From 25a716393433a0dab6c9c465a04c9604f36ab4b1 Mon Sep 17 00:00:00 2001
From: CyberCatQ <yuhangxmu@foxmail.com>
Date: Tue, 26 Dec 2023 11:45:42 +0800
Subject: [PATCH] doc update

---
 .buildinfo                         |   2 +-
 README.html                        |  12 +++++--
 _modules/index.html                |   4 +--
 _modules/pyCADD/Demand/config.html |  51 +++++++++++++++++++++++++++--
 _modules/pyCADD/Demand/core.html   |  41 +++++++++++++++++++----
 _modules/pyCADD/Dock/common.html   |  21 +++++++++---
 _modules/pyCADD/utils/env.html     |   4 +--
 _sources/README.md.txt             |   5 +++
 _sources/dock.md.txt               |  13 ++++++--
 _static/documentation_options.js   |   2 +-
 dance.html                         |   4 +--
 demand.html                        |   4 +--
 density.html                       |   4 +--
 dock.html                          |  21 ++++++++----
 dynamic.html                       |   4 +--
 genindex.html                      |  20 +++++++----
 index.html                         |   6 ++--
 modules.html                       |   4 +--
 objects.inv                        | Bin 3217 -> 3233 bytes
 py-modindex.html                   |   4 +--
 pyCADD.Dance.algorithm.html        |   4 +--
 pyCADD.Dance.html                  |   4 +--
 pyCADD.Demand.html                 |  20 +++++++++--
 pyCADD.Density.html                |   4 +--
 pyCADD.Dock.html                   |   4 +--
 pyCADD.Dynamic.html                |   4 +--
 pyCADD.VSW.html                    |   4 +--
 pyCADD.html                        |   9 +++--
 pyCADD.utils.html                  |   4 +--
 search.html                        |   4 +--
 searchindex.js                     |   2 +-
 31 files changed, 216 insertions(+), 73 deletions(-)

diff --git a/.buildinfo b/.buildinfo
index d5188a1..0a12126 100644
--- a/.buildinfo
+++ b/.buildinfo
@@ -1,4 +1,4 @@
 # 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
diff --git a/README.html b/README.html
index f827511..12051ca 100644
--- a/README.html
+++ b/README.html
@@ -4,7 +4,7 @@
   <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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -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>
diff --git a/_modules/index.html b/_modules/index.html
index 83a2153..4c75d9a 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -3,7 +3,7 @@
 <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" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
   
         <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>
diff --git a/_modules/pyCADD/Demand/config.html b/_modules/pyCADD/Demand/config.html
index a7c7c52..6f7163c 100644
--- a/_modules/pyCADD/Demand/config.html
+++ b/_modules/pyCADD/Demand/config.html
@@ -3,7 +3,7 @@
 <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]>
@@ -12,7 +12,7 @@
   
         <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>
@@ -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>
@@ -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>
 
diff --git a/_modules/pyCADD/Demand/core.html b/_modules/pyCADD/Demand/core.html
index 658591d..5784998 100644
--- a/_modules/pyCADD/Demand/core.html
+++ b/_modules/pyCADD/Demand/core.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pyCADD.Demand.core &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Demand.core &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]>
@@ -12,7 +12,7 @@
   
