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cctbx · Feb 28, 2024 · 840f1d2 · 840f1d2
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diff --git a/cctbx/cctbx.command_line.precession_view.html b/cctbx/cctbx.command_line.precession_view.html
@@ -121,7 +121,7 @@ <h3>Navigation</h3>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="cctbx.command_line.precession_view.run">
-<span class="sig-prename descclassname"><span class="pre">cctbx.command_line.precession_view.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.command_line.precession_view.run" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">cctbx.command_line.precession_view.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.command_line.precession_view.run" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </section>

diff --git a/cctbx/cctbx.euclidean_model_matching.html b/cctbx/cctbx.euclidean_model_matching.html
@@ -167,7 +167,7 @@ <h3>Navigation</h3>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="cctbx.euclidean_model_matching.match_refine.get_transformed_model2">
-<span class="sig-name descname"><span class="pre">get_transformed_model2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_pdb=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scattering_type='SE'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_superposed_model2=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_pdb_inp=None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.match_refine.get_transformed_model2" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_transformed_model2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_pdb=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scattering_type='SE'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_superposed_model2=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_pdb_inp=None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.match_refine.get_transformed_model2" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
@@ -218,7 +218,7 @@ <h3>Navigation</h3>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="cctbx.euclidean_model_matching.model.best_superpositions_on_other">
-<span class="sig-name descname"><span class="pre">best_superpositions_on_other</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance=1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">models_are_diffraction_index_equivalent=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">break_if_match_with_no_singles=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">specifically_test_inverse=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.model.best_superpositions_on_other" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">best_superpositions_on_other</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance=1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">models_are_diffraction_index_equivalent=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">break_if_match_with_no_singles=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">specifically_test_inverse=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.model.best_superpositions_on_other" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
@@ -238,7 +238,7 @@ <h3>Navigation</h3>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="cctbx.euclidean_model_matching.model.combine_with_other">
-<span class="sig-name descname"><span class="pre">combine_with_other</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance=1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">models_are_diffraction_index_equivalent=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">break_if_match_with_no_singles=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">improved_only=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_model_number=0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.model.combine_with_other" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">combine_with_other</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance=1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">models_are_diffraction_index_equivalent=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">break_if_match_with_no_singles=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">improved_only=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_model_number=0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.euclidean_model_matching.model.combine_with_other" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">

diff --git a/cctbx/cctbx.maptbx.mem.html b/cctbx/cctbx.maptbx.mem.html
@@ -115,7 +115,7 @@ <h3>Navigation</h3>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="cctbx.maptbx.mem.show_map_stat">
-<span class="sig-prename descclassname"><span class="pre">cctbx.maptbx.mem.</span></span><span class="sig-name descname"><span class="pre">show_map_stat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.maptbx.mem.show_map_stat" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">cctbx.maptbx.mem.</span></span><span class="sig-name descname"><span class="pre">show_map_stat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">m</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out=&lt;_io.TextIOWrapper</span> <span class="pre">name='&lt;stdout&gt;'</span> <span class="pre">mode='w'</span> <span class="pre">encoding='utf-8'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.maptbx.mem.show_map_stat" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </section>