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LBC-LNBio · Oct 19, 2022 · e9ef6e1 · e9ef6e1
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diff --git a/docs/.buildinfo b/docs/.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: a8e686330cd82d1e1e428ef58223c494
+config: dc0dc5212cfdc73f6c712028918bddd0
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/_about/index.doctree b/docs/.doctrees/_about/index.doctree
diff --git a/docs/.doctrees/_api_reference/index.doctree b/docs/.doctrees/_api_reference/index.doctree
diff --git a/docs/.doctrees/_installation/index.doctree b/docs/.doctrees/_installation/index.doctree
diff --git a/docs/.doctrees/_tutorial/index.doctree b/docs/.doctrees/_tutorial/index.doctree
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/_about/index.html b/docs/_about/index.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+  <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>Issues &mdash; SERD 0.1.1 documentation</title>
+  <title>Issues &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/icon.ico"/>

diff --git a/docs/_api_reference/index.html b/docs/_api_reference/index.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+  <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>SERD.detect &mdash; SERD 0.1.1 documentation</title>
+  <title>SERD.detect &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/icon.ico"/>
@@ -278,7 +278,7 @@ <h1>SERD.r2g<a class="headerlink" href="#serd-r2g" title="Permalink to this head
 <li><p><strong>cutoff</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>]</em><em>, </em><em>optional</em>) – A limit of distance to define an edge between two solvent-exposed residues, by default None.
 If None, cutoff depends on selection argument. If “CA”, cutoff is 10.0. If “CB”, cutoff is 8.0.</p></li>
 <li><p><strong>intraresidual</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to consider intraresidual contacts to create adjacency matrix, by default False.</p></li>
-<li><p><strong>weighted_edges</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>False</em>) – Whether to include the interresidual distances as edge weights, by default False.</p></li>
+<li><p><strong>weighted_edges</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to include the distances as weight of the edges.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

diff --git a/docs/_installation/index.html b/docs/_installation/index.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+  <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>Requirements &mdash; SERD 0.1.1 documentation</title>
+  <title>Requirements &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/icon.ico"/>

diff --git a/docs/_modules/SERD/SERD.html b/docs/_modules/SERD/SERD.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>SERD.SERD &mdash; SERD 0.1.1 documentation</title>
+  <title>SERD.SERD &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../../_static/icon.ico"/>
@@ -874,8 +874,8 @@ <h1>Source code for SERD.SERD</h1><div class="highlight"><pre>
 <span class="sd">        If None, cutoff depends on selection argument. If &quot;CA&quot;, cutoff is 10.0. If &quot;CB&quot;, cutoff is 8.0.</span>
 <span class="sd">    intraresidual : bool, optional</span>
 <span class="sd">        Whether to consider intraresidual contacts to create adjacency matrix, by default False.</span>
-<span class="sd">    weighted_edges : bool, False</span>
-<span class="sd">        Whether to include the interresidual distances as edge weights, by default False.</span>
+<span class="sd">    weighted_edges : bool, optional</span>
+<span class="sd">        Whether to include the distances as weight of the edges.</span>
 
 <span class="sd">    Returns</span>
 <span class="sd">    -------</span>
@@ -926,6 +926,15 @@ <h1>Source code for SERD.SERD</h1><div class="highlight"><pre>
     <span class="c1"># Create networkx.Graph</span>
     <span class="n">G</span> <span class="o">=</span> <span class="n">networkx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
     <span class="n">G</span><span class="o">.</span><span class="n">add_edges_from</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">argwhere</span><span class="p">(</span><span class="n">adjacency</span><span class="p">))</span>
+    <span class="k">if</span> <span class="n">weighted_edges</span><span class="p">:</span>
+        <span class="n">weighted_edges</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="p">(</span><span class="n">edges</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">edges</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">distance</span><span class="p">[</span><span class="n">edges</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">edges</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
+            <span class="k">for</span> <span class="n">edges</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="p">]</span>
+        <span class="n">G</span><span class="o">.</span><span class="n">add_weighted_edges_from</span><span class="p">(</span><span class="n">weighted_edges</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">weighted_edges</span> <span class="o">=</span> <span class="p">[(</span><span class="n">edges</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">edges</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mf">1.0</span><span class="p">)</span> <span class="k">for</span> <span class="n">edges</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
+        <span class="n">G</span><span class="o">.</span><span class="n">add_weighted_edges_from</span><span class="p">(</span><span class="n">weighted_edges</span><span class="p">)</span>
 