         <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>
@@ -89,8 +89,12 @@ <h1>Source code for pyCADD.Demand.core</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">import</span> <span class="nn">requests</span>
 <span class="kn">import</span> <span class="nn">yaml</span>
-<span class="kn">from</span> <span class="nn">pyCADD.Demand.config</span> <span class="kn">import</span> <span class="n">BaseQueryCfg</span><span class="p">,</span> <span class="n">IGNORE_LIG</span>
-<span class="kn">from</span> <span class="nn">pyCADD.Demand.config</span> <span class="kn">import</span> <span class="n">DATA_KEYS</span><span class="p">,</span> <span class="n">PDBID_KEYS</span><span class="p">,</span> <span class="n">TITLE_KEYS</span><span class="p">,</span> <span class="n">RESOLUTION_KEYS</span><span class="p">,</span> <span class="n">AUTHOR_KEYS</span><span class="p">,</span> <span class="n">REFERENCE_KEYS</span><span class="p">,</span> <span class="n">REF_DOI_KEYS</span><span class="p">,</span> <span class="n">POLYMER_ENTITY_NUM_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_ENTITY_NUM_KEYS</span><span class="p">,</span> <span class="n">POLYMER_ENTITY_KEYS</span><span class="p">,</span> <span class="n">POLYMER_NAME_KEYS</span><span class="p">,</span> <span class="n">POLYMER_CHAIN_ID_KEYS</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_NUM_KEYS</span><span class="p">,</span> <span class="n">POLYMER_TYPE_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_CHAIN_ID_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_ENTITY_KEYS</span><span class="p">,</span><span class="n">NONPOLYMER_ID_KEYS</span><span class="p">,</span><span class="n">NONPOLYMER_NAME_KEYS</span><span class="p">,</span><span class="n">NONPOLYMER_SMILES_KEYS</span><span class="p">,</span> <span class="n">POLYMER_UNIPROT_ID_KEYS</span>
+<span class="kn">from</span> <span class="nn">pyCADD.Demand.config</span> <span class="kn">import</span> <span class="n">BaseQueryCfg</span><span class="p">,</span> <span class="n">BaseQueryPDB</span><span class="p">,</span> <span class="n">IGNORE_LIG</span>
+<span class="kn">from</span> <span class="nn">pyCADD.Demand.config</span> <span class="kn">import</span> <span class="p">(</span><span class="n">DATA_KEYS</span><span class="p">,</span> <span class="n">PDBID_KEYS</span><span class="p">,</span> <span class="n">TITLE_KEYS</span><span class="p">,</span> <span class="n">RESOLUTION_KEYS</span><span class="p">,</span> <span class="n">AUTHOR_KEYS</span><span class="p">,</span> 
+                                  <span class="n">REFERENCE_KEYS</span><span class="p">,</span> <span class="n">REF_DOI_KEYS</span><span class="p">,</span> <span class="n">POLYMER_ENTITY_NUM_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_ENTITY_NUM_KEYS</span><span class="p">,</span> 
+                                  <span class="n">POLYMER_ENTITY_KEYS</span><span class="p">,</span> <span class="n">POLYMER_NAME_KEYS</span><span class="p">,</span> <span class="n">POLYMER_CHAIN_ID_KEYS</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_NUM_KEYS</span><span class="p">,</span> 
+                                  <span class="n">POLYMER_TYPE_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_CHAIN_ID_KEYS</span><span class="p">,</span> <span class="n">NONPOLYMER_ENTITY_KEYS</span><span class="p">,</span><span class="n">NONPOLYMER_ID_KEYS</span><span class="p">,</span>
+                                  <span class="n">NONPOLYMER_NAME_KEYS</span><span class="p">,</span><span class="n">NONPOLYMER_SMILES_KEYS</span><span class="p">,</span> <span class="n">POLYMER_UNIPROT_ID_KEYS</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_KEYS</span><span class="p">)</span>
 <span class="kn">from</span> <span class="nn">pyCADD.utils.tool</span> <span class="kn">import</span> <span class="n">makedirs_from_list</span><span class="p">,</span> <span class="n">Myconfig</span>
 
 <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
@@ -98,6 +102,7 @@ <h1>Source code for pyCADD.Demand.core</h1><div class="highlight"><pre>
 <span class="c1"># API 接口</span>
 <span class="n">UNIPROT_URL</span> <span class="o">=</span> <span class="s1">&#39;https://rest.uniprot.org/uniprotkb/&#39;</span>
 <span class="n">PDB_URL</span> <span class="o">=</span> <span class="s1">&#39;https://data.rcsb.org/graphql?query=&#39;</span>
+<span class="n">PDB_SEARCH_URL</span> <span class="o">=</span> <span class="s1">&#39;https://search.rcsb.org/rcsbsearch/v2/query?json=&#39;</span>
 
 <div class="viewcode-block" id="query_uniprot"><a class="viewcode-back" href="../../../pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot">[docs]</a><span class="k">def</span> <span class="nf">query_uniprot</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="n">save_path</span><span class="p">:</span><span class="nb">str</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 
@@ -136,6 +141,23 @@ <h1>Source code for pyCADD.Demand.core</h1><div class="highlight"><pre>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Uniprot ID </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">uniprot_file_path</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1"> has no PDB crystal data.&#39;</span><span class="p">)</span>
     <span class="k">return</span> <span class="n">pdb_list</span></div>
 
