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NPLinker · Apr 12, 2024 · 730b948 · 730b948
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diff --git a/dev/api/antismash/index.html b/dev/api/antismash/index.html
diff --git a/dev/api/arranger/index.html b/dev/api/arranger/index.html
diff --git a/dev/api/bigscape/index.html b/dev/api/bigscape/index.html
diff --git a/dev/api/genomics/index.html b/dev/api/genomics/index.html
diff --git a/dev/api/genomics_abc/index.html b/dev/api/genomics_abc/index.html
diff --git a/dev/api/genomics_utils/index.html b/dev/api/genomics_utils/index.html
diff --git a/dev/api/gnps/index.html b/dev/api/gnps/index.html
diff --git a/dev/api/loader/index.html b/dev/api/loader/index.html
diff --git a/dev/api/metabolomics/index.html b/dev/api/metabolomics/index.html
diff --git a/dev/api/metabolomics_abc/index.html b/dev/api/metabolomics_abc/index.html
diff --git a/dev/api/metabolomics_utils/index.html b/dev/api/metabolomics_utils/index.html
diff --git a/dev/api/mibig/index.html b/dev/api/mibig/index.html
diff --git a/dev/api/nplinker/index.html b/dev/api/nplinker/index.html
@@ -741,6 +741,15 @@
     <nav class="md-nav" aria-label=" nplinker">
       <ul class="md-nav__list">
 
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.logger" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;logger
+    </span>
+  </a>
+
+</li>
+
           <li class="md-nav__item">
   <a href="#nplinker.nplinker.NPLinker" class="md-nav__link">
     <span class="md-ellipsis">
@@ -751,6 +760,24 @@
     <nav class="md-nav" aria-label=" NPLinker">
       <ul class="md-nav__list">
 
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.OBJ_CLASSES" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;OBJ_CLASSES
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.SCORING_METHODS" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;SCORING_METHODS
+    </span>
+  </a>
+
+</li>
+
           <li class="md-nav__item">
   <a href="#nplinker.nplinker.NPLinker.root_dir" class="md-nav__link">
     <span class="md-ellipsis">
@@ -821,6 +848,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.metadata" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;metadata
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -875,6 +911,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.save_repro_data" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;save_repro_data
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1513,6 +1558,15 @@
     <nav class="md-nav" aria-label=" nplinker">
       <ul class="md-nav__list">
 
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.logger" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;logger
+    </span>
+  </a>
+
+</li>
+
           <li class="md-nav__item">
   <a href="#nplinker.nplinker.NPLinker" class="md-nav__link">
     <span class="md-ellipsis">
@@ -1523,6 +1577,24 @@
     <nav class="md-nav" aria-label=" NPLinker">
       <ul class="md-nav__list">
 
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.OBJ_CLASSES" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;OBJ_CLASSES
+    </span>
+  </a>
+
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.SCORING_METHODS" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;SCORING_METHODS
+    </span>
+  </a>
+
+</li>
+
           <li class="md-nav__item">
   <a href="#nplinker.nplinker.NPLinker.root_dir" class="md-nav__link">
     <span class="md-ellipsis">
@@ -1593,6 +1665,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.metadata" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-attribute"></code>&nbsp;metadata
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1647,6 +1728,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nplinker.nplinker.NPLinker.save_repro_data" class="md-nav__link">
+    <span class="md-ellipsis">
+      <code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;save_repro_data
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1782,6 +1872,27 @@ <h2 id="nplinker.nplinker" class="doc doc-heading">
 
 
 
+<div class="doc doc-object doc-attribute">
+
+
+
+<h3 id="nplinker.nplinker.logger" class="doc doc-heading">
+<code class="doc-symbol doc-symbol-heading doc-symbol-attribute"></code>          <span class="doc doc-object-name doc-attribute-name">logger</span>
+
+
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-module-attribute"><code>module-attribute</code></small>
+  </span>
+
+<a href="#nplinker.nplinker.logger" class="headerlink" title="Permanent link">&para;</a></h3>
+<div class="language-python doc-signature highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">logger</span> <span class="o">=</span> <span class="n"><span title="nplinker.logconfig.LogConfig.getLogger">getLogger</span></span><span class="p">(</span><span class="n"><a class="autorefs autorefs-external" href="https://docs.python.org/3/reference/import.html#name__">__name__</a></span><span class="p">)</span>
+</code></pre></div>
+
+  <div class="doc doc-contents ">
+  </div>
+
+</div>
+
 
