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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How-to Guides
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_3">
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How-to Guides
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</label>
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<a href="../../how-to/jobs/" class="md-nav__link">
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<span class="md-ellipsis">
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Jobs and Results
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<span class="md-ellipsis">
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Scatter and Reduce
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
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<span class="md-ellipsis">
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Troubleshooting
|
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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_4" checked>
|
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627
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|
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628
|
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|
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629
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<div class="md-nav__link md-nav__container">
|
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630
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<a href="../" class="md-nav__link ">
|
|
631
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|
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632
|
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|
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633
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|
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634
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<span class="md-ellipsis">
|
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635
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|
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636
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|
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Core
|
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638
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|
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639
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|
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640
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|
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641
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</span>
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</a>
|
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646
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647
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648
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<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
649
|
+
<span class="md-nav__icon md-icon"></span>
|
|
650
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</label>
|
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651
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652
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</div>
|
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653
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654
|
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
|
|
655
|
+
<label class="md-nav__title" for="__nav_4">
|
|
656
|
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<span class="md-nav__icon md-icon"></span>
|
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657
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658
|
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|
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Core
|
|
660
|
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|
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661
|
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|
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662
|
+
</label>
|
|
663
|
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<ul class="md-nav__list" data-md-scrollfix>
|
|
664
|
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|
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665
|
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666
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667
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669
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<li class="md-nav__item md-nav__item--active">
|
|
674
|
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|
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675
|
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
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<label class="md-nav__link md-nav__link--active" for="__toc">
|
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682
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683
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684
|
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|
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<span class="md-ellipsis">
|
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686
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|
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Concepts
|
|
689
|
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690
|
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691
|
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692
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</span>
|
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693
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694
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696
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<span class="md-nav__icon md-icon"></span>
|
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697
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</label>
|
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698
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699
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<a href="./" class="md-nav__link md-nav__link--active">
|
|
700
|
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|
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701
|
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702
|
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703
|
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<span class="md-ellipsis">
|
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704
|
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|
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705
|
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|
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706
|
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Concepts
|
|
707
|
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|
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708
|
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|
|
709
|
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|
|
710
|
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</span>
|
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711
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|
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712
|
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713
|
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|
|
714
|
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</a>
|
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715
|
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|
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716
|
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|
|
717
|
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|
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718
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
719
|
+
|
|
720
|
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|
|
721
|
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722
|
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|
|
723
|
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|
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724
|
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|
|
725
|
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<label class="md-nav__title" for="__toc">
|
|
726
|
+
<span class="md-nav__icon md-icon"></span>
|
|
727
|
+
Table of contents
|
|
728
|
+
</label>
|
|
729
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
730
|
+
|
|
731
|
+
<li class="md-nav__item">
|
|
732
|
+
<a href="#dataset-and-moleculeset" class="md-nav__link">
|
|
733
|
+
<span class="md-ellipsis">
|
|
734
|
+
|
|
735
|
+
Dataset and MoleculeSet
|
|
736
|
+
|
|
737
|
+
</span>
|
|
738
|
+
</a>
|
|
739
|
+
|
|
740
|
+
</li>
|
|
741
|
+
|
|
742
|
+
<li class="md-nav__item">
|
|
743
|
+
<a href="#workflow" class="md-nav__link">
|
|
744
|
+
<span class="md-ellipsis">
|
|
745
|
+
|
|
746
|
+
Workflow
|
|
747
|
+
|
|
748
|
+
</span>
|
|
749
|
+
</a>
|
|
750
|
+
|
|
751
|
+
</li>
|
|
752
|
+
|
|
753
|
+
<li class="md-nav__item">
|
|
754
|
+
<a href="#job" class="md-nav__link">
|
|
755
|
+
<span class="md-ellipsis">
|
|
756
|
+
|
|
757
|
+
Job
|
|
758
|
+
|
|
759
|
+
</span>
|
|
760
|
+
</a>
|
|
761
|
+
|
|
762
|
+
</li>
|
|
763
|
+
|
|
764
|
+
<li class="md-nav__item">
|
|
765
|
+
<a href="#backend" class="md-nav__link">
|
|
766
|
+
<span class="md-ellipsis">
|
|
767
|
+
|
|
768
|
+
Backend
|
|
769
|
+
|
|
770
|
+
</span>
|
|
771
|
+
</a>
|
|
772
|
+
|
|
773
|
+
</li>
|
|
774
|
+
|
|
775
|
+
<li class="md-nav__item">
|
|
776
|
+
<a href="#result" class="md-nav__link">
|
|
777
|
+
<span class="md-ellipsis">
|
|
778
|
+
|
|
779
|
+
Result
|
|
780
|
+
|
|
781
|
+
</span>
|
|
782
|
+
</a>
|
|
783
|
+
|
|
784
|
+
</li>
|
|
785
|
+
|
|
786
|
+
</ul>
|
|
787
|
+
|
|
788
|
+
</nav>
|
|
789
|
+
|
|
790
|
+
</li>
|
|
791
|
+
|
|
792
|
+
|
|
793
|
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|
|
794
|
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|
|
795
|
+
|
|
796
|
+
|
|
797
|
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|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
<li class="md-nav__item">
|
|
802
|
+
<a href="../configuration/" class="md-nav__link">
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
<span class="md-ellipsis">
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
Configuration
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
</span>
|
|
814
|
+