+<div class="viewcode-block" id="query_uniprot_id_on_pdb"><a class="viewcode-back" href="../../../pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot_id_on_pdb">[docs]</a><span class="k">def</span> <span class="nf">query_uniprot_id_on_pdb</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="n">save_path</span><span class="p">:</span><span class="nb">str</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
+    <span class="n">query</span> <span class="o">=</span> <span class="n">BaseQueryPDB</span><span class="p">(</span><span class="n">uniprot_id</span><span class="o">=</span><span class="n">uniprot_id</span><span class="p">)</span><span class="o">.</span><span class="n">get_query</span><span class="p">()</span>
+    <span class="n">query</span> <span class="o">=</span> <span class="n">parse</span><span class="o">.</span><span class="n">quote</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+    <span class="n">req</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">PDB_SEARCH_URL</span> <span class="o">+</span> <span class="n">query</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Query failed: </span><span class="si">{</span><span class="n">req</span><span class="o">.</span><span class="n">text</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">save_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">save_path</span><span class="p">,</span> <span class="n">uniprot_id</span> <span class="o">+</span> <span class="s1">&#39;.json&#39;</span><span class="p">),</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+            
+    <span class="n">search_result</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">json</span><span class="p">()</span>
+    <span class="n">result_length</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">search_result</span><span class="p">[</span><span class="s1">&#39;total_count&#39;</span><span class="p">])</span>
+    <span class="n">pdb_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">result</span><span class="p">[</span><span class="s1">&#39;identifier&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">result</span> <span class="ow">in</span> <span class="n">search_result</span><span class="p">[</span><span class="s1">&#39;result_set&#39;</span><span class="p">]]</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdb_list</span><span class="p">)</span> <span class="o">!=</span> <span class="n">result_length</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Uniprot ID </span><span class="si">{</span><span class="n">uniprot_id</span><span class="si">}</span><span class="s1"> has </span><span class="si">{</span><span class="n">result_length</span><span class="si">}</span><span class="s1"> PDB crystal data, but only </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">pdb_list</span><span class="p">)</span><span class="si">}</span><span class="s1"> is returned.&#39;</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">pdb_list</span></div>
+    
 <div class="viewcode-block" id="query_pdb"><a class="viewcode-back" href="../../../pyCADD.Demand.html#pyCADD.Demand.core.query_pdb">[docs]</a><span class="k">def</span> <span class="nf">query_pdb</span><span class="p">(</span><span class="n">pdb_list</span><span class="p">,</span> <span class="n">save_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">quert_cfg</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 
     <span class="n">query_cfg</span> <span class="o">=</span> <span class="n">BaseQueryCfg</span><span class="p">(</span><span class="n">pdb_list</span><span class="p">)</span> <span class="k">if</span> <span class="n">quert_cfg</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">quert_cfg</span><span class="p">(</span><span class="n">pdb_list</span><span class="p">)</span>
@@ -189,11 +211,15 @@ <h1>Source code for pyCADD.Demand.core</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">_query_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">save_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_save_dir</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="s1">&#39;.json&#39;</span><span class="p">)</span>
         <span class="n">query_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span><span class="p">,</span> <span class="n">save_path</span><span class="p">)</span>
+        
+    <span class="k">def</span> <span class="nf">_query_uniprot_id</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdb_list</span> <span class="o">=</span> <span class="n">query_uniprot_id_on_pdb</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_save_dir</span><span class="p">)</span>
     