     <span class="c1"># Add interresidual distances as edge weights</span>
     <span class="k">if</span> <span class="n">weighted_edges</span><span class="p">:</span>

diff --git a/docs/_modules/index.html b/docs/_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; SERD 0.1.1 documentation</title>
+  <title>Overview: module code &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/icon.ico"/>

diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pyKVFinder.utils &mdash; SERD 0.1.1 documentation</title>
+  <title>pyKVFinder.utils &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../../_static/icon.ico"/>
@@ -353,7 +353,7 @@ <h1>Source code for pyKVFinder.utils</h1><div class="highlight"><pre>
             <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</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">4</span><span class="p">:</span>
                 <span class="c1"># Get PDB information</span>
-                <span class="n">atom_symbol</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">atom_symbol</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">upper</span><span class="p">()</span>
                 <span class="n">x</span> <span class="o">=</span> <span class="nb">float</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="n">y</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
                 <span class="n">z</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>

diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -326,13 +326,15 @@ p.sidebar-title {
 }
 nav.contents,
 aside.topic,
+
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
 nav.contents,
 aside.topic,
+
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -373,6 +375,7 @@ div.sidebar > :last-child,
 aside.sidebar > :last-child,
 nav.contents > :last-child,
 aside.topic > :last-child,
+
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
@@ -382,6 +385,7 @@ div.sidebar::after,
 aside.sidebar::after,
 nav.contents::after,
 aside.topic::after,
+
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -606,6 +610,26 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
+
+/* Docutils 0.17 and older (footnotes & citations) */
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+    margin-right: 0.5em;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -630,6 +654,8 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
+/* Footnotes & citations ends */
+
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -642,6 +668,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.1.1',
+    VERSION: '0.1.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
@@ -10,5 +10,5 @@ var DOCUMENTATION_OPTIONS = {
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false,
     SHOW_SEARCH_SUMMARY: true,
-    ENABLE_SEARCH_SHORTCUTS: true,
+    ENABLE_SEARCH_SHORTCUTS: false,
 };
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -88,7 +88,7 @@ const _displayItem = (item, highlightTerms, searchTerms) => {
   linkEl.href = linkUrl + "?" + params.toString() + anchor;
   linkEl.innerHTML = title;
   if (descr)
-    listItem.appendChild(document.createElement("span")).innerHTML =
+    listItem.appendChild(document.createElement("span")).innerText =
       " (" + descr + ")";
   else if (showSearchSummary)
     fetch(requestUrl)
@@ -155,8 +155,10 @@ const Search = {
   _pulse_status: -1,
 
   htmlToText: (htmlString) => {
-    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+    const htmlElement = document
+      .createRange()
+      .createContextualFragment(htmlString);
+    _removeChildren(htmlElement.querySelectorAll(".headerlink"));
     const docContent = htmlElement.querySelector('[role="main"]');
     if (docContent !== undefined) return docContent.textContent;
     console.warn(
@@ -502,22 +504,21 @@ const Search = {
    * latter for highlighting it.
    */
   makeSearchSummary: (htmlText, keywords, highlightWords) => {
-    const text = Search.htmlToText(htmlText);
+    const text = Search.htmlToText(htmlText).toLowerCase();
     if (text === "") return null;
 
-    const textLower = text.toLowerCase();
     const actualStartPosition = [...keywords]
-      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .map((k) => text.indexOf(k.toLowerCase()))
       .filter((i) => i > -1)
       .slice(-1)[0];
     const startWithContext = Math.max(actualStartPosition - 120, 0);
 
     const top = startWithContext === 0 ? "" : "...";
     const tail = startWithContext + 240 < text.length ? "..." : "";
 
-    let summary = document.createElement("p");
+    let summary = document.createElement("div");
     summary.classList.add("context");
-    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+    summary.innerText = top + text.substr(startWithContext, 240).trim() + tail;
 
     highlightWords.forEach((highlightWord) =>
       _highlightText(summary, highlightWord, "highlighted")

diff --git a/docs/_tutorial/index.html b/docs/_tutorial/index.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+  <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>Full workflow &mdash; SERD 0.1.1 documentation</title>
+  <title>Full workflow &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/icon.ico"/>

diff --git a/docs/genindex.html b/docs/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; SERD 0.1.1 documentation</title>
+  <title>Index &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="_static/icon.ico"/>

diff --git a/docs/index.html b/docs/index.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+  <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>Welcome to SERD’s documentation! &mdash; SERD 0.1.1 documentation</title>
+  <title>Welcome to SERD’s documentation! &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="_static/icon.ico"/>

diff --git a/docs/search.html b/docs/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; SERD 0.1.1 documentation</title>
+  <title>Search &mdash; SERD 0.1.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
     <link rel="shortcut icon" href="_static/icon.ico"/>