htdocs update

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>

mmtbx/mmtbx.maps.html

@@ -118,7 +118,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.maps.composite_omit_map.omit_box.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.maps.composite_omit_map.omit_box.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.maps.composite_omit_map.omit_box.show" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -193,14 +193,14 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="mmtbx.maps.composite_omit_map.omit_regions.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.maps.composite_omit_map.omit_regions.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.maps.composite_omit_map.omit_regions.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.maps.composite_omit_map.run">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.maps.composite_omit_map.</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">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">crystal_gridding</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box_size_as_fraction=0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_boxes=2000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neutral_volume_box_cushion_width=2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_resolution_map=True</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.composite_omit_map.run" 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.composite_omit_map.</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">fmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">crystal_gridding</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box_size_as_fraction=0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_boxes=2000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neutral_volume_box_cushion_width=2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_resolution_map=True</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.composite_omit_map.run" 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="simple">
 <dt>Composite residual OMIT map. Details:</dt><dd><p>Afonine et al. (2014). FEM: Feature Enhanced Map</p>
@@ -465,7 +465,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <span id="mmtbx-maps-superpose-module"></span><h2>mmtbx.maps.superpose module<a class="headerlink" href="#module-mmtbx.maps.superpose" title="Link to this heading">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="mmtbx.maps.superpose.common_frame_of_reference">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.maps.superpose.</span></span><span class="sig-name descname"><span class="pre">common_frame_of_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_sites_cart</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsq_fits</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer=10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">move_to_frame_of_reference=True</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.superpose.common_frame_of_reference" 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.superpose.</span></span><span class="sig-name descname"><span class="pre">common_frame_of_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_sites_cart</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsq_fits</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer=10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">move_to_frame_of_reference=True</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.superpose.common_frame_of_reference" 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.superpose.common_frame_of_reference.apply_new_sites_to_hierarchies">
@@ -506,7 +506,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="mmtbx.maps.superpose.transform_map_by_lsq_fit">
-<span class="sig-prename descclassname"><span class="pre">mmtbx.maps.superpose.</span></span><span class="sig-name descname"><span class="pre">transform_map_by_lsq_fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fft_map</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit_cell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsq_fit_obj</span></span></em>, <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">d_min</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer=10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution_factor=0.25</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>, <em class="sig-param"><span class="n"><span class="pre">mask_map_grid=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format='xplor'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.maps.superpose.transform_map_by_lsq_fit" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mmtbx.maps.superpose.</span></span><span class="sig-name descname"><span class="pre">transform_map_by_lsq_fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fft_map</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit_cell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsq_fit_obj</span></span></em>, <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">d_min</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer=10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution_factor=0.25</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>, <em class="sig-param"><span class="n"><span class="pre">mask_map_grid=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format='xplor'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.maps.superpose.transform_map_by_lsq_fit" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py class">
@@ -553,7 +553,7 @@ <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.utils.fast_maps_from_hkl_file">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mmtbx.maps.utils.</span></span><span class="sig-name descname"><span class="pre">fast_maps_from_hkl_file</span></span><span class="sig-paren">(</span><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">xray_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scattering_table='wk1995'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_label=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_free_label=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_out=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">auto_run=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quiet=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anomalous_map=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fill_maps=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_fmodel=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">llg_map=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assume_pdb_data=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.maps.utils.fast_maps_from_hkl_file" 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.utils.</span></span><span class="sig-name descname"><span class="pre">fast_maps_from_hkl_file</span></span><span class="sig-paren">(</span><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">xray_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scattering_table='wk1995'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_label=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_free_label=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_out=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">auto_run=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quiet=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anomalous_map=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fill_maps=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_fmodel=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">llg_map=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assume_pdb_data=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#mmtbx.maps.utils.fast_maps_from_hkl_file" 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>Automation wrapper for calculating standard 2mFo-DFc, mFo-DFc, and optional
 anomalous difference map coefficients, starting from an X-ray structure and