     <span class="k">def</span> <span class="nf">_query_pdb</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_list</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_query_uniprot</span><span class="p">()</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">pdb_list</span> <span class="o">=</span> <span class="n">parse_uniport</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_save_dir</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="s1">&#39;.json&#39;</span><span class="p">))</span>
+            <span class="c1"># self._query_uniprot()</span>
+            <span class="c1"># self.pdb_list = parse_uniport(os.path.join(self.uniprot_save_dir, self.uniprot_id + &#39;.json&#39;))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_query_uniprot_id</span><span class="p">()</span>
         <span class="n">save_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdb_save_dir</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="s1">&#39;.json&#39;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">data_dict</span> <span class="o">=</span> <span class="n">query_pdb</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdb_list</span><span class="p">,</span> <span class="n">save_path</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_query_cfg</span><span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_dict</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -220,7 +246,8 @@ <h1>Source code for pyCADD.Demand.core</h1><div class="highlight"><pre>
             <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">polymer</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">polymer_entities</span><span class="p">):</span>
                 <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_NAME_KEYS</span><span class="p">)</span>  <span class="c1"># 名称</span>
                 <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_TYPE_KEYS</span><span class="p">)</span>  <span class="c1"># 类型</span>
-                <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_mutation&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_NUM_KEYS</span><span class="p">)</span>  <span class="c1"># 突变数</span>
+                <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_mutation_num&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_NUM_KEYS</span><span class="p">)</span>  <span class="c1"># 突变数</span>
+                <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_mutation&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_MUTATION_KEYS</span><span class="p">)</span>  <span class="c1"># 突变数</span>
                 <span class="n">d</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;polymer_entities_</span><span class="si">{</span><span class="n">index</span><span class="si">}</span><span class="s1">_chain&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_nested_value</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">POLYMER_CHAIN_ID_KEYS</span><span class="p">)</span>  <span class="c1"># 所在链</span>
                 <span class="k">try</span><span class="p">:</span>
                     <span class="n">d</span><span class="p">[</span><span class="s1">&#39;polymer_entities_&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">index</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;_source_organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">polymer</span><span class="p">[</span><span class="s1">&#39;rcsb_entity_source_organism&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s1">&#39;rcsb_gene_name&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">polymer</span><span class="p">[</span><span class="s1">&#39;rcsb_entity_source_organism&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>  <span class="c1"># 结构来源蛋白</span>
diff --git a/_modules/pyCADD/Dock/common.html b/_modules/pyCADD/Dock/common.html
index 29a57a3..7ed6f10 100644
--- a/_modules/pyCADD/Dock/common.html
+++ b/_modules/pyCADD/Dock/common.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pyCADD.Dock.common &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Dock.common &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]>
@@ -12,7 +12,7 @@
   
         <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>
@@ -282,8 +282,8 @@ <h1>Source code for pyCADD.Dock.common</h1><div class="highlight"><pre>
 <span class="sd">        &#39;&#39;&#39;</span>
         
         <span class="n">ligand_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ligid</span> <span class="k">if</span> <span class="n">ligand_id</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">ligand_id</span>
-        <span class="n">ligand_id</span> <span class="o">=</span> <span class="n">ligand_id</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
         <span class="k">assert</span> <span class="n">ligand_id</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;Ligand ID is not specified.&#39;</span>
+        <span class="n">ligand_id</span> <span class="o">=</span> <span class="n">ligand_id</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
         <span class="n">_all_match_lig</span> <span class="o">=</span> <span class="p">[</span><span class="n">res</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">residue</span> <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">pdbres</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="n">ligand_id</span><span class="p">]</span>
 
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">_all_match_lig</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
@@ -800,7 +800,20 @@ <h1>Source code for pyCADD.Dock.common</h1><div class="highlight"><pre>
         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
             <span class="n">raw_list</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
         
-        <span class="n">pairs_list</span> <span class="o">=</span> <span class="p">[(</span><span class="n">pdbid</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> <span class="n">ligid</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">pdbid</span><span class="p">,</span> <span class="n">ligid</span> <span class="ow">in</span> <span class="p">[</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">raw_list</span><span class="p">]]</span>
+        <span class="c1"># pairs_list = [(pdbid.strip(), ligid.strip()) for pdbid, ligid in [line.split(&#39;,&#39;) for line in raw_list]]</span>
+        <span class="n">pairs_list</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">raw_list</span><span class="p">:</span>
+            <span class="n">line</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="n">pdbid</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">ligid</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="mi">2</span><span class="p">:</span>
+                <span class="n">pdbid</span><span class="p">,</span> <span class="n">ligid</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> <span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">&#39;Input file may not be a csv file.&#39;</span><span class="p">)</span>
+
+            <span class="n">pairs_list</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">pdbid</span><span class="p">,</span> <span class="n">ligid</span><span class="p">))</span>
+        
         <span class="c1"># ligand_list = [ligid for pdbid, ligid in pairs_list]</span>
         <span class="n">mappings</span> <span class="o">=</span> <span class="p">[{</span><span class="s1">&#39;receptor&#39;</span><span class="p">:</span> <span class="n">receptor_name</span><span class="p">,</span> <span class="s1">&#39;pdb&#39;</span><span class="p">:</span> <span class="n">pdbid</span><span class="p">,</span> <span class="s1">&#39;ligand&#39;</span><span class="p">:</span> <span class="n">ligid</span><span class="p">}</span> <span class="k">for</span> <span class="n">pdbid</span><span class="p">,</span> <span class="n">ligid</span> <span class="ow">in</span> <span class="n">pairs_list</span><span class="p">]</span>
         <span class="k">return</span> <span class="n">pairs_list</span><span class="p">,</span> <span class="n">mappings</span>
diff --git a/_modules/pyCADD/utils/env.html b/_modules/pyCADD/utils/env.html
index ea8d24d..b8d158a 100644
--- a/_modules/pyCADD/utils/env.html
+++ b/_modules/pyCADD/utils/env.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pyCADD.utils.env &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.utils.env &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]>
@@ -12,7 +12,7 @@
   
