rugnux/Gitea-pages
0
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
f16068f65ba26b44c06ba65cb76309e0b89720a9
Gitea-pages/python_client/docs/RugnuxLiveRefinement.html
T

14 lines
18 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
<!DOCTYPE html> <html lang=en data-content_root="../../"> <meta charset=utf-8 /> <meta name=viewport content="width=device-width, initial-scale=1.0" /><meta name=viewport content="width=device-width, initial-scale=1" /> <meta name=viewport content="width=device-width,initial-scale=1"> <meta http-equiv=x-ua-compatible content="ie=edge"> <meta name="lang:clipboard.copy" content="Copy to clipboard"> <meta name="lang:clipboard.copied" content="Copied to clipboard"> <meta name="lang:search.language" content=en > <meta name="lang:search.pipeline.stopwords" content=True > <meta name="lang:search.pipeline.trimmer" content=True > <meta name="lang:search.result.none" content="No matching documents"> <meta name="lang:search.result.one" content="1 matching document"> <meta name="lang:search.result.other" content="# matching documents"> <meta name="lang:search.tokenizer" content="[\s\-]+"> <link href="https://fonts.gstatic.com/" rel=preconnect crossorigin> <link href="https://fonts.googleapis.com/css?family=Roboto+Mono:400,500,700|Roboto:300,400,400i,700&display=fallback" rel=stylesheet > <style> body, input { font-family: "Roboto", "Helvetica Neue", Helvetica, Arial, sans-serif } code, kbd, pre { font-family: "Roboto Mono", "Courier New", Courier, monospace } </style> <link rel=stylesheet href="../../_static/stylesheets/application.css"/> <link rel=stylesheet href="../../_static/stylesheets/application-palette.css"/> <link rel=stylesheet href="../../_static/stylesheets/application-fixes.css"/> <link rel=stylesheet href="../../_static/fonts/material-icons.css"/> <meta name=theme-color content="#3f51b5"> <script src="../../_static/javascripts/modernizr.js"></script> <title>RugnuxLiveRefinement &#8212; Jungfraujoch 1.0.0-rc.180 documentation</title> <link rel=stylesheet type="text/css" href="../../_static/pygments.css?v=83e35b93" /> <link rel=stylesheet type="text/css" href="../../_static/material.css?v=79c92029" /> <link rel=stylesheet type="text/css" href="../../_static/jfjoch.css?v=bb6ed8b7" /> <script src="../../_static/documentation_options.js?v=b43f58b8"></script> <script src="../../_static/doctools.js?v=9bcbadda"></script> <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script> <script src="../../_static/jfjoch_downloads.js?v=9e84fe5a"></script> <link rel=icon href="../../_static/jfjoch.png"/> <link rel=index title=Index href="../../genindex.html" /> <link rel=search title=Search href="../../search.html" /> <link rel=next title=RugnuxLiveStatus href=RugnuxLiveStatus.html /> <link rel=prev title=RugnuxLiveModel href=RugnuxLiveModel.html /> <body dir=ltr data-md-color-primary=indigo data-md-color-accent=lime> <svg class=md-svg > <defs data-children-count=0 > <svg xmlns="http://www.w3.org/2000/svg" width=500 height=500 viewBox="0 0 500 500" id=__gitlab ><path fill=currentColor d="M93.667 473.347l90.684-279.097H2.983l90.684 279.097z" transform="translate(156.198 1.16)"/><path fill=currentColor d="M221.333 473.345L130.649 194.25H3.557l217.776 279.095z" transform="translate(28.531 1.16)" opacity=.7 /><path fill=currentColor d="M32 195.155L4.441 279.97a18.773 18.773 0 0 0 6.821 20.99l238.514 173.29L32 195.155z" transform="translate(.089 .256)" opacity=.5 /><path fill=currentColor d="M2.667-84.844h127.092L75.14-252.942c-2.811-8.649-15.047-8.649-17.856 0L2.667-84.844z" transform="translate(29.422 280.256)"/><path fill=currentColor d="M2.667 473.345L93.351 194.25h127.092L2.667 473.345z" transform="translate(247.198 1.16)" opacity=.7 /><path fill=currentColor d="M221.334 195.155l27.559 84.815a18.772 18.772 0 0 1-6.821 20.99L3.557 474.25l217.777-279.095z" transform="translate(246.307 .256)" opacity=.5 /><path fill=currentColor d="M130.667-84.844H3.575l54.618-168.098c2.811-8.649 15.047-8.649 17.856 0l54.618 168.098z" transform="translate(336.974 280.256)"/></svg> </defs> </svg> <input class=md-toggle data-md-toggle=drawer type=checkbox id=__drawer > <input class=md-toggle data-md-toggle=search type=checkbox id=__search > <label class=md-overlay data-md-component=overlay for=__drawer ></label> <a href="#python_client/docs/RugnuxLiveRefinement" tabindex=1 class=md-skip > Skip to content </a> <header class=md-header data-md-component=header > <nav class="md-header-nav