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doc update
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CyberCatQ committed Dec 26, 2023
1 parent e46274c commit 25a7163
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2 changes: 1 addition & 1 deletion .buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: fe3df20c2fdb917b4801700aa2227b33
config: 9a65cd1615ddaaf09306780b19b5ff39
tags: 645f666f9bcd5a90fca523b33c5a78b7
12 changes: 10 additions & 2 deletions README.html
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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pyCADD &mdash; pyCADD 1.6.8 documentation</title>
<title>pyCADD &mdash; pyCADD 1.6.9 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
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<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=733169e8"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=d749edf1"></script>
<script src="_static/doctools.js?v=888ff710"></script>
<script src="_static/sphinx_highlight.js?v=4825356b"></script>
<script src="_static/js/theme.js"></script>
Expand Down Expand Up @@ -291,6 +291,14 @@ <h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading">
<section id="id1">
<h2>更新日志<a class="headerlink" href="#id1" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>1.6.9 (2023-12-26)</p>
<ul>
<li><p>将 Demand 数据获取修改为直接与PDB服务器API交互，确保获取最新PDB数据</p></li>
<li><p>添加了对PDB蛋白链突变信息的解析</p></li>
<li><p>为 Dock 添加了多线程批量下载PDB的接口 <code class="docutils literal notranslate"><span class="pre">pycadd-dock</span> <span class="pre">download</span></code></p></li>
<li><p>其他 BUG 修复</p></li>
</ul>
</li>
<li><p>1.6.8 (2023-11-21)</p>
<ul>
<li><p>为 Dock 模块 CLI 接口 pycadd-dock 添加了自动创建 schrodinger 虚拟环境的功能</p></li>
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4 changes: 2 additions & 2 deletions _modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; pyCADD 1.6.8 documentation</title>
<title>Overview: module code &mdash; pyCADD 1.6.9 documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
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<script src="../_static/jquery.js?v=5d32c60e"></script>
<script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=733169e8"></script>
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=d749edf1"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../_static/js/theme.js"></script>
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51 changes: 49 additions & 2 deletions _modules/pyCADD/Demand/config.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pyCADD.Demand.config &mdash; pyCADD 1.6.8 documentation</title>
<title>pyCADD.Demand.config &mdash; pyCADD 1.6.9 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=733169e8"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=d749edf1"></script>
<script src="../../../_static/doctools.js?v=888ff710"></script>
<script src="../../../_static/sphinx_highlight.js?v=4825356b"></script>
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Expand Down Expand Up @@ -156,6 +156,52 @@ <h1>Source code for pyCADD.Demand.config</h1><div class="highlight"><pre>
<span class="s1"> }</span>
<span class="s1"> }</span>
<span class="s1"> &#39;&#39;&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span></div>

<div class="viewcode-block" id="BaseQueryPDB"><a class="viewcode-back" href="../../../pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB">[docs]</a><span class="k">class</span> <span class="nc">BaseQueryPDB</span><span class="p">:</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot_id</span><span class="p">:</span><span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span> <span class="o">=</span> <span class="n">uniprot_id</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>

<div class="viewcode-block" id="BaseQueryPDB.get_query"><a class="viewcode-back" href="../../../pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB.get_query">[docs]</a> <span class="k">def</span> <span class="nf">get_query</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_search_pdb_list</span></div>

<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">_search_pdb_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s1">&#39;&#39;&#39;{</span>
<span class="s1"> &quot;query&quot;: {</span>
<span class="s1"> &quot;type&quot;: &quot;group&quot;,</span>
<span class="s1"> &quot;nodes&quot;: [</span>
<span class="s1"> {</span>
<span class="s1"> &quot;type&quot;: &quot;terminal&quot;,</span>
<span class="s1"> &quot;service&quot;: &quot;text&quot;,</span>
<span class="s1"> &quot;parameters&quot;: {</span>
<span class="s1"> &quot;attribute&quot;: &quot;rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession&quot;,</span>
<span class="s1"> &quot;operator&quot;: &quot;in&quot;,</span>
<span class="s1"> &quot;value&quot;: [</span>
<span class="s1"> &quot;</span><span class="si">%s</span><span class="s1">&quot;</span>
<span class="s1"> ]</span>
<span class="s1"> }</span>
<span class="s1"> },</span>
<span class="s1"> {</span>
<span class="s1"> &quot;type&quot;: &quot;terminal&quot;,</span>
<span class="s1"> &quot;service&quot;: &quot;text&quot;,</span>
<span class="s1"> &quot;parameters&quot;: {</span>
<span class="s1"> &quot;attribute&quot;: &quot;rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name&quot;,</span>
<span class="s1"> &quot;operator&quot;: &quot;exact_match&quot;,</span>
<span class="s1"> &quot;value&quot;: &quot;UniProt&quot;</span>
<span class="s1"> }</span>
<span class="s1"> }</span>
<span class="s1"> ],</span>
<span class="s1"> &quot;logical_operator&quot;: &quot;and&quot;,</span>
<span class="s1"> &quot;label&quot;: &quot;nested-attribute&quot;</span>
<span class="s1"> },</span>
<span class="s1"> &quot;return_type&quot;: &quot;entry&quot;,</span>
<span class="s1"> &quot;request_options&quot;: {</span>
<span class="s1"> &quot;paginate&quot;: {</span>
<span class="s1"> &quot;start&quot;: 0,</span>
<span class="s1"> &quot;rows&quot;: 10000</span>
<span class="s1"> }</span>
<span class="s1"> }</span>
<span class="s1"> }&#39;&#39;&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span></div>

<span class="n">DATA_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;data&#39;</span><span class="p">,</span> <span class="s1">&#39;entries&#39;</span><span class="p">]</span>
<span class="n">PDBID_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;rcsb_id&#39;</span><span class="p">]</span>
Expand All @@ -171,6 +217,7 @@ <h1>Source code for pyCADD.Demand.config</h1><div class="highlight"><pre>
<span class="n">POLYMER_NAME_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;rcsb_polymer_entity&#39;</span><span class="p">,</span> <span class="s1">&#39;pdbx_description&#39;</span><span class="p">]</span>
<span class="n">POLYMER_TYPE_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;entity_poly&#39;</span><span class="p">,</span> <span class="s1">&#39;rcsb_entity_polymer_type&#39;</span><span class="p">]</span>
<span class="n">POLYMER_MUTATION_NUM_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;entity_poly&#39;</span><span class="p">,</span> <span class="s1">&#39;rcsb_mutation_count&#39;</span><span class="p">]</span>
<span class="n">POLYMER_MUTATION_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;rcsb_polymer_entity&#39;</span><span class="p">,</span> <span class="s1">&#39;pdbx_mutation&#39;</span><span class="p">]</span>
<span class="n">POLYMER_CHAIN_ID_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;entity_poly&#39;</span><span class="p">,</span> <span class="s1">&#39;pdbx_strand_id&#39;</span><span class="p">]</span>
<span class="n">POLYMER_UNIPROT_ID_KEYS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;rcsb_polymer_entity_container_identifiers&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_ids&#39;</span><span class="p">]</span>

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