htdocs update

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;_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>
+<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>
 <dd></dd></dl>
 
 </section>

mmtbx/mmtbx.disorder.html

@@ -207,7 +207,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.disordered_segment.show">
-<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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="#mmtbx.disorder.analyze_model.disordered_segment.show" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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="#mmtbx.disorder.analyze_model.disordered_segment.show" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -233,7 +233,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.process_pdb_hierarchy">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.disorder.analyze_model.</span></span><span class="sig-name descname"><span class="pre">process_pdb_hierarchy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_inconsistent_occupancy=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&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="#mmtbx.disorder.analyze_model.process_pdb_hierarchy" title="Link 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">mmtbx.disorder.analyze_model.</span></span><span class="sig-name descname"><span class="pre">process_pdb_hierarchy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_inconsistent_occupancy=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.analyze_model.process_pdb_hierarchy" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_distance_between_conformers">
@@ -252,18 +252,18 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.process_pdb_hierarchy.show">
-<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.analyze_model.process_pdb_hierarchy.show" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.analyze_model.process_pdb_hierarchy.show" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.process_residue_groups">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.disorder.analyze_model.</span></span><span class="sig-name descname"><span class="pre">process_residue_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multi_criterion_validation=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_inconsistent_occupancy=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&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="#mmtbx.disorder.analyze_model.process_residue_groups" title="Link 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">mmtbx.disorder.analyze_model.</span></span><span class="sig-name descname"><span class="pre">process_residue_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multi_criterion_validation=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_inconsistent_occupancy=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.analyze_model.process_residue_groups" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.disorder.analyze_model.process_residue_groups.show">
-<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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="#mmtbx.disorder.analyze_model.process_residue_groups.show" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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="#mmtbx.disorder.analyze_model.process_residue_groups.show" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -336,7 +336,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.disorder.backbone.backrub_residue.show">
-<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><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>, <em class="sig-param"><span class="n"><span class="pre">prefix=''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.backbone.backrub_residue.show" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix=''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.disorder.backbone.backrub_residue.show" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py attribute">

mmtbx/mmtbx.scaling.html

@@ -1794,7 +1794,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <p>Main program driver for Xtriage.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.scaling.xtriage.change_symmetry">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.scaling.xtriage.</span></span><span class="sig-name descname"><span class="pre">change_symmetry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">space_group_symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&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="#mmtbx.scaling.xtriage.change_symmetry" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.scaling.xtriage.</span></span><span class="sig-name descname"><span class="pre">change_symmetry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">space_group_symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.scaling.xtriage.change_symmetry" title="Link to this definition">¶</a></dt>
 <dd><p>Encapsulates all operations required to convert the original data to a
 different symmetry as suggested by Xtriage.</p>
 </dd></dl>

mmtbx/mmtbx.solvent.html

@@ -117,7 +117,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <span id="mmtbx-solvent-ordered-solvent-module"></span><h2>mmtbx.solvent.ordered_solvent module<a class="headerlink" href="#module-mmtbx.solvent.ordered_solvent" title="Link to this heading">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.solvent.ordered_solvent.manager">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.solvent.ordered_solvent.</span></span><span class="sig-name descname"><span class="pre">manager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_neutron_scat_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params=&lt;libtbx.phil.scope_extract</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_peaks_params=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&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="#mmtbx.solvent.ordered_solvent.manager" title="Link 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">mmtbx.solvent.ordered_solvent.</span></span><span class="sig-name descname"><span class="pre">manager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmodels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_neutron_scat_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params=&lt;libtbx.phil.scope_extract</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_peaks_params=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.solvent.ordered_solvent.manager" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.solvent.ordered_solvent.manager.refine_adp">