|
|
2265
|
+
</code></pre></div>
|
|
2266
|
+
<h2 id="requirements-and-example-status">Requirements and example status<a class="headerlink" href="#requirements-and-example-status" title="Permanent link">¶</a></h2>
|
|
2267
|
+
<p>The <a href="../../examples/">example library</a> provides downloadable configuration
|
|
2268
|
+
templates for every workflow on this page, plus a shared Python runner. File paths
|
|
2269
|
+
refer to inputs you must prepare; these are not bundled research datasets. Schema
|
|
2270
|
+
validation does not establish scientific validity or engine availability. See the
|
|
2271
|
+
<a href="../version-matrix/">version matrix</a> for release tags and publication status.</p>
|
|
2272
|
+
<h2 id="unidock"><code>unidock</code><a class="headerlink" href="#unidock" title="Permanent link">¶</a></h2>
|
|
2273
|
+
<p>Runs GPU-accelerated docking with Uni-Dock.</p>
|
|
2274
|
+
<p>CLI:</p>
|
|
2275
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>docking<span class="w"> </span>unidock<span class="w"> </span>--config<span class="w"> </span>unidock.yaml
|
|
2276
|
+
</code></pre></div>
|
|
2277
|
+
<p>YAML:</p>
|
|
2278
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nt">receptor_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/protein.pdbqt</span>
|
|
2279
|
+
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nt">ligand_multisdf_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligands.sdf</span>
|
|
2280
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nt">center_x</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
|
|
2281
|
+
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="nt">center_y</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
|
|
2282
|
+
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="nt">center_z</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.0</span>
|
|
2283
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="nt">size_x</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">20</span>
|
|
2284
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="nt">size_y</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">20</span>
|
|
2285
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="nt">size_z</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">20</span>
|
|
2286
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a><span class="nt">search_mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">fast</span>
|
|
2287
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="nt">exhaustiveness</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">384</span>
|
|
2288
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="nt">batch_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">50000</span>
|
|
2289
|
+
</code></pre></div>
|
|
2290
|
+
<p>Python:</p>
|
|
2291
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></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>
|
|
2292
|
+
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></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>
|
|
2293
|
+
<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
|
|
2294
|
+
<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"docking"</span><span class="p">,</span> <span class="s2">"unidock"</span><span class="p">)</span>
|
|
2295
|
+
<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></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>
|
|
2296
|
+
<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a> <span class="n">receptor_path</span><span class="o">=</span><span class="s2">"data/protein.pdbqt"</span><span class="p">,</span>
|
|
2297
|
+
<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a> <span class="n">ligand_multisdf_path</span><span class="o">=</span><span class="s2">"data/ligands.sdf"</span><span class="p">,</span>
|
|
2298
|
+
<a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a> <span class="n">center_x</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span>
|
|
2299
|
+
<a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a> <span class="n">center_y</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span>
|
|
2300
|
+
<a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a> <span class="n">center_z</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span>
|
|
2301
|
+
<a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a> <span class="n">size_x</span><span class="o">=</span><span class="mf">20.0</span><span class="p">,</span>
|
|
2302
|
+
<a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a> <span class="n">size_y</span><span class="o">=</span><span class="mf">20.0</span><span class="p">,</span>
|
|
2303
|
+
<a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a> <span class="n">size_z</span><span class="o">=</span><span class="mf">20.0</span><span class="p">,</span>
|
|
2304
|
+
<a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2305
|
+
<a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a><span class="p">)</span>
|
|
2306
|
+
<a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></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>
|
|
2307
|
+
<a id="__codelineno-3-17" name="__codelineno-3-17" href="#__codelineno-3-17"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2308
|
+
<a id="__codelineno-3-18" name="__codelineno-3-18" href="#__codelineno-3-18"></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>
|
|
2309
|
+
<a id="__codelineno-3-19" name="__codelineno-3-19" href="#__codelineno-3-19"></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>
|
|
2310
|
+
<a id="__codelineno-3-20" name="__codelineno-3-20" href="#__codelineno-3-20"></a><span class="p">)</span>
|
|
2311
|
+
<a id="__codelineno-3-21" name="__codelineno-3-21" href="#__codelineno-3-21"></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>
|
|
2312
|
+
<a id="__codelineno-3-22" name="__codelineno-3-22" href="#__codelineno-3-22"></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>
|
|
2313
|
+
<a id="__codelineno-3-23" name="__codelineno-3-23" href="#__codelineno-3-23"></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">"best_scores_csv"</span><span class="p">])</span>