 <div class="doc doc-object doc-class">
 
@@ -1797,8 +1908,6 @@ <h3 id="nplinker.nplinker.NPLinker" class="doc doc-heading">
 
   <div class="doc doc-contents ">
 
-
-      <p>Initialise an NPLinker instance.</p>
 
                 <details class="quote">
                   <summary>Source code in <code>src/nplinker/nplinker.py</code></summary>
@@ -1910,6 +2019,50 @@ <h3 id="nplinker.nplinker.NPLinker" class="doc doc-heading">
 
 
 
+<div class="doc doc-object doc-attribute">
+
+
+
+<h4 id="nplinker.nplinker.NPLinker.OBJ_CLASSES" class="doc doc-heading">
+<code class="doc-symbol doc-symbol-heading doc-symbol-attribute"></code>          <span class="doc doc-object-name doc-attribute-name">OBJ_CLASSES</span>
+
+
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-class-attribute"><code>class-attribute</code></small>
+      <small class="doc doc-label doc-label-instance-attribute"><code>instance-attribute</code></small>
+  </span>
+
+<a href="#nplinker.nplinker.NPLinker.OBJ_CLASSES" class="headerlink" title="Permanent link">&para;</a></h4>
+<div class="language-python doc-signature highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">OBJ_CLASSES</span> <span class="o">=</span> <span class="p">[</span><span class="n"><a class="autorefs autorefs-internal" title="nplinker.metabolomics.Spectrum" href="../metabolomics/#nplinker.metabolomics.Spectrum">Spectrum</a></span><span class="p">,</span> <span class="n"><a class="autorefs autorefs-internal" title="nplinker.metabolomics.MolecularFamily" href="../metabolomics/#nplinker.metabolomics.MolecularFamily">MolecularFamily</a></span><span class="p">,</span> <span class="n"><a class="autorefs autorefs-internal" title="nplinker.genomics.GCF" href="../genomics/#nplinker.genomics.GCF">GCF</a></span><span class="p">,</span> <span class="n"><a class="autorefs autorefs-internal" title="nplinker.genomics.BGC" href="../genomics/#nplinker.genomics.BGC">BGC</a></span><span class="p">]</span>
+</code></pre></div>
+
+  <div class="doc doc-contents ">
+  </div>
+
+</div>
+
+<div class="doc doc-object doc-attribute">
+
+
+
+<h4 id="nplinker.nplinker.NPLinker.SCORING_METHODS" class="doc doc-heading">
+<code class="doc-symbol doc-symbol-heading doc-symbol-attribute"></code>          <span class="doc doc-object-name doc-attribute-name">SCORING_METHODS</span>
+
+
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-class-attribute"><code>class-attribute</code></small>
+      <small class="doc doc-label doc-label-instance-attribute"><code>instance-attribute</code></small>
+  </span>
+
+<a href="#nplinker.nplinker.NPLinker.SCORING_METHODS" class="headerlink" title="Permanent link">&para;</a></h4>
+<div class="language-python doc-signature highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">SCORING_METHODS</span> <span class="o">=</span> <span class="p">{</span><span class="n"><a class="autorefs autorefs-internal" title="nplinker.scoring.metcalf_scoring.MetcalfScoring.NAME" href="../scoring/#nplinker.scoring.MetcalfScoring.NAME">NAME</a></span><span class="p">:</span> <span class="n"><a class="autorefs autorefs-internal" title="nplinker.scoring.metcalf_scoring.MetcalfScoring" href="../scoring/#nplinker.scoring.MetcalfScoring">MetcalfScoring</a></span><span class="p">,</span> <span class="n"><span title="nplinker.scoring.rosetta_scoring.RosettaScoring.NAME">NAME</span></span><span class="p">:</span> <span class="n"><span title="nplinker.scoring.rosetta_scoring.RosettaScoring">RosettaScoring</span></span><span class="p">,</span> <span class="n"><span title="nplinker.scoring.np_class_scoring.NPClassScoring.NAME">NAME</span></span><span class="p">:</span> <span class="n"><span title="nplinker.scoring.np_class_scoring.NPClassScoring">NPClassScoring</span></span><span class="p">}</span>
+</code></pre></div>
+
+  <div class="doc doc-contents ">
+  </div>
+
+</div>
+
 <div class="doc doc-object doc-attribute">
 