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
</a>
|
|
818
|
+
</li>
|
|
819
|
+
|
|
820
|
+
|
|
821
|
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|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
|
|
826
|
+
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
<li class="md-nav__item">
|
|
830
|
+
<a href="../cli/" class="md-nav__link">
|
|
831
|
+
|
|
832
|
+
|
|
833
|
+
|
|
834
|
+
<span class="md-ellipsis">
|
|
835
|
+
|
|
836
|
+
|
|
837
|
+
CLI
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
</span>
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
</a>
|
|
846
|
+
</li>
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
|
|
853
|
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|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
<li class="md-nav__item">
|
|
858
|
+
<a href="../jobs-results/" class="md-nav__link">
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
<span class="md-ellipsis">
|
|
863
|
+
|
|
864
|
+
|
|
865
|
+
Jobs and Results
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
|
|
869
|
+
</span>
|
|
870
|
+
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
</a>
|
|
874
|
+
</li>
|
|
875
|
+
|
|
876
|
+
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
|
|
880
|
+
|
|
881
|
+
|
|
882
|
+
|
|
883
|
+
|
|
884
|
+
|
|
885
|
+
<li class="md-nav__item">
|
|
886
|
+
<a href="../slurm/" class="md-nav__link">
|
|
887
|
+
|
|
888
|
+
|
|
889
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<span class="md-ellipsis">
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Slurm Backend
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<li class="md-nav__item">
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<a href="../plugins/" class="md-nav__link">
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915
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Plugins
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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971
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
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975
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<div class="md-nav__link md-nav__container">
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976
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<a href="../../pipelines/" class="md-nav__link ">
|
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977
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978
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979
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980
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<span class="md-ellipsis">
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981
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982
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Pipelines
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987
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988
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989
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</a>
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992
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993
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994
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<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
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995
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<span class="md-nav__icon md-icon"></span>
|
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996
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</label>
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997
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998
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</div>
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999
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|
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1000
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
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1001
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+
<label class="md-nav__title" for="__nav_5">
|
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1002
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<span class="md-nav__icon md-icon"></span>
|
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1003
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|
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1004
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1005
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Pipelines
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1006
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1007
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1008
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</label>
|
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1009
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<ul class="md-nav__list" data-md-scrollfix>
|
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1010
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1011
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1016
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|
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1017
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<li class="md-nav__item">
|
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1018
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<a href="../../pipelines/specification/" class="md-nav__link">
|
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1019
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|
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1020
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|
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1021
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|
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1022
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<span class="md-ellipsis">
|
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1023
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|
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1024
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|
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1025
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Specification
|
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1026
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1027
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1028
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1029
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</span>
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1038
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1044
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1045
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<li class="md-nav__item">
|
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1046
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<a href="../../pipelines/artifacts/" class="md-nav__link">
|
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1047
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1048
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1049
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<span class="md-ellipsis">
|
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1051
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|
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1052
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|
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1053
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Artifacts
|
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1056
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1057
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1073
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<li class="md-nav__item">
|
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1074
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<a href="../../pipelines/built-ins/" class="md-nav__link">
|
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1075
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1076
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1077
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1078
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<span class="md-ellipsis">
|
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1079
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|
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1080
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|
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1081
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Built-in Stages
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1082
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1083
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1084
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1085
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1100
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1101
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<li class="md-nav__item">
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1102
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<a href="../../pipelines/examples/" class="md-nav__link">
|
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1103
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1104
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1105
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1106
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<span class="md-ellipsis">
|
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1107
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|
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1109
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Examples
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1110
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1111
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1112
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1120
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1123
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</ul>
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</nav>
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|
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<div class="md-nav__link md-nav__container">
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<a href="../../plugins/" class="md-nav__link ">
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1177