md-grid"> <div class="md-flex navheader"> <div class="md-flex__cell md-flex__cell--shrink"> <a href="../../documentation.html" title="Jungfraujoch 1.0.0-rc.180 documentation" class="md-header-nav__button md-logo"> <i class=md-icon >&#xe30d</i> </a> </div> <div class="md-flex__cell md-flex__cell--shrink"> <label class="md-icon md-icon--menu md-header-nav__button" for=__drawer ></label> </div> <div class="md-flex__cell md-flex__cell--stretch"> <div class="md-flex__ellipsis md-header-nav__title" data-md-component=title > <span class=md-header-nav__topic >PSI Jungfraujoch</span> <span class=md-header-nav__topic > RugnuxLiveRefinement </span> </div> </div> <div class="md-flex__cell md-flex__cell--shrink"> <label class="md-icon md-icon--search md-header-nav__button" for=__search ></label> <div class=md-search data-md-component=search role=dialog > <label class=md-search__overlay for=__search ></label> <div class=md-search__inner role=search > <form class=md-search__form action="../../search.html" method=get name=search > <input type=text class=md-search__input name=q placeholder=""Search"" autocapitalize=off autocomplete=off spellcheck=false data-md-component=query data-md-state=active > <label class="md-icon md-search__icon" for=__search ></label> <button type=reset class="md-icon md-search__icon" data-md-component=reset tabindex=-1 > &#xE5CD; </button> </form> <div class=md-search__output > <div class=md-search__scrollwrap data-md-scrollfix> <div class=md-search-result data-md-component=result > <div class=md-search-result__meta > Type to start searching </div> <ol class=md-search-result__list ></ol> </div> </div> </div> </div> </div> </div> <div class="md-flex__cell md-flex__cell--shrink"> <div class=md-header-nav__source > <a href="https://gitea.psi.ch/mx/jungfraujoch" title="Go to repository" class=md-source data-md-source=github > <div class=md-source__icon > <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width=28 height=28 > <use xlink:href="#__gitlab" width=24 height=24 ></use> </svg> </div> <div class=md-source__repository > Jungfraujoch </div> </a> </div> </div> <script src="../../_static/javascripts/version_dropdown.js"></script> <script> var json_loc = "../../"versions.json"", target_loc = "../../../", text = "Versions"; $( document ).ready( add_version_dropdown(json_loc, target_loc, text)); </script> </div> </nav> </header> <div class=md-container > <nav class=md-tabs data-md-component=tabs > <div class="md-tabs__inner md-grid"> <ul class=md-tabs__list > <li class=md-tabs__item ><a href="../../documentation.html" class=md-tabs__link >Jungfraujoch 1.0.0-rc.180 documentation</a> <li class=md-tabs__item ><a href="../../PYTHON_CLIENT.html" class=md-tabs__link >OpenAPI Python client</a> </ul> </div> </nav> <main class=md-main > <div class="md-main__inner md-grid" data-md-component=container > <div class="md-sidebar md-sidebar--primary" data-md-component=navigation > <div class=md-sidebar__scrollwrap > <div class=md-sidebar__inner > <nav class="md-nav md-nav--primary" data-md-level=0 > <label class="md-nav__title md-nav__title--site" for=__drawer > <a href="../../documentation.html" title="Jungfraujoch 1.0.0-rc.180 documentation" class="md-nav__button md-logo"> <i class=md-icon >&#xe30d</i> </a> <a href="../../documentation.html" title="Jungfraujoch 1.0.0-rc.180 documentation">PSI Jungfraujoch</a> </label> <div class=md-nav__source > <a href="https://gitea.psi.ch/mx/jungfraujoch" title="Go to repository" class=md-source data-md-source=github > <div class=md-source__icon > <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width=28 height=28 > <use xlink:href="#__gitlab" width=24 height=24 ></use> </svg> </div> <div class=md-source__repository > Jungfraujoch </div> </a> </div> <ul class=md-nav__list > <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Rugnux</span></span> <li class=md-nav__item > <a href="../../RUGNUX.html" class=md-nav__link >Getting started</a> <li class=md-nav__item > <a href="../../RUGNUX_DOWNLOAD.html" class=md-nav__link >Download</a> <li class=md-nav__item > <a href="../../RUGNUX_OVERVIEW.html" class=md-nav__link >What Rugnux does</a> <li class=md-nav__item > <a href="../../RUGNUX_INSTALL.html" class=md-nav__link >Installing Rugnux</a> <li class=md-nav__item > <a href="../../RUGNUX_FORMATS.html" class=md-nav__link >What Rugnux reads</a> <li class=md-nav__item > <a href="../../RUGNUX_TUTORIAL.html" class=md-nav__link >Running Rugnux</a> <li