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<!DOCTYPE html>
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<h1 class="logo"><a href="index.html">ReactionUtils</a></h1>
<p class="blurb">Utilities for working with reactions, reaction templates and template extraction</p>
<h3>Navigation</h3>
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<li class="toctree-l1"><a class="reference internal" href="templates.html">Templates</a></li>
<li class="toctree-l1"><a class="reference internal" href="uspto.html">USPTO</a></li>
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<li class="toctree-l7"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow</span></code></a><ul>
<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.data_prefix"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.data_prefix</span></code></a></li>
<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.start"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.start()</span></code></a></li>
<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.combine_files"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.combine_files()</span></code></a></li>
<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.setup_cleaning"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.setup_cleaning()</span></code></a></li>
<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.do_cleaning"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.do_cleaning()</span></code></a></li>
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<li class="toctree-l8"><a class="reference internal" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.end"><code class="docutils literal notranslate"><span class="pre">UsptoDataPreparationFlow.end()</span></code></a></li>
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<li class="toctree-l7"><a class="reference internal" href="#rxnutils.data.uspto.uspto_yield.UsptoYieldCuration"><code class="docutils literal notranslate"><span class="pre">UsptoYieldCuration</span></code></a><ul>
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<section id="rxnutils-data-uspto-package">
<h1>rxnutils.data.uspto package<a class="headerlink" href="#rxnutils-data-uspto-package" title="Link to this heading">¶</a></h1>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading">¶</a></h2>
</section>
<section id="module-rxnutils.data.uspto.combine">
<span id="rxnutils-data-uspto-combine-module"></span><h2>rxnutils.data.uspto.combine module<a class="headerlink" href="#module-rxnutils.data.uspto.combine" title="Link to this heading">¶</a></h2>
<p>Module containing script to combine raw USPTO files</p>
<dl class="simple">
<dt>It will:</dt><dd><ul class="simple">
<li><p>preserve the ReactionSmiles and Year columns</p></li>
<li><p>create an ID from PatentNumber and ParagraphNum and row index in the original file</p></li>
</ul>
</dd>
</dl>
<dl class="py function">
<dt class="sig sig-object py" id="rxnutils.data.uspto.combine.main">
<span class="sig-prename descclassname"><span class="pre">rxnutils.data.uspto.combine.</span></span><span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.combine.main" title="Link to this definition">¶</a></dt>
<dd><p>Function for command-line tool</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>args</strong> (<em>Sequence</em><em>[</em><em>str</em><em>] </em><em>| </em><em>None</em>)</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-rxnutils.data.uspto.download">
<span id="rxnutils-data-uspto-download-module"></span><h2>rxnutils.data.uspto.download module<a class="headerlink" href="#module-rxnutils.data.uspto.download" title="Link to this heading">¶</a></h2>
<p>Module containing a script to download USPTO files Figshare</p>
<dl class="py function">
<dt class="sig sig-object py" id="rxnutils.data.uspto.download.main">
<span class="sig-prename descclassname"><span class="pre">rxnutils.data.uspto.download.</span></span><span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.download.main" title="Link to this definition">¶</a></dt>
<dd><p>Function for command-line tool</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>args</strong> (<em>Sequence</em><em>[</em><em>str</em><em>] </em><em>| </em><em>None</em>)</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-rxnutils.data.uspto.preparation_pipeline">
<span id="rxnutils-data-uspto-preparation-pipeline-module"></span><h2>rxnutils.data.uspto.preparation_pipeline module<a class="headerlink" href="#module-rxnutils.data.uspto.preparation_pipeline" title="Link to this heading">¶</a></h2>
<p>Module containing pipeline for downloading, transforming and cleaning USPTO data
This needs to be run in an environment with rxnutils installed</p>
<dl class="py class">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">rxnutils.data.uspto.preparation_pipeline.</span></span><span class="sig-name descname"><span class="pre">UsptoDataPreparationFlow</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_cli</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow" title="Link to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="rxnutils.data.html#rxnutils.data.base_pipeline.DataPreparationBaseFlow" title="rxnutils.data.base_pipeline.DataPreparationBaseFlow"><code class="xref py py-class docutils literal notranslate"><span class="pre">DataPreparationBaseFlow</span></code></a></p>
