deploy: b82c513

api/kinoml/datasets/pkis2/index.html

@@ -431,7 +431,7 @@ <h2 id="module-contents">Module Contents<a class="headerlink" href="#module-cont
 <dd></dd></dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="kinoml.datasets.pkis2.PKIS2DatasetProvider">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">kinoml.datasets.pkis2.</span></span><span class="sig-name descname"><span class="pre">PKIS2DatasetProvider</span></span><a class="headerlink" href="#kinoml.datasets.pkis2.PKIS2DatasetProvider" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">kinoml.datasets.pkis2.</span></span><span class="sig-name descname"><span class="pre">PKIS2DatasetProvider</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">measurements</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="../../core/measurements/index.html#kinoml.core.measurements.BaseMeasurement" title="kinoml.core.measurements.BaseMeasurement"><span class="pre">kinoml.core.measurements.BaseMeasurement</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#kinoml.datasets.pkis2.PKIS2DatasetProvider" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference internal" href="../core/index.html#kinoml.datasets.core.DatasetProvider" title="kinoml.datasets.core.DatasetProvider"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kinoml.datasets.core.DatasetProvider</span></code></a></p>
 <p>Loads the PKIS2 dataset as provided in _Progress towards a public chemogenomic set for protein
 kinases and a call for contributions [1].</p>

api/kinoml/features/protein/index.html

@@ -483,8 +483,7 @@ <h2 id="module-contents">Module Contents<a class="headerlink" href="#module-cont
 <dl class="py method">
 <dt class="sig sig-object py" id="kinoml.features.protein.OneHotEncodedSequenceFeaturizer._retrieve_sequence">
 <span class="sig-name descname"><span class="pre">_retrieve_sequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">system</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="../../core/systems/index.html#kinoml.core.systems.ProteinSystem" title="kinoml.core.systems.ProteinSystem"><span class="pre">kinoml.core.systems.ProteinSystem</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="../../core/systems/index.html#kinoml.core.systems.ProteinLigandComplex" title="kinoml.core.systems.ProteinLigandComplex"><span class="pre">kinoml.core.systems.ProteinLigandComplex</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="headerlink" href="#kinoml.features.protein.OneHotEncodedSequenceFeaturizer._retrieve_sequence" title="Permalink to this definition">¶</a></dt>
-<dd><p>Implement in your component-specific subclass!</p>
-</dd></dl>
+<dd></dd></dl>
 </dd></dl>
 <dl class="py class">
 <dt class="sig sig-object py" id="kinoml.features.protein.OEProteinStructureFeaturizer">

api/kinoml/ml/torch_geometric_models/index.html

@@ -449,7 +449,17 @@ <h2 id="module-contents">Module Contents<a class="headerlink" href="#module-cont
 <dl class="py method">
 <dt class="sig sig-object py" id="kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork.estimate_input_shape">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">estimate_input_shape</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_sample</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork.estimate_input_shape" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><p>This static method takes the same input
+as <code class="docutils literal notranslate"><span class="pre">.forward()</span></code> would and estimates the
+incoming shape so the layers can be initialized
+properly.</p>
+<p>Most of the time, <code class="docutils literal notranslate"><span class="pre">input_sample</span></code> would be a
+Tensor, in which the first dimension corresponds
+to systems, and the second is the input shape
+we need.</p>
+<p>If your <code class="docutils literal notranslate"><span class="pre">.forward()</span></code> method takes something else
+than a Tensor, please adapt this method accordingly.</p>
+</dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork.forward" title="Permalink to this definition">¶</a></dt>

notebooks/getting_started.ipynb

@@ -32,7 +32,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8ede9514",
+   "id": "05090503",
    "metadata": {},
    "source": [
     "![KinoML object model](../../kinoml/data/fig_1_kinomltechpaper_v2.png)  \n",