         <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>
diff --git a/_sources/README.md.txt b/_sources/README.md.txt
index 3286013..479cb07 100644
--- a/_sources/README.md.txt
+++ b/_sources/README.md.txt
@@ -117,6 +117,11 @@ Copyight © 2023 XMU
 2023-11-21
 
 ## 更新日志
+* 1.6.9 (2023-12-26)
+  * 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
+  * 添加了对PDB蛋白链突变信息的解析
+  * 为 Dock 添加了多线程批量下载PDB的接口 `pycadd-dock download`
+  * 其他 BUG 修复
 
 * 1.6.8 (2023-11-21)
   * 为 Dock 模块 CLI 接口 pycadd-dock 添加了自动创建 schrodinger 虚拟环境的功能
diff --git a/_sources/dock.md.txt b/_sources/dock.md.txt
index 8951884..cca0107 100644
--- a/_sources/dock.md.txt
+++ b/_sources/dock.md.txt
@@ -14,10 +14,17 @@ Dock 模块是通过串联分子对接软件 python API 来实现各类分子设
     ```
     命令可在当前目录下创建名为 `schrodinger.ve` 的虚拟环境，激活并在其中安装 `pyCADD`。 更多信息请参阅 [如何建立Schrodinger Python Virtual Env](https://content.schrodinger.com/Docs/r2022-1/python_api/intro.html#per-user-virtual-environments-for-installing-additional-modules)。
 
-## Docking of Many-to-One
+## Download PDB file(s)
+`pyCADD` 的 `pycadd-dock download` 提供了从PDB数据库进行多线程批量下载PDB结构文件的功能（需要互联网）。
+使用 `pycadd-dock download -i PDBID` 下载单一结构，或在一个文件 `example.csv` 中列出您想要下载的PDB ID：
 
-`pyCADD` UI 的 `Dock Mode` 提供了将一个或多个配体对接于单个受体结构的功能。
-运行 `pyCADD` 选择模式1 并使用功能6，提供包含一个多个配体的单一 `.mae` 或 `.maegz` 的文件路径即可
+```
+1FBY
+3OAP
+4K6I
+5JI0
+```
+然后使用 `pycadd-dock download -f example.csv [-s SAVE_DIR]` (在当前目录或指定目录SAVE_DIR) 批量下载它们。
 