<p>Pipeline for download UPSTO source file, combining them and do some clean-up</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.data_prefix">
<span class="sig-name descname"><span class="pre">data_prefix</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'uspto'</span></em><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.data_prefix" title="Link to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.start">
<span class="sig-name descname"><span class="pre">start</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.start" title="Link to this definition">¶</a></dt>
<dd><p>Download USPTO data from Figshare</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.combine_files">
<span class="sig-name descname"><span class="pre">combine_files</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.combine_files" title="Link to this definition">¶</a></dt>
<dd><p>Combine USPTO data files and add IDs</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.setup_cleaning">
<span class="sig-name descname"><span class="pre">setup_cleaning</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.setup_cleaning" title="Link to this definition">¶</a></dt>
<dd><p>Setup cleaning</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.do_cleaning">
<span class="sig-name descname"><span class="pre">do_cleaning</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.do_cleaning" title="Link to this definition">¶</a></dt>
<dd><p>Perform cleaning of data</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.join_cleaning">
<span class="sig-name descname"><span class="pre">join_cleaning</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">_</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.join_cleaning" title="Link to this definition">¶</a></dt>
<dd><p>Combined cleaned batches of data</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.end">
<span class="sig-name descname"><span class="pre">end</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow.end" title="Link to this definition">¶</a></dt>
<dd><p>Final step, just print information</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-rxnutils.data.uspto.uspto_yield">
<span id="rxnutils-data-uspto-uspto-yield-module"></span><h2>rxnutils.data.uspto.uspto_yield module<a class="headerlink" href="#module-rxnutils.data.uspto.uspto_yield" title="Link to this heading">¶</a></h2>
<p>Code for curating USPTO yields.</p>
<p>Inspiration from this code: <a class="reference external" href="https://github.com/DocMinus/Yield_curation_USPTO">https://github.com/DocMinus/Yield_curation_USPTO</a></p>
<p>This could potentially be an action, but since it only make sens to use it
with USPTO data, it resides here for now.</p>
<dl class="py class">
<dt class="sig sig-object py" id="rxnutils.data.uspto.uspto_yield.UsptoYieldCuration">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">rxnutils.data.uspto.uspto_yield.</span></span><span class="sig-name descname"><span class="pre">UsptoYieldCuration</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">text_yield_column</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'TextMinedYield'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">calc_yield_column</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'CalculatedYield'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_column</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'CuratedYield'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rxnutils.data.uspto.uspto_yield.UsptoYieldCuration" title="Link to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Action for curating USPTO yield columns</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>text_yield_column</strong> (<em>str</em>)</p></li>
<li><p><strong>calc_yield_column</strong> (<em>str</em>)</p></li>
<li><p><strong>out_column</strong> (<em>str</em>)</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.text_yield_column">
<span class="sig-name descname"><span class="pre">text_yield_column</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'TextMinedYield'</span></em><a class="headerlink" href="#rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.text_yield_column" title="Link to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.calc_yield_column">
<span class="sig-name descname"><span class="pre">calc_yield_column</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'CalculatedYield'</span></em><a class="headerlink" href="#rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.calc_yield_column" title="Link to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.out_column">
<span class="sig-name descname"><span class="pre">out_column</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'CuratedYield'</span></em><a class="headerlink" href="#rxnutils.data.uspto.uspto_yield.UsptoYieldCuration.out_column" title="Link to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
</section>
<section id="module-rxnutils.data.uspto">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-rxnutils.data.uspto" title="Link to this heading">¶</a></h2>
</section>
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