deploy: 51f73c8

Author: liugangcode

_modules/index.html

@@ -274,6 +274,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="torch_molecule/generator/digress/modeling_digress.html">torch_molecule.generator.digress.modeling_digress</a></li>
 <li><a href="torch_molecule/generator/graph_dit/modeling_graph_dit.html">torch_molecule.generator.graph_dit.modeling_graph_dit</a></li>
 <li><a href="torch_molecule/generator/graph_ga/modeling_graph_ga.html">torch_molecule.generator.graph_ga.modeling_graph_ga</a></li>
+<li><a href="torch_molecule/generator/graph_ga/oracle.html">torch_molecule.generator.graph_ga.oracle</a></li>
 <li><a href="torch_molecule/generator/molgpt/modeling_molgpt.html">torch_molecule.generator.molgpt.modeling_molgpt</a></li>
 <li><a href="torch_molecule/nn/attention.html">torch_molecule.nn.attention</a></li>
 <li><a href="torch_molecule/nn/embedder.html">torch_molecule.nn.embedder</a></li>

_modules/torch_molecule/generator/graph_ga/oracle.html

@@ -54,6 +54,12 @@ Modeling Molecules as Graphs with Heuristic-based Generators
    :undoc-members:
    :show-inheritance:
 
+.. rubric:: Default Oracles in GraphGA
+.. autoclass:: torch_molecule.generator.graph_ga.oracle.Oracle
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Modeling Molecules as Sequences with Transformer-based Generators
 -----------------------------------------------------------------
 

_sources/api/generator.rst.txt

@@ -503,6 +503,45 @@ <h2>Modeling Molecules as Graphs with Heuristic-based Generators<a class="header
 
 </dd></dl>
 
+<p class="rubric">Default Oracles in GraphGA</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="torch_molecule.generator.graph_ga.oracle.Oracle">
+<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">torch_molecule.generator.graph_ga.oracle.</span></span><span class="sig-name descname"><span class="pre">Oracle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">models</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_task</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/torch_molecule/generator/graph_ga/oracle.html#Oracle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#torch_molecule.generator.graph_ga.oracle.Oracle" 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>Oracle class for scoring molecules.</p>
+<p>This class wraps predictive models (like RandomForestRegressor) to score molecules
+based on their properties. It handles conversion of SMILES to fingerprints.</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>models</strong> (<em>List</em><em>[</em><em>Any</em><em>]</em><em>, </em><em>optional</em>) – List of trained models that implement a predict method.
+If None, RandomForestRegressors will be created when fit is called.</p></li>
+<li><p><strong>num_task</strong> (<em>int</em><em>, </em><em>default=1</em>) – Number of properties to predict.</p></li>
+</ul>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="torch_molecule.generator.graph_ga.oracle.Oracle.fit">
+<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X_train</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_train</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/torch_molecule/generator/graph_ga/oracle.html#Oracle.fit"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#torch_molecule.generator.graph_ga.oracle.Oracle.fit" title="Link to this definition">¶</a></dt>
+<dd><p>Fit the underlying models with training data.</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>X_train</strong> (<em>List</em><em>[</em><em>str</em><em>] or </em><em>List</em><em>[</em><em>RDKit.Mol</em><em>]</em>) – Training molecules as SMILES strings or RDKit Mol objects.</p></li>
+<li><p><strong>y_train</strong> (<em>np.ndarray</em>) – Training labels with shape (n_samples, num_task).</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>self</strong> – Fitted oracle.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference internal" href="#torch_molecule.generator.graph_ga.oracle.Oracle" title="torch_molecule.generator.graph_ga.oracle.Oracle">Oracle</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 </section>
 <section id="modeling-molecules-as-sequences-with-transformer-based-generators">
 <h2>Modeling Molecules as Sequences with Transformer-based Generators<a class="headerlink" href="#modeling-molecules-as-sequences-with-transformer-based-generators" title="Link to this heading">¶</a></h2>
@@ -668,6 +707,10 @@ <h2>Modeling Molecules as Sequences with Transformer-based Generators<a class="h
 <li><a class="reference internal" href="#torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator.generate"><code class="docutils literal notranslate"><span class="pre">GraphGAMolecularGenerator.generate()</span></code></a></li>
 </ul>
 </li>
+<li><a class="reference internal" href="#torch_molecule.generator.graph_ga.oracle.Oracle"><code class="docutils literal notranslate"><span class="pre">Oracle</span></code></a><ul>
+<li><a class="reference internal" href="#torch_molecule.generator.graph_ga.oracle.Oracle.fit"><code class="docutils literal notranslate"><span class="pre">Oracle.fit()</span></code></a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li><a class="reference internal" href="#modeling-molecules-as-sequences-with-transformer-based-generators">Modeling Molecules as Sequences with Transformer-based Generators</a><ul>