 ## Docking of Many-to-many (Ensemble Docking)
 
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 11cf6de..bcdeb2e 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.6.8',
+    VERSION: '1.6.9',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/dance.html b/dance.html
index 88fedc0..a52b8c1 100644
--- a/dance.html
+++ b/dance.html
@@ -4,7 +4,7 @@
   <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>Dance User Guide &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Dance User Guide &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/demand.html b/demand.html
index f72cf74..42cced4 100644
--- a/demand.html
+++ b/demand.html
@@ -4,7 +4,7 @@
   <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>Demand User Guide &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Demand User Guide &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/density.html b/density.html
index ca24db5..9b51355 100644
--- a/density.html
+++ b/density.html
@@ -4,7 +4,7 @@
   <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>Density User Guide &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Density User Guide &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/dock.html b/dock.html
index 9d467cb..4e5147a 100644
--- a/dock.html
+++ b/dock.html
@@ -4,7 +4,7 @@
   <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>Dock User Guide &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Dock User Guide &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -49,7 +49,7 @@
 <p class="caption" role="heading"><span class="caption-text">Module User Guide</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Dock User Guide</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#docking-of-many-to-one">Docking of Many-to-One</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#download-pdb-file-s">Download PDB file(s)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#docking-of-many-to-many-ensemble-docking">Docking of Many-to-many (Ensemble Docking)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#generate-docking-reports">Generate Docking Reports</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#dock">为系综对接构建Dock输入文件的示例</a></li>
@@ -104,10 +104,17 @@ <h1>Dock User Guide<a class="headerlink" href="#dock-user-guide" title="Permalin
 <p>命令可在当前目录下创建名为 <code class="docutils literal notranslate"><span class="pre">schrodinger.ve</span></code> 的虚拟环境，激活并在其中安装 <code class="docutils literal notranslate"><span class="pre">pyCADD</span></code>。 更多信息请参阅 <a class="reference external" href="https://content.schrodinger.com/Docs/r2022-1/python_api/intro.html#per-user-virtual-environments-for-installing-additional-modules">如何建立Schrodinger Python Virtual Env</a>。</p>
 </li>
 </ul>
-<section id="docking-of-many-to-one">
-<h2>Docking of Many-to-One<a class="headerlink" href="#docking-of-many-to-one" title="Permalink to this heading"></a></h2>
-<p><code class="docutils literal notranslate"><span class="pre">pyCADD</span></code> UI 的 <code class="docutils literal notranslate"><span class="pre">Dock</span> <span class="pre">Mode</span></code> 提供了将一个或多个配体对接于单个受体结构的功能。
-运行 <code class="docutils literal notranslate"><span class="pre">pyCADD</span></code> 选择模式1 并使用功能6，提供包含一个多个配体的单一 <code class="docutils literal notranslate"><span class="pre">.mae</span></code> 或 <code class="docutils literal notranslate"><span class="pre">.maegz</span></code> 的文件路径即可</p>
+<section id="download-pdb-file-s">
+<h2>Download PDB file(s)<a class="headerlink" href="#download-pdb-file-s" title="Permalink to this heading"></a></h2>
+<p><code class="docutils literal notranslate"><span class="pre">pyCADD</span></code> 的 <code class="docutils literal notranslate"><span class="pre">pycadd-dock</span> <span class="pre">download</span></code> 提供了从PDB数据库进行多线程批量下载PDB结构文件的功能（需要互联网）。
+使用 <code class="docutils literal notranslate"><span class="pre">pycadd-dock</span> <span class="pre">download</span> <span class="pre">-i</span> <span class="pre">PDBID</span></code> 下载单一结构，或在一个文件 <code class="docutils literal notranslate"><span class="pre">example.csv</span></code> 中列出您想要下载的PDB ID：</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">1</span><span class="n">FBY</span>
+<span class="mi">3</span><span class="n">OAP</span>
+<span class="mi">4</span><span class="n">K6I</span>
+<span class="mi">5</span><span class="n">JI0</span>
+</pre></div>
+</div>
+<p>然后使用 <code class="docutils literal notranslate"><span class="pre">pycadd-dock</span> <span class="pre">download</span> <span class="pre">-f</span> <span class="pre">example.csv</span> <span class="pre">[-s</span> <span class="pre">SAVE_DIR]</span></code> (在当前目录或指定目录SAVE_DIR) 批量下载它们。</p>
 </section>
 <section id="docking-of-many-to-many-ensemble-docking">
 <h2>Docking of Many-to-many (Ensemble Docking)<a class="headerlink" href="#docking-of-many-to-many-ensemble-docking" title="Permalink to this heading"></a></h2>
diff --git a/dynamic.html b/dynamic.html
index 34824b3..e708952 100644
--- a/dynamic.html
+++ b/dynamic.html
@@ -4,7 +4,7 @@
   <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>Dynamic User Guide &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Dynamic User Guide &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/genindex.html b/genindex.html
index 08322a7..7ecaa8b 100644
--- a/genindex.html
+++ b/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Index &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]>
@@ -12,7 +12,7 @@
   
