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drugilsberg committed Feb 9, 2024
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1 change: 1 addition & 0 deletions _modules/index.html
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Expand Up @@ -80,6 +80,7 @@ <h1>All modules for which code is available</h1>
<li><a href="rxn/chemutils/reaction_smiles.html">rxn.chemutils.reaction_smiles</a></li>
<li><a href="rxn/chemutils/smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li><a href="rxn/chemutils/smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li><a href="rxn/chemutils/smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li><a href="rxn/chemutils/tokenization.html">rxn.chemutils.tokenization</a></li>
<li><a href="rxn/chemutils/utils.html">rxn.chemutils.utils</a></li>
</ul>
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1 change: 1 addition & 0 deletions _modules/rxn/chemutils/multicomponent_smiles.html
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Expand Up @@ -69,6 +69,7 @@ <h1>Source code for rxn.chemutils.multicomponent_smiles</h1><div class="highligh
<span class="sd">Utilities related to &quot;multi-component SMILES&quot;, i.e. strings containing multiple compounds</span>
<span class="sd">in SMILES notation, which may include fragment bonds.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">from</span> <span class="nn">functools</span> <span class="kn">import</span> <span class="n">partial</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span>

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1 change: 1 addition & 0 deletions _modules/rxn/chemutils/reaction_smiles.html
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Expand Up @@ -71,6 +71,7 @@ <h1>Source code for rxn.chemutils.reaction_smiles</h1><div class="highlight"><pr
<span class="sd">In a separate file than miscellaneous.py or conversion.py in order to avoid</span>
<span class="sd">cyclic dependencies.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">from</span> <span class="nn">enum</span> <span class="kn">import</span> <span class="n">auto</span>

<span class="kn">from</span> <span class="nn">rxn.utilities.types</span> <span class="kn">import</span> <span class="n">RxnEnum</span>
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4 changes: 2 additions & 2 deletions _modules/rxn/chemutils/tokenization.html
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Expand Up @@ -95,8 +95,8 @@ <h1>Source code for rxn.chemutils.tokenization</h1><div class="highlight"><pre>
<span class="sd"> Initialize TokenizationError.</span>

<span class="sd"> Args:</span>
<span class="sd"> title (str): title of the error.</span>
<span class="sd"> detail (str): decscription of the error.</span>
<span class="sd"> title: title of the error.</span>
<span class="sd"> detail: decscription of the error.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s2">&quot;TokenizationError&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="n">title</span>
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1 change: 0 additions & 1 deletion _modules/rxn/chemutils/utils.html
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<h1>Source code for rxn.chemutils.utils</h1><div class="highlight"><pre>
<span></span><span class="sd">&quot;&quot;&quot;Simple utilities not involving RDKit.&quot;&quot;&quot;</span>


<span class="kn">import</span> <span class="nn">re</span>


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1 change: 1 addition & 0 deletions _sources/generated/rxn.chemutils.rst.txt
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Expand Up @@ -41,6 +41,7 @@
rxn.chemutils.scripts
rxn.chemutils.smiles_augmenter
rxn.chemutils.smiles_randomization
rxn.chemutils.smiles_standardization
rxn.chemutils.tokenization
rxn.chemutils.utils

31 changes: 31 additions & 0 deletions _sources/generated/rxn.chemutils.smiles_standardization.rst.txt
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rxn.chemutils.smiles\_standardization
=====================================

.. automodule:: rxn.chemutils.smiles_standardization







.. rubric:: Functions

.. autosummary::
:toctree:

standardize_molecules
standardize_smiles













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rxn.chemutils.smiles\_standardization.standardize\_molecules
============================================================

.. currentmodule:: rxn.chemutils.smiles_standardization

.. autofunction:: standardize_molecules
6 changes: 6 additions & 0 deletions _sources/generated/rxn.chemutils.smiles_standardization.standardize_smiles.rst.txt
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rxn.chemutils.smiles\_standardization.standardize\_smiles
=========================================================

.. currentmodule:: rxn.chemutils.smiles_standardization

.. autofunction:: standardize_smiles
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.scripts.html">rxn.chemutils.scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_augmenter.html">rxn.chemutils.smiles_augmenter</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_randomization.html">rxn.chemutils.smiles_randomization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.smiles_standardization.html">rxn.chemutils.smiles_standardization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.tokenization.html">rxn.chemutils.tokenization</a></li>
<li class="toctree-l3"><a class="reference internal" href="rxn.chemutils.utils.html">rxn.chemutils.utils</a></li>
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