api/generator.html

@@ -261,7 +261,7 @@
 
 <section class="genindex-section">
   <h1 id="index">Index</h1>
-  <div class="genindex-jumpbox"><a href="#A"><strong>A</strong></a> | <a href="#B"><strong>B</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a> | <a href="#U"><strong>U</strong></a> | <a href="#V"><strong>V</strong></a></div>
+  <div class="genindex-jumpbox"><a href="#A"><strong>A</strong></a> | <a href="#B"><strong>B</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#O"><strong>O</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a> | <a href="#U"><strong>U</strong></a> | <a href="#V"><strong>V</strong></a></div>
 </section>
 <section id="A" class="genindex-section">
   <h2>A</h2>
@@ -439,6 +439,8 @@ <h2>F</h2>
           <li><a href="api/generator.html#torch_molecule.generator.graph_dit.modeling_graph_dit.GraphDITMolecularGenerator.fit">(torch_molecule.generator.graph_dit.modeling_graph_dit.GraphDITMolecularGenerator method)</a>
 </li>
           <li><a href="api/generator.html#torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator.fit">(torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator method)</a>
+</li>
+          <li><a href="api/generator.html#torch_molecule.generator.graph_ga.oracle.Oracle.fit">(torch_molecule.generator.graph_ga.oracle.Oracle method)</a>
 </li>
           <li><a href="api/generator.html#torch_molecule.generator.molgpt.modeling_molgpt.MolGPTMolecularGenerator.fit">(torch_molecule.generator.molgpt.modeling_molgpt.MolGPTMolecularGenerator method)</a>
 </li>
@@ -710,6 +712,16 @@ <h2>N</h2>
   </tr></table>
 </section>
 
+<section id="O" class="genindex-section">
+  <h2>O</h2>
+  <table style="width: 100%" class="indextable genindextable"><tr>
+    <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="api/generator.html#torch_molecule.generator.graph_ga.oracle.Oracle">Oracle (class in torch_molecule.generator.graph_ga.oracle)</a>
+</li>
+    </ul></td>
+  </tr></table>
+</section>
+
 <section id="P" class="genindex-section">
   <h2>P</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>

genindex.html

@@ -314,6 +314,7 @@ <h2>Model Persistence<a class="headerlink" href="#model-persistence" title="Link
 </li>
 <li class="toctree-l2"><a class="reference internal" href="api/generator.html#modeling-molecules-as-graphs-with-heuristic-based-generators">Modeling Molecules as Graphs with Heuristic-based Generators</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="api/generator.html#torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator"><code class="docutils literal notranslate"><span class="pre">GraphGAMolecularGenerator</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="api/generator.html#torch_molecule.generator.graph_ga.oracle.Oracle"><code class="docutils literal notranslate"><span class="pre">Oracle</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="api/generator.html#modeling-molecules-as-sequences-with-transformer-based-generators">Modeling Molecules as Sequences with Transformer-based Generators</a><ul>