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Doc sphinx (#6)
* sphinx docs * Create CNAME * completed the documentation and benchmarks for search, discovery and restrictions * Update README.md * test * fixed few bugs in main.py * test files added * test files/npz added * command to run test * Update CNAME * Update CNAME * docs removed * compiled docs for web Co-authored-by: cysloth <[email protected]>
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‎.gitattributes

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models/model_final_002.pth filter=lfs diff=lfs merge=lfs -text
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data/test_npz.tgz filter=lfs diff=lfs merge=lfs -text

‎README.md

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# Surface Similarity Search via Geometric Deep Learning: SurfaceID
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![alt text](https://github.com/Sanofi-GitHub/LMR-SurfaceID/blob/main/data/toc.png?raw=true)
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![alt text](https://github.com/Sanofi-GitHub/LMR-SurfaceID/blob/doc_sphinx/data/toc.png)
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A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein’s function such as its ability to interact with other molecules. While many methods have been developed for comparing similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited. Here, we describe “Surface ID”, a geometric deep learning system for high-throughput surface comparison based on geometric and chemical features. Surface ID offers a novel grouping and alignment algorithm useful for clustering proteins by function, visualization, and in-silico screening of potential binding partners to a target molecule. Our method demonstrates top performance in surface similarity assessment, indicating great potential for protein functional annotation, a major need in protein engineering and therapeutic design.
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```bash
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python3.9 -m venv sandbox
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source sandbox/bin/activate
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python main.py
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#untar the test_npz file and run:
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python main.py --params data/config.yml --library data/test.tsv
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```
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## Data
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year={2022},
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publisher={Nature}
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}
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```
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```

‎data/config.yml

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---
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# Generall varaibles
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CONTACT : True
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DESC : True
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SEARCH : True
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RESTRICT: False
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ALIGN : True
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SAVEPLY : False
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HEATMAP : False
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# Model Name
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MODEL:
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NAME: final_002
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# Model related variables
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MODEL_PARAMETER:
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rho_max: 6.0
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nbins_rho: 5
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nbins_theta: 16
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num_in: 5
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neg_margin: 10.
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add_center_pixel: True
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share_soft_grid_across_channel: True
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conv_type: sep
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num_filters: 512
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weight_decay: 1.e-2
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dropout: 0.1
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min_sig: 5.e-2
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lr: 5e-4
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SPATIAL_PARAMETER:
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thres: 5.0
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expand_radius : 2.0
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neighbor_dist : 3.0
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nmin_pts : 40
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nmin_pts_library: 30
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contact_thres1: 3.0
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contact_thres2: None
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contact_mode: dist
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npatience: 100
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# Path related variables
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PATH:
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CATALOG_PAIRS : data/test.tsv
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OUTDIR : data/npz
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SAVEDIR : models
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MODEL: final_002
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TARGET: 4FQI_AB
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CASE: test
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HIT_COLUMNS:
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- target
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- library epitope
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- target_nhits
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- target_nexpanded
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- mean_desc_dist
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- library_nhits
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- library_nexpanded
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- frac_library_hits
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- target_expanded_indices
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- library_epitope_indices

‎data/test.tsv

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id Ag Ab
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4FQI AB HL
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4FQY AB HL

‎data/test_npz.tgz

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version https://git-lfs.github.com/spec/v1
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oid sha256:56432dbec8718bd889fbba9273466303f1fd3739b03d2f51d2633915dead9069
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size 560709960

‎data/toc.png

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‎docs/.buildinfo

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 49a2f8507e1b6d15500265e4cdd2009c
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tags: 645f666f9bcd5a90fca523b33c5a78b7

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‎docs/html/.buildinfo

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 49a2f8507e1b6d15500265e4cdd2009c
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎docs/html/_modules/index.html

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<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Overview: module code &mdash; LMR-SurfaceID 0.1 documentation</title>
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<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
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<!--[if lt IE 9]>
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<script src="../_static/js/html5shiv.min.js"></script>
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<![endif]-->
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<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
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<script src="../_static/jquery.js"></script>
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<script src="../_static/underscore.js"></script>
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<script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
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<script src="../_static/doctools.js"></script>
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<script src="../_static/sphinx_highlight.js"></script>
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<script src="../_static/js/theme.js"></script>
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<link rel="index" title="Index" href="../genindex.html" />
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<link rel="search" title="Search" href="../search.html" />
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</head>
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<body class="wy-body-for-nav">
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<div class="wy-grid-for-nav">
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<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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<div class="wy-side-scroll">
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<div class="wy-side-nav-search" >
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<a href="../index.html" class="icon icon-home"> LMR-SurfaceID
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</a>
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<div role="search">
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<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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<input type="text" name="q" placeholder="Search docs" />
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<input type="hidden" name="check_keywords" value="yes" />
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<input type="hidden" name="area" value="default" />
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</form>
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</div>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="../util.html">util package</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../modules.html">util</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../setup.html">Setup</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../model.html">model package</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../model.html#module-surfaceid.surfaceid.model.model">model.model module</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../aligner.html">aligner package</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../aligner.html#model-aligner-module">model.aligner module</a></li>
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</ul>
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</div>
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</div>
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</nav>
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<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
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<a href="../index.html">LMR-SurfaceID</a>
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</nav>
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<div class="wy-nav-content">
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<div class="rst-content">
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<div role="navigation" aria-label="Page navigation">
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<ul class="wy-breadcrumbs">
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<li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
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<li>Overview: module code</li>
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<li class="wy-breadcrumbs-aside">
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</li>
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</ul>
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<hr/>
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<h1>All modules for which code is available</h1>
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<ul><li><a href="surfaceid/surfaceid/model/model.html">surfaceid.surfaceid.model.model</a></li>
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<li><a href="surfaceid/surfaceid/util/Config.html">surfaceid.surfaceid.util.Config</a></li>
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<li><a href="surfaceid/surfaceid/util/mol.html">surfaceid.surfaceid.util.mol</a></li>
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<li><a href="surfaceid/surfaceid/util/utils.html">surfaceid.surfaceid.util.utils</a></li>
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</ul>
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</div>
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</div>
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<footer>
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<hr/>
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<div role="contentinfo">
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<p>&#169; Copyright 2022, sansrs.</p>
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</div>
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Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
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provided by <a href="https://readthedocs.org">Read the Docs</a>.
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jQuery(function () {
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