         <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>
@@ -167,13 +167,15 @@ <h2 id="B">B</h2>
 </li>
       <li><a href="pyCADD.Dynamic.html#pyCADD.Dynamic.template.BaseConstructor">BaseConstructor (class in pyCADD.Dynamic.template)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="pyCADD.utils.html#pyCADD.utils.common.BaseFile">BaseFile (class in pyCADD.utils.common)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="pyCADD.Dynamic.html#pyCADD.Dynamic.core.BaseProcess">BaseProcess (class in pyCADD.Dynamic.core)</a>
 </li>
       <li><a href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryCfg">BaseQueryCfg (class in pyCADD.Demand.config)</a>
+</li>
+      <li><a href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB">BaseQueryPDB (class in pyCADD.Demand.config)</a>
 </li>
       <li><a href="pyCADD.utils.html#pyCADD.utils.ui.UI.basic_info">basic_info (pyCADD.utils.ui.UI property)</a>
 </li>
@@ -431,10 +433,10 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.PDBFile.get_lig">get_lig() (pyCADD.Dock.common.PDBFile method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.ComplexFile.get_lig_molnum">get_lig_molnum() (pyCADD.Dock.common.ComplexFile method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.PDBFile.get_lig_name">get_lig_name() (pyCADD.Dock.common.PDBFile method)</a>
 </li>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.DockResultFile.get_ligand_file">get_ligand_file() (pyCADD.Dock.common.DockResultFile method)</a>
@@ -470,7 +472,11 @@ <h2 id="G">G</h2>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.get_predict_structure">get_predict_structure() (in module pyCADD.Dock.common)</a>
 </li>
       <li><a href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryCfg.get_query">get_query() (pyCADD.Demand.config.BaseQueryCfg method)</a>
+
+      <ul>
+        <li><a href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB.get_query">(pyCADD.Demand.config.BaseQueryPDB method)</a>
 </li>
+      </ul></li>
       <li><a href="pyCADD.Dock.html#pyCADD.Dock.common.DockResultFile.get_receptor_file">get_receptor_file() (pyCADD.Dock.common.DockResultFile method)</a>
 </li>
       <li><a href="pyCADD.VSW.html#pyCADD.VSW.base.VSW.get_receptor_list">get_receptor_list() (pyCADD.VSW.base.VSW method)</a>
@@ -1119,6 +1125,8 @@ <h2 id="Q">Q</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot">query_uniprot() (in module pyCADD.Demand.core)</a>
+</li>
+      <li><a href="pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot_id_on_pdb">query_uniprot_id_on_pdb() (in module pyCADD.Demand.core)</a>
 </li>
       <li><a href="pyCADD.Demand.html#pyCADD.Demand.core.QueryClient">QueryClient (class in pyCADD.Demand.core)</a>
 </li>
diff --git a/index.html b/index.html
index 058fb54..07f51f4 100644
--- a/index.html
+++ b/index.html
@@ -4,7 +4,7 @@
   <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 Documentation &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD Documentation &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -103,7 +103,7 @@ <h1>pyCADD Documentation<a class="headerlink" href="#pycadd-documentation" title
 <p class="caption" role="heading"><span class="caption-text">Module User Guide</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="dock.html">Dock User Guide</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="dock.html#docking-of-many-to-one">Docking of Many-to-One</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dock.html#download-pdb-file-s">Download PDB file(s)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dock.html#docking-of-many-to-many-ensemble-docking">Docking of Many-to-many (Ensemble Docking)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dock.html#generate-docking-reports">Generate Docking Reports</a></li>
 <li class="toctree-l2"><a class="reference internal" href="dock.html#dock">为系综对接构建Dock输入文件的示例</a></li>
diff --git a/modules.html b/modules.html
index d248ee2..b5dee27 100644
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     <script src="_static/js/theme.js"></script>
diff --git a/pyCADD.Dance.html b/pyCADD.Dance.html
index 5e01ab0..383f131 100644
--- a/pyCADD.Dance.html
+++ b/pyCADD.Dance.html
@@ -4,7 +4,7 @@
   <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.Dance package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Dance package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/pyCADD.Demand.html b/pyCADD.Demand.html
index 76c7a17..a008ce4 100644
--- a/pyCADD.Demand.html
+++ b/pyCADD.Demand.html
@@ -4,7 +4,7 @@
   <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.Demand package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Demand package &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -122,6 +122,17 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 </dd></dl>
 