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Plugins
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1190
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
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1191
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+
<span class="md-nav__icon md-icon"></span>
|
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1192
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+
</label>
|
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1193
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|
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1194
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</div>
|
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1195
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1196
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
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1197
|
+
<label class="md-nav__title" for="__nav_6">
|
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1198
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+
<span class="md-nav__icon md-icon"></span>
|
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1199
|
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|
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1200
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|
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1201
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Plugins
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1202
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|
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1203
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|
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1204
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</label>
|
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1205
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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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1214
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<a href="../../plugins/version-matrix/" class="md-nav__link">
|
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1215
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|
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1216
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|
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1217
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|
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<span class="md-ellipsis">
|
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1219
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|
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1220
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|
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1221
|
+
Version Matrix
|
|
1222
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|
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1223
|
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|
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1224
|
+
|
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1225
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</span>
|
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1226
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|
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1227
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1228
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|
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1229
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</a>
|
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1230
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1232
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1233
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|
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1234
|
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1235
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1236
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1238
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1239
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1240
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|
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1241
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<li class="md-nav__item">
|
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1242
|
+
<a href="../../plugins/docking/" class="md-nav__link">
|
|
1243
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+
|
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1244
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|
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1245
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|
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1246
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<span class="md-ellipsis">
|
|
1247
|
+
|
|
1248
|
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|
|
1249
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+
Docking
|
|
1250
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|
|
1251
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+
|
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1252
|
+
|
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1253
|
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</span>
|
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1254
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1255
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1256
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|
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1257
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</a>
|
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1258
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1267
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1268
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|
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1269
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<li class="md-nav__item">
|
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1270
|
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<a href="../../plugins/descriptors/" class="md-nav__link">
|
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1271
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+
|
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1272
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|
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1273
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|
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1274
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<span class="md-ellipsis">
|
|
1275
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+
|
|
1276
|
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|
|
1277
|
+
Descriptors
|
|
1278
|
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|
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1279
|
+
|
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1280
|
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|
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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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1287
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1288
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1289
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1290
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1291
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1295
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1296
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|
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1297
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<li class="md-nav__item">
|
|
1298
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
|
|
1302
|
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<span class="md-ellipsis">
|
|
1303
|
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|
|
1304
|
+
|
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1305
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+
MD
|
|
1306
|
+
|
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1307
|
+
|
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1308
|
+
|
|
1309
|
+
</span>
|
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1310
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|
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1311
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|
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1312
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|
|
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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1316
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1317
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1318
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1319
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1320
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1321
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1322
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|
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1323
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|
|
1324
|
+
|
|
1325
|
+
<li class="md-nav__item">
|
|
1326
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1327
|
+
|
|
1328
|
+
|
|
1329
|
+
|
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Data Science
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" >
|
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|
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<a href="../../gui/" class="md-nav__link ">
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1471
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GUI
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|
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|
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|
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
|
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<label class="md-nav__title" for="__nav_7">
|
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|
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|
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Walkthrough
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Plugin GUI Authoring
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|
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|
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<a href="../../reference/" class="md-nav__link ">