|
|
2314
|
+
</code></pre></div>
|
|
2315
|
+
<p>Outputs to inspect: <code>results/docked_out/</code>, <code>results/best_scores.csv</code>,
|
|
2316
|
+
<code>results/result_record.json</code>.</p>
|
|
2317
|
+
<p><code>exhaustiveness</code> defaults to <code>384</code> in this release. Set it explicitly when reproducing runs made
|
|
2318
|
+
with an earlier default.</p>
|
|
2319
|
+
<h2 id="idockya"><code>idockya</code><a class="headerlink" href="#idockya" title="Permanent link">¶</a></h2>
|
|
2320
|
+
<p>Runs docking with OpenChemLib iDockYa through <code>pyocl</code>, provided by
|
|
2321
|
+
<code>pyocl-idor>=0.8.3</code>. Java 21 or newer is required; configure <code>JAVA_HOME</code> accordingly.</p>
|
|
2322
|
+
<p>CLI:</p>
|
|
2323
|
+
<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>docking<span class="w"> </span>idockya<span class="w"> </span>--config<span class="w"> </span>idockya.yaml
|
|
2324
|
+
</code></pre></div>
|
|
2325
|
+
<p>YAML:</p>
|
|
2326
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="nt">receptor_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/receptor.sdf</span>
|
|
2327
|
+
<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="nt">native_ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/native_ligand.sdf</span>
|
|
2328
|
+
<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="nt">ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligands.sdf</span>
|
|
2329
|
+
<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="nt">output_format</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">sdf</span>
|
|
2330
|
+
<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="nt">output_dir_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">docked_out</span>
|
|
2331
|
+
<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a><span class="nt">num_workers</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
|
|
2332
|
+
<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a><span class="nt">max_inflight_tasks</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
|
|
2333
|
+
</code></pre></div>
|
|
2334
|
+
<p>Python:</p>
|
|
2335
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></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>
|
|
2336
|
+
<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></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>
|
|
2337
|
+
<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>
|
|
2338
|
+
<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"docking"</span><span class="p">,</span> <span class="s2">"idockya"</span><span class="p">)</span>
|
|
2339
|
+
<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></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>
|
|
2340
|
+
<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a> <span class="n">receptor_path</span><span class="o">=</span><span class="s2">"data/receptor.sdf"</span><span class="p">,</span>
|
|
2341
|
+
<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a> <span class="n">native_ligand_path</span><span class="o">=</span><span class="s2">"data/native_ligand.sdf"</span><span class="p">,</span>
|
|
2342
|
+
<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a> <span class="n">ligand_path</span><span class="o">=</span><span class="s2">"data/ligands.sdf"</span><span class="p">,</span>
|
|
2343
|
+
<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a> <span class="n">output_format</span><span class="o">=</span><span class="s2">"sdf"</span><span class="p">,</span>
|
|
2344
|
+
<a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2345
|
+
<a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="p">)</span>
|
|
2346
|
+
<a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></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>
|
|
2347
|
+
<a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2348
|
+
<a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></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>
|
|
2349
|
+
<a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></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>
|
|
2350
|
+
<a id="__codelineno-6-16" name="__codelineno-6-16" href="#__codelineno-6-16"></a><span class="p">)</span>
|
|
2351
|
+
<a id="__codelineno-6-17" name="__codelineno-6-17" href="#__codelineno-6-17"></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>
|
|
2352
|
+
<a id="__codelineno-6-18" name="__codelineno-6-18" href="#__codelineno-6-18"></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>
|
|
2353
|
+
<a id="__codelineno-6-19" name="__codelineno-6-19" href="#__codelineno-6-19"></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>
|
|
2354
|
+
</code></pre></div>
|
|
2355
|
+
<p>Outputs to inspect: <code>results/docked_out/</code>, <code>results/best_scores.csv</code>,
|
|
2356
|
+
<code>results/result_record.json</code>.</p>
|
|
2357
|
+
<h2 id="gnina"><code>gnina</code><a class="headerlink" href="#gnina" title="Permanent link">¶</a></h2>
|
|
2358
|
+
<p>Runs docking or rescoring with the <code>gnina</code> executable.</p>
|
|
2359
|
+
<p>CLI:</p>
|
|
2360
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>docking<span class="w"> </span>gnina<span class="w"> </span>--config<span class="w"> </span>gnina.yaml
|
|
2361
|
+
</code></pre></div>
|
|
2362
|
+
<p>YAML:</p>
|
|
2363
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="nt">receptor_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/protein.pdb</span>
|
|
2364
|
+
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="nt">ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/ligands.sdf</span>
|
|
2365
|
+
<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="nt">autobox_ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/reference_ligand.sdf</span>
|
|
2366
|
+
<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="nt">flexres</span><span class="p">:</span>
|
|
2367
|
+
<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">A:194</span>
|
|
2368
|
+
<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">A:244</span>