class=md-nav__item > <a href="../../RUGNUX_REPORT.html" class=md-nav__link >The results report</a> <li class=md-nav__item > <a href="../../RUGNUX_INTEGRATION.html" class=md-nav__link >Rugnux with other programs</a> <li class=md-nav__item > <a href="../../RUGNUX_ADVANCED.html" class=md-nav__link >Advanced Rugnux</a> <li class=md-nav__item > <a href="../../RUGNUX_MODEL_AND_REFERENCE.html" class=md-nav__link >Models and reference data</a> <li class=md-nav__item > <a href="../../RUGNUX_CALIBRATION.html" class=md-nav__link >Detector calibration</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Jungfraujoch Viewer</span></span> <li class=md-nav__item > <a href="../../JFJOCH_VIEWER.html" class=md-nav__link >Using the viewer</a> <li class=md-nav__item > <a href="../../VIEWER_DOWNLOAD.html" class=md-nav__link >Download</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Jungfraujoch</span></span> <li class=md-nav__item > <a href="../../JUNGFRAUJOCH.html" class=md-nav__link >Overview</a> <li class=md-nav__item > <a href="../../DEPLOYMENT.html" class=md-nav__link >Deployment</a> <li class=md-nav__item > <a href="../../REPOSITORIES.html" class=md-nav__link >Linux package repositories</a> <li class=md-nav__item > <a href="../../RELEASE_CONTENTS.html" class=md-nav__link >Release contents</a> <li class=md-nav__item > <a href="../../JFJOCH_BROKER.html" class=md-nav__link >jfjoch_broker</a> <li class=md-nav__item > <a href="../../JFJOCH_WRITER.html" class=md-nav__link >jfjoch_writer</a> <li class=md-nav__item > <a href="../../WEB_FRONTEND.html" class=md-nav__link >Web frontend</a> <li class=md-nav__item > <a href="../../SOFTWARE_INTEGRATION.html" class=md-nav__link >MX software integration</a> <li class=md-nav__item > <a href="../../TOOLS.html" class=md-nav__link >Tools</a> <li class=md-nav__item > <a href="../../PYTHON_CLIENT.html" class=md-nav__link >Python client</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Reference</span></span> <li class=md-nav__item > <a href="../../TECHNICAL.html" class=md-nav__link >Technical reference</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Project</span></span> <li class=md-nav__item > <a href="../../ACKNOWLEDGEMENT.html" class=md-nav__link >Acknowledgements</a> <li class=md-nav__item > <a href="../../LICENSE.html" class=md-nav__link >License</a> <li class=md-nav__item > <a href="../../THIRD_PARTY_NOTICES.html" class=md-nav__link >Third-party software notices</a> <li class=md-nav__item > <a href="../../NAMING.html" class=md-nav__link >Naming</a> <li class=md-nav__item > <a href="../../CHANGELOG.html" class=md-nav__link >Changelog</a> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component=toc > <div class=md-sidebar__scrollwrap > <div class=md-sidebar__inner > <nav class="md-nav md-nav--secondary"> <ul class=md-nav__list data-md-scrollfix=""> </ul> </nav> </div> </div> </div> <div class=md-content > <article class="md-content__inner md-typeset" role=main > <section class="tex2jax_ignore mathjax_ignore" id=rugnuxliverefinement > <h1 id=python-client-docs-rugnuxliverefinement--page-root >RugnuxLiveRefinement<a class=headerlink href="#python-client-docs-rugnuxliverefinement--page-root" title="Link to this heading"></a></h1> <p>The placed model refined against the merge it was placed on, as the report’s REFINE_ keys state it. Set where a placed model was refined or its refinement failed; absent where the model was not placed or refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run’s deadline or cancel can cut it.</p> <section id=properties > <h2 id=properties >Properties<a class=headerlink href="#properties" title="Link to this heading"></a></h2> <table> <thead> <tr class=row-odd ><th class=head ><p>Name</p> <th class=head ><p>Type</p> <th class=head ><p>Description</p> <th class=head ><p>Notes</p> <tr class=row-even ><td><p><strong>performed</strong></p> <td><p><strong>bool</strong></p> <td><p>Refinement ran; false with `reason` where it failed</p> <td><p></p> <tr class=row-odd ><td><p><strong>cancelled</strong></p> <td><p><strong>bool</strong></p> <td><p>The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the rest left out (cut before the first, the model is the placement’s)</p> <td><p></p> <tr class=row-even ><td><p><strong>reason</strong></p> <td><p><strong>str</strong></p> <td><p>Why refinement did not run to the end; empty otherwise</p> <td><p></p> <tr class=row-odd ><td><p><strong>on_gpu</strong></p> <td><p><strong>bool</strong></p> <td><p></p> <td><p></p> <tr