htdocs update

cctbx/cctbx.geometry_restraints.manager.html

@@ -518,7 +518,7 @@ <h3>Navigation</h3>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="cctbx.geometry_restraints.manager.manager.write_geo_file">
-<span class="sig-name descname"><span class="pre">write_geo_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sites_cart=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_labels=None</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">file_descriptor=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">header='#</span> <span class="pre">Geometry</span> <span class="pre">restraints\n'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.geometry_restraints.manager.manager.write_geo_file" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">write_geo_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sites_cart=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_labels=None</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">file_descriptor=&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">header='#</span> <span class="pre">Geometry</span> <span class="pre">restraints\n'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cctbx.geometry_restraints.manager.manager.write_geo_file" title="Link to this definition">¶</a></dt>
 <dd><p>Define this if you want the .geo file</p>
 </dd></dl>
 

iotbx/iotbx.file_reader.html

@@ -275,7 +275,7 @@ <h1>iotbx.file_reader - generic file input<a class="headerlink" href="#iotbx-fil
 
 <dl class="py method">
 <dt class="sig sig-object py" id="iotbx.file_reader.any_file_input.show_summary">
-<span class="sig-name descname"><span class="pre">show_summary</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><span class="sig-paren">)</span><a class="headerlink" href="#iotbx.file_reader.any_file_input.show_summary" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">show_summary</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><span class="sig-paren">)</span><a class="headerlink" href="#iotbx.file_reader.any_file_input.show_summary" title="Link to this definition">¶</a></dt>
 <dd><p>Print out some basic information about the file.</p>
 </dd></dl>
 

mmtbx/mmtbx.command_line.html

@@ -109,13 +109,13 @@ <h1>mmtbx.command_line package<a class="headerlink" href="#mmtbx-command-line-pa
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.command_line.load_and_validate_unmerged_data">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.command_line.</span></span><span class="sig-name descname"><span class="pre">load_and_validate_unmerged_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f_obs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_labels</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.command_line.load_and_validate_unmerged_data" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.command_line.</span></span><span class="sig-name descname"><span class="pre">load_and_validate_unmerged_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f_obs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_labels</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.command_line.load_and_validate_unmerged_data" title="Link to this definition">¶</a></dt>
 <dd><p>Read in (and verify) unmerged intensities, e.g. from scalepack or XDS.</p>
 </dd></dl>
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.command_line.load_model_and_data">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.command_line.</span></span><span class="sig-name descname"><span class="pre">load_model_and_data</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">master_phil</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>, <em class="sig-param"><span class="n"><span class="pre">process_pdb_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">require_data=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_fmodel=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefer_anomalous=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_non_anomalous=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">set_wavelength_from_model_header=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">set_inelastic_form_factors=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usage_string=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_log_buffer=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_unknown_scatterers=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">generate_input_phil=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.command_line.load_model_and_data" 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.command_line.</span></span><span class="sig-name descname"><span class="pre">load_model_and_data</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">master_phil</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>, <em class="sig-param"><span class="n"><span class="pre">process_pdb_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">require_data=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_fmodel=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefer_anomalous=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_non_anomalous=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">set_wavelength_from_model_header=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">set_inelastic_form_factors=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usage_string=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_log_buffer=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_unknown_scatterers=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">generate_input_phil=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.command_line.load_model_and_data" 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>
 <p>Class for processing command-line input and creating necessary objects.
 The master_phil object should include cmdline_input_phil_str above, plus

mmtbx/mmtbx.geometry_restraints.html

@@ -116,7 +116,7 @@ <h2>mmtbx.geometry_restraints.hbond module<a class="headerlink" href="#mmtbx-geo
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.geometry_restraints.ramachandran.ramachandran_manager">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.geometry_restraints.ramachandran.</span></span><span class="sig-name descname"><span class="pre">ramachandran_manager</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">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>, <em class="sig-param"><span class="n"><span class="pre">proxies=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tables=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialize=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.geometry_restraints.ramachandran.ramachandran_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.geometry_restraints.ramachandran.</span></span><span class="sig-name descname"><span class="pre">ramachandran_manager</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">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>, <em class="sig-param"><span class="n"><span class="pre">proxies=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tables=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialize=True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.geometry_restraints.ramachandran.ramachandran_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.geometry_restraints.ramachandran.ramachandran_manager.append_emsley8k_proxies">

mmtbx/mmtbx.maps.html

@@ -665,7 +665,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.maps.compute_map_coefficients">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.maps.</span></span><span class="sig-name descname"><span class="pre">compute_map_coefficients</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">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtz_dataset=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">post_processing_callback=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy=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.maps.compute_map_coefficients" 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.maps.</span></span><span class="sig-name descname"><span class="pre">compute_map_coefficients</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">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mtz_dataset=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">post_processing_callback=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_hierarchy=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.maps.compute_map_coefficients" 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.maps.compute_map_coefficients.write_mtz_file">