|
|
2369
|
+
<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">A:252</span>
|
|
2370
|
+
<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="nt">scoring</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">dkoes_fast</span>
|
|
2371
|
+
<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="nt">cnn_scoring</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">rescore</span>
|
|
2372
|
+
<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="nt">no_gpu</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2373
|
+
<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="nt">output_format</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">sdf</span>
|
|
2374
|
+
</code></pre></div>
|
|
2375
|
+
<p>Python:</p>
|
|
2376
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></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>
|
|
2377
|
+
<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></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>
|
|
2378
|
+
<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>
|
|
2379
|
+
<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"docking"</span><span class="p">,</span> <span class="s2">"gnina"</span><span class="p">)</span>
|
|
2380
|
+
<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></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>
|
|
2381
|
+
<a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a> <span class="n">receptor_path</span><span class="o">=</span><span class="s2">"data/protein.pdb"</span><span class="p">,</span>
|
|
2382
|
+
<a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a> <span class="n">ligand_path</span><span class="o">=</span><span class="s2">"data/ligands.sdf"</span><span class="p">,</span>
|
|
2383
|
+
<a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a> <span class="n">autobox_ligand_path</span><span class="o">=</span><span class="s2">"data/reference_ligand.sdf"</span><span class="p">,</span>
|
|
2384
|
+
<a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a> <span class="n">flexres</span><span class="o">=</span><span class="p">[</span><span class="s2">"A:194"</span><span class="p">,</span> <span class="s2">"A:244"</span><span class="p">,</span> <span class="s2">"A:252"</span><span class="p">],</span>
|
|
2385
|
+
<a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a> <span class="n">no_gpu</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
|
|
2386
|
+
<a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2387
|
+
<a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a><span class="p">)</span>
|
|
2388
|
+
<a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></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>
|
|
2389
|
+
<a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2390
|
+
<a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></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>
|
|
2391
|
+
<a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></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>
|
|
2392
|
+
<a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a><span class="p">)</span>
|
|
2393
|
+
<a id="__codelineno-9-18" name="__codelineno-9-18" href="#__codelineno-9-18"></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>
|
|
2394
|
+
<a id="__codelineno-9-19" name="__codelineno-9-19" href="#__codelineno-9-19"></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>
|
|
2395
|
+
<a id="__codelineno-9-20" name="__codelineno-9-20" href="#__codelineno-9-20"></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><span class="s2">"best_scores_csv"</span><span class="p">])</span>
|
|
2396
|
+
</code></pre></div>
|
|
2397
|
+
<p>Outputs to inspect: <code>results/docked_out/</code>, <code>results/gnina_logs/</code>,
|
|
2398
|
+
<code>results/best_scores.csv</code>, <code>results/result_record.json</code>.</p>
|
|
2399
|
+
<p>Flexible docking also writes raw gnina flex receptor outputs when <code>write_flex_receptor_output</code> is
|
|
2400
|
+
enabled. By default, gnina additionally writes one full protein-ligand complex PDB, one protein-only
|
|
2401
|
+
PDB, and one ligand-only SDF per generated pose under <code>results/flexible_complexes/</code>. These artifacts
|
|
2402
|
+
preserve protein and ligand hydrogen presence from the input receptor and ligand records. Ligand
|
|
2403
|
+
bond orders and formal charges are copied from the input ligand; PDB complexes emit ligand bond
|
|
2404
|
+
orders as <code>CONECT</code> records, but downstream support for interpreting those bond orders is
|
|
2405
|
+
reader-dependent. Use a PDB receptor for this mode, or set
|
|
2406
|
+
<code>write_flexible_complexes: false</code> to keep only the raw gnina outputs.</p>
|
|
2407
|
+
<p>Pipeline output aliases include <code>scores</code>, <code>poses</code>, <code>flexible_complexes_manifest</code>,
|
|
2408
|
+
<code>flexible_complexes</code>, <code>flexible_proteins</code>, and <code>flexible_ligand_poses</code>. The flexible artifact
|
|
2409
|
+
aliases are optional and are emitted only when flexible complex generation produces them.</p>
|
|
2410
|
+
<p>On Slurm, GNINA stages static inputs once in node-local scratch, synchronizes live text logs, and
|
|
2411
|
+
publishes completed ligand artifacts asynchronously. <code>log_sync_interval_seconds</code> and
|
|
2412
|
+
<code>result_sync_interval_seconds</code> control those retry intervals. A temporary shared-filesystem outage
|
|
2413
|
+
does not interrupt docking, but the workflow does not report success if required artifacts remain
|
|
2414
|
+
unpublished after the final retry.</p>
|
|
2415
|
+
<h2 id="compressed-inputs">Compressed inputs<a class="headerlink" href="#compressed-inputs" title="Permanent link">¶</a></h2>
|
|
2416
|
+
<p>Declared receptor, ligand, and reference inputs may use a trailing <code>.gz</code>; CADDForge expands
|
|
2417
|
+
them in runtime scratch. UniDock indexes can reference <code>.sdf.gz</code> ligands.</p>
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+
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