+<dl class="py class">
+<dt class="sig sig-object py" id="pyCADD.Demand.config.BaseQueryPDB">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pyCADD.Demand.config.</span></span><span class="sig-name descname"><span class="pre">BaseQueryPDB</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pyCADD/Demand/config.html#BaseQueryPDB"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyCADD.Demand.config.BaseQueryPDB" title="Permalink to this definition"></a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pyCADD.Demand.config.BaseQueryPDB.get_query">
+<span class="sig-name descname"><span class="pre">get_query</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pyCADD/Demand/config.html#BaseQueryPDB.get_query"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyCADD.Demand.config.BaseQueryPDB.get_query" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
 </section>
 <section id="module-pyCADD.Demand.core">
 <span id="pycadd-demand-core-module"></span><h2>pyCADD.Demand.core module<a class="headerlink" href="#module-pyCADD.Demand.core" title="Permalink to this heading"></a></h2>
@@ -213,6 +224,11 @@ <h3>Parameters<a class="headerlink" href="#parameters" title="Permalink to this
 <span class="sig-prename descclassname"><span class="pre">pyCADD.Demand.core.</span></span><span class="sig-name descname"><span class="pre">query_uniprot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pyCADD/Demand/core.html#query_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyCADD.Demand.core.query_uniprot" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="pyCADD.Demand.core.query_uniprot_id_on_pdb">
+<span class="sig-prename descclassname"><span class="pre">pyCADD.Demand.core.</span></span><span class="sig-name descname"><span class="pre">query_uniprot_id_on_pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference internal" href="_modules/pyCADD/Demand/core.html#query_uniprot_id_on_pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyCADD.Demand.core.query_uniprot_id_on_pdb" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 </section>
 <section id="module-pyCADD.Demand">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-pyCADD.Demand" title="Permalink to this heading"></a></h2>
diff --git a/pyCADD.Density.html b/pyCADD.Density.html
index f8855c8..5f27088 100644
--- a/pyCADD.Density.html
+++ b/pyCADD.Density.html
@@ -4,7 +4,7 @@
   <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.Density package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Density package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/pyCADD.Dock.html b/pyCADD.Dock.html
index 0e7d026..e4c3288 100644
--- a/pyCADD.Dock.html
+++ b/pyCADD.Dock.html
@@ -4,7 +4,7 @@
   <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.Dock package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Dock package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/pyCADD.Dynamic.html b/pyCADD.Dynamic.html
index 8dda568..4832dfb 100644
--- a/pyCADD.Dynamic.html
+++ b/pyCADD.Dynamic.html
@@ -4,7 +4,7 @@
   <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.Dynamic package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.Dynamic package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/pyCADD.VSW.html b/pyCADD.VSW.html
index ace492c..b63affd 100644
--- a/pyCADD.VSW.html
+++ b/pyCADD.VSW.html
@@ -4,7 +4,7 @@
   <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.VSW package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.VSW package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/pyCADD.html b/pyCADD.html
index e8852c5..c8fd372 100644
--- a/pyCADD.html
+++ b/pyCADD.html
@@ -4,7 +4,7 @@
   <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 package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD package &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -183,6 +183,10 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l4"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryCfg.get_query"><code class="docutils literal notranslate"><span class="pre">BaseQueryCfg.get_query()</span></code></a></li>
 </ul>
 </li>
+<li class="toctree-l3"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB"><code class="docutils literal notranslate"><span class="pre">BaseQueryPDB</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.config.BaseQueryPDB.get_query"><code class="docutils literal notranslate"><span class="pre">BaseQueryPDB.get_query()</span></code></a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="pyCADD.Demand.html#module-pyCADD.Demand.core">pyCADD.Demand.core module</a><ul>
@@ -199,6 +203,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l3"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.core.parse_uniport"><code class="docutils literal notranslate"><span class="pre">parse_uniport()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.core.query_pdb"><code class="docutils literal notranslate"><span class="pre">query_pdb()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot"><code class="docutils literal notranslate"><span class="pre">query_uniprot()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pyCADD.Demand.html#pyCADD.Demand.core.query_uniprot_id_on_pdb"><code class="docutils literal notranslate"><span class="pre">query_uniprot_id_on_pdb()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="pyCADD.Demand.html#module-pyCADD.Demand">Module contents</a></li>
diff --git a/pyCADD.utils.html b/pyCADD.utils.html
index 430bdab..c09e35d 100644
--- a/pyCADD.utils.html
+++ b/pyCADD.utils.html
@@ -4,7 +4,7 @@
   <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.utils package &mdash; pyCADD 1.6.8 documentation</title>
+  <title>pyCADD.utils package &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]>
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/search.html b/search.html
index 7517fa3..48383fd 100644
--- a/search.html
+++ b/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; pyCADD 1.6.8 documentation</title>
+  <title>Search &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" />
     
@@ -13,7 +13,7 @@
   
         <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>
diff --git a/searchindex.js b/searchindex.js
index 0c57c9c..065415e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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