class=row-even ><td><p><strong>seconds</strong></p> <td><p><strong>float</strong></p> <td><p>Wall time of the refinement</p> <td><p></p> <tr class=row-odd ><td><p><strong>r_work</strong></p> <td><p><strong>float</strong></p> <td><p>R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>r_free</strong></p> <td><p><strong>float</strong></p> <td><p>R-free of the refined model, on the same reflections as `r_work`</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>rmsd_bonds_a</strong></p> <td><p><strong>float</strong></p> <td><p>RMS deviation of the bond lengths from the dictionary, where the restrained stage ran</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>rmsd_angles_deg</strong></p> <td><p><strong>float</strong></p> <td><p>RMS deviation of the bond angles from the dictionary, where the restrained stage ran</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>blob_count</strong></p> <td><p><strong>int</strong></p> <td><p>Unexplained blobs of the refined model’s mFo-DFc map (above 3 sigma, peaking above 4)</p> <td><p></p> <tr class=row-even ><td><p><strong>blobs</strong></p> <td><p><a class="reference internal" href=RugnuxLiveBlob.html ><span class="std std-doc"><strong>List[RugnuxLiveBlob]</strong></span></a></p> <td><p>The strongest blobs, at most 50, strongest first</p> <td><p></p> </table> </section> <section id=example > <h2 id=example >Example<a class=headerlink href="#example" title="Link to this heading"></a></h2> <div class="highlight-python notranslate"><div class=highlight ><pre><span></span><span class=kn >from</span> <span class=nn >jfjoch_client.models.rugnux_live_refinement</span> <span class=kn >import</span> <span class=n >RugnuxLiveRefinement</span>
<span class=c1 ># TODO update the JSON string below</span>
<span class=n >json</span> <span class=o >=</span> <span class=s2 >"</span><span class=si >{}</span><span class=s2 >"</span>
<span class=c1 ># create an instance of RugnuxLiveRefinement from a JSON string</span>
<span class=n >rugnux_live_refinement_instance</span> <span class=o >=</span> <span class=n >RugnuxLiveRefinement</span><span class=o >.</span><span class=n >from_json</span><span class=p >(</span><span class=n >json</span><span class=p >)</span>
<span class=c1 ># print the JSON string representation of the object</span>
<span class=nb >print</span><span class=p >(</span><span class=n >RugnuxLiveRefinement</span><span class=o >.</span><span class=n >to_json</span><span class=p >())</span>
<span class=c1 ># convert the object into a dict</span>
<span class=n >rugnux_live_refinement_dict</span> <span class=o >=</span> <span class=n >rugnux_live_refinement_instance</span><span class=o >.</span><span class=n >to_dict</span><span class=p >()</span>
<span class=c1 ># create an instance of RugnuxLiveRefinement from a dict</span>
<span class=n >rugnux_live_refinement_from_dict</span> <span class=o >=</span> <span class=n >RugnuxLiveRefinement</span><span class=o >.</span><span class=n >from_dict</span><span class=p >(</span><span class=n >rugnux_live_refinement_dict</span><span class=p >)</span>
</pre></div> </div> <p><a class="reference internal" href="../README.html#documentation-for-models"><span class="std std-ref">[Back to Model list]</span></a> <a class="reference internal" href="../README.html#documentation-for-api-endpoints"><span class="std std-ref">[Back to API list]</span></a> <a class="reference internal" href="../README.html"><span class="std std-doc">[Back to README]</span></a></p> </section> </section> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=RugnuxLiveModel.html title=RugnuxLiveModel class="md-flex md-footer-nav__link md-footer-nav__link--prev" rel=prev > <div class="md-flex__cell md-flex__cell--shrink"> <i class="md-icon md-icon--arrow-back md-footer-nav__button"></i> </div> <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"> <span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Previous" </span> RugnuxLiveModel </span> </div> </a> <a href=RugnuxLiveStatus.html title=RugnuxLiveStatus class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> RugnuxLiveStatus </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > &#169; Copyright 2024, Paul Scherrer Institute. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 8.1.3. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="../../_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script>
Reference in new issue View Git Blame Copy Permalink