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@@ -237,7 +237,7 @@ <h2>Returns:<a class="headerlink" href="#id8" title="Permalink to this heading">
 
 <dl class="py function">
 <dt class="sig sig-object py" id="colav.extract_data.generate_strain_matrix">
-<span class="sig-prename descclassname"><span class="pre">colav.extract_data.</span></span><span class="sig-name descname"><span class="pre">generate_strain_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference_pdb</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resnum_bounds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atoms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['N',</span> <span class="pre">'C',</span> <span class="pre">'CA',</span> <span class="pre">'CB',</span> <span class="pre">'O']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alt_locs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['',</span> <span class="pre">'A']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_prefix</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">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#colav.extract_data.generate_strain_matrix" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">colav.extract_data.</span></span><span class="sig-name descname"><span class="pre">generate_strain_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference_pdb</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resnum_bounds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atoms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['N',</span> <span class="pre">'C',</span> <span class="pre">'CA',</span> <span class="pre">'CB',</span> <span class="pre">'O']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alt_locs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">['',</span> <span class="pre">'A']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_prefix</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">save_additional</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#colav.extract_data.generate_strain_matrix" title="Permalink to this definition"></a></dt>
 <dd><p>Extracts strain tensors, shear tensors, or shear energies from given structures.</p>
 <p>Extracts and returns a data matrix of (observations x features) with the given structures as observations
 and strain tensors, shear tensors, or shear energies. For tensor features, only the off-diagonal
@@ -262,6 +262,8 @@ <h2>Parameters:<a class="headerlink" href="#id9" title="Permalink to this headin
 </dd>
 <dt>save_prefix<span class="classifier">str</span></dt><dd><p>If saving results, prefix for pickle save file.</p>
 </dd>
+<dt>save_additional<span class="classifier">bool, optional</span></dt><dd><p>Indicator to save results of nested calculations.</p>
+</dd>
 <dt>verbose<span class="classifier">bool, optional</span></dt><dd><p>Indicator for verbose output.</p>
 </dd>
 </dl>