|
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Reference
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|
|
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+
<span class="md-nav__icon md-icon"></span>
|
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+
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|
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</div>
|
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
|
|
1623
|
+
<label class="md-nav__title" for="__nav_8">
|
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<span class="md-nav__icon md-icon"></span>
|
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1627
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Reference
|
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1628
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|
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|
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<a href="../../reference/api/" class="md-nav__link">
|
|
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|
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|
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|
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|
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|
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1647
|
+
Public Python API
|
|
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|
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|
|
1649
|
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|
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1650
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|
|
1651
|
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|
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|
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|
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1654
|
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|
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|
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|
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|
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|
|
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<a href="../../examples/" class="md-nav__link">
|
|
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|
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|
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|
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|
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1671
|
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|
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+
<span class="md-ellipsis">
|
|
1673
|
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|
|
1674
|
+
|
|
1675
|
+
Example Library
|
|
1676
|
+
|
|
1677
|
+
|
|
1678
|
+
|
|
1679
|
+
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|
|
1680
|
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|
|
1681
|
+
|
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1682
|
+
|
|
1683
|
+
</a>
|
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1684
|
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|
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|
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<a href="../../examples/quickstart/" class="md-nav__link">
|
|
1697
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|
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1698
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1699
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|
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<span class="md-ellipsis">
|
|
1701
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|
|
1702
|
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|
|
1703
|
+
Example Data Provenance
|
|
1704
|
+
|
|
1705
|
+
|
|
1706
|
+
|
|
1707
|
+
</span>
|
|
1708
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|
|
1709
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|
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1710
|
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|
|
1711
|
+
</a>
|
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1712
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</li>
|
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1714
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1715
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1716
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1717
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</ul>
|
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1718
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</nav>
|
|
1719
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1720
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</li>
|
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1721
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1723
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1725
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1726
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1727
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1728
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1729
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1730
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1732
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1733
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1735
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1744
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|
|
1745
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|
|
1746
|
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|
|
1747
|
+
|
|
1748
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1749
|
+
|
|
1750
|
+
|
|
1751
|
+
|
|
1752
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1753
|
+
|
|
1754
|
+
|
|
1755
|
+
<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
1756
|
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|
|
1757
|
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|
|
1758
|
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|
|
1759
|
+
<span class="md-ellipsis">
|
|
1760
|
+
|
|
1761
|
+
|
|
1762
|
+
Explanation
|
|
1763
|
+
|
|
1764
|
+
|
|
1765
|
+
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2175
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2176
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2177
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2178
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2181
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<span class="md-ellipsis">
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2182
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2183
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Dataset and MoleculeSet
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2184
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2185
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2186
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2197
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</a>
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<h1 id="concepts">Concepts<a class="headerlink" href="#concepts" title="Permanent link">¶</a></h1>
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<h2 id="dataset-and-moleculeset">Dataset and MoleculeSet<a class="headerlink" href="#dataset-and-moleculeset" title="Permanent link">¶</a></h2>
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<p><code>Dataset</code> represents a reproducible collection of data such as molecules and labels. <code>MoleculeSet</code>
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represents a collection of molecules used by workflows and models. Both are frozen
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dataclasses, but contained lists and molecular objects are not deeply immutable.
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<code>Dataset.from_molecules()</code> is implemented; <code>Dataset.from_file()</code> currently raises
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<code>NotImplementedError</code>. File input is handled by tool-specific configuration/workflows.</p>
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<p>See the <a href="../../reference/api/">public API reference</a> for constructors and fields.</p>
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<p>Future data sources may include databases, but tool APIs should continue to accept stable core data
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objects rather than tool-specific containers.</p>
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<h2 id="workflow">Workflow<a class="headerlink" href="#workflow" title="Permanent link">¶</a></h2>
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<p>A <code>Workflow</code> orchestrates one scientific protocol, such as docking, MD, FEP, QM, or property
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prediction. Workflows are backend-agnostic and delegate execution to backends through the core job
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infrastructure.</p>
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<h2 id="job">Job<a class="headerlink" href="#job" title="Permanent link">¶</a></h2>
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<p>A <code>Job</code> represents one execution of a workflow. Jobs carry a unique ID, status, timestamps, backend
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metadata, and paths to the standardized run directory and logs.</p>
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<h2 id="backend">Backend<a class="headerlink" href="#backend" title="Permanent link">¶</a></h2>
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<p>A <code>Backend</code> submits, tracks, and cancels jobs. Core backends include local execution and Slurm.
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Workflows should not know Slurm-specific or local-process details.</p>
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<h2 id="result">Result<a class="headerlink" href="#result" title="Permanent link">¶</a></h2>
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<p>A <code>Result</code> is the canonical outcome of a job. Results include the job ID, tool name, status,
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metrics, and paths to important output files. Tools may store richer tool-specific data under their
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result directory, but the canonical result should remain loadable through the core helpers.</p>
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