 
@@ -2122,6 +2275,27 @@ <h4 id="nplinker.nplinker.NPLinker.molfams" class="doc doc-heading">
 
 
 
+<h4 id="nplinker.nplinker.NPLinker.metadata" class="doc doc-heading">
+<code class="doc-symbol doc-symbol-heading doc-symbol-attribute"></code>          <span class="doc doc-object-name doc-attribute-name">metadata</span>
+
+
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-property"><code>property</code></small>
+  </span>
+
+<a href="#nplinker.nplinker.NPLinker.metadata" class="headerlink" title="Permanent link">&para;</a></h4>
+<div class="language-python doc-signature highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">metadata</span>
+</code></pre></div>
+
+  <div class="doc doc-contents ">
+  </div>
+
+</div>
+
+<div class="doc doc-object doc-attribute">
+
+
+
 <h4 id="nplinker.nplinker.NPLinker.mibig_bgcs" class="doc doc-heading">
 <code class="doc-symbol doc-symbol-heading doc-symbol-attribute"></code>          <span class="doc doc-object-name doc-attribute-name">mibig_bgcs</span>
 
@@ -2263,6 +2437,40 @@ <h4 id="nplinker.nplinker.NPLinker.class_matches" class="doc doc-heading">
 
 
 
+<h4 id="nplinker.nplinker.NPLinker.save_repro_data" class="doc doc-heading">
+<code class="doc-symbol doc-symbol-heading doc-symbol-method"></code>          <span class="doc doc-object-name doc-function-name">save_repro_data</span>
+
+
+<a href="#nplinker.nplinker.NPLinker.save_repro_data" class="headerlink" title="Permanent link">&para;</a></h4>
+<div class="language-python doc-signature highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">save_repro_data</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+</code></pre></div>
+
+  <div class="doc doc-contents ">
+
+          <details class="quote">
+            <summary>Source code in <code>src/nplinker/nplinker.py</code></summary>
+            <div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-115">115</a></span>
+<span class="normal"><a href="#__codelineno-0-116">116</a></span>
+<span class="normal"><a href="#__codelineno-0-117">117</a></span>
+<span class="normal"><a href="#__codelineno-0-118">118</a></span>
+<span class="normal"><a href="#__codelineno-0-119">119</a></span>
+<span class="normal"><a href="#__codelineno-0-120">120</a></span></pre></div></td><td class="code"><div><pre><span></span><code><a id="__codelineno-0-115" name="__codelineno-0-115"></a><span class="k">def</span> <span class="nf">save_repro_data</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+<a id="__codelineno-0-116" name="__codelineno-0-116"></a>    <span class="bp">self</span><span class="o">.</span><span class="n">_collect_repro_data</span><span class="p">()</span>
+<a id="__codelineno-0-117" name="__codelineno-0-117"></a>    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s2">&quot;wb&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">repro_file</span><span class="p">:</span>
+<a id="__codelineno-0-118" name="__codelineno-0-118"></a>        <span class="c1"># TODO is pickle the best format to use?</span>
+<a id="__codelineno-0-119" name="__codelineno-0-119"></a>        <span class="n">save_pickled_data</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_repro_data</span><span class="p">,</span> <span class="n">repro_file</span><span class="p">)</span>
+<a id="__codelineno-0-120" name="__codelineno-0-120"></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Saving reproducibility data to </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
 <h4 id="nplinker.nplinker.NPLinker.load_data" class="doc doc-heading">
 <code class="doc-symbol doc-symbol-heading doc-symbol-method"></code>          <span class="doc doc-object-name doc-function-name">load_data</span>