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>

iotbx/iotbx.managers.html

@@ -803,7 +803,7 @@ <h3>Parameters:<a class="headerlink" href="#parameters" title="Link to this head
 
 <dl class="py method">
 <dt class="sig sig-object py" id="iotbx.map_manager.map_manager.set_log">
-<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_manager.map_manager.set_log" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_manager.map_manager.set_log" title="Link to this definition">¶</a></dt>
 <dd><p>Set output log file</p>
 </dd></dl>
 
@@ -1266,7 +1266,7 @@ <h3>Parameters:<a class="headerlink" href="#parameters" title="Link to this head
 
 <dl class="py function">
 <dt class="sig sig-object py" id="iotbx.map_model_manager.get_selections_and_boxes_to_split_model">
-<span class="sig-prename descclassname"><span class="pre">iotbx.map_model_manager.</span></span><span class="sig-name descname"><span class="pre">get_selections_and_boxes_to_split_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_id=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_model_manager=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selection_method='by_chain'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selection_list=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_waters=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_hetero=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_for_boxes=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box_cushion=3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">select_final_boxes_based_on_model=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_empty_boxes=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_around_unselected_atoms=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_all_maps_around_edges=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_radius=3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">masked_value=-10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_unique_set_for_boxes=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_id=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_points_outside_density=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimum_boxes_inside_density=25</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="#iotbx.map_model_manager.get_selections_and_boxes_to_split_model" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">iotbx.map_model_manager.</span></span><span class="sig-name descname"><span class="pre">get_selections_and_boxes_to_split_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_id=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_model_manager=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selection_method='by_chain'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selection_list=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_waters=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_hetero=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_for_boxes=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box_cushion=3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">select_final_boxes_based_on_model=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_empty_boxes=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_around_unselected_atoms=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_all_maps_around_edges=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_radius=3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">masked_value=-10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_unique_set_for_boxes=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_id=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_points_outside_density=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimum_boxes_inside_density=25</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="#iotbx.map_model_manager.get_selections_and_boxes_to_split_model" title="Link to this definition">¶</a></dt>
 <dd><p>Split up model into pieces using selection_method
 Choices are [‘by_chain’, ‘by_segment’,’all’, ‘boxes’]
 by_chain:  each chain is a selection
@@ -1346,7 +1346,7 @@ <h3>Parameters:<a class="headerlink" href="#parameters" title="Link to this head
 
 <dl class="py function">
 <dt class="sig sig-object py" id="iotbx.map_model_manager.get_tlso_group_info_from_model">
-<span class="sig-prename descclassname"><span class="pre">iotbx.map_model_manager.</span></span><span class="sig-name descname"><span class="pre">get_tlso_group_info_from_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nproc=1</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="#iotbx.map_model_manager.get_tlso_group_info_from_model" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">iotbx.map_model_manager.</span></span><span class="sig-name descname"><span class="pre">get_tlso_group_info_from_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nproc=1</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="#iotbx.map_model_manager.get_tlso_group_info_from_model" title="Link to this definition">¶</a></dt>
 <dd><p>Extract tlso_group_info from aniso records in model</p>
 </dd></dl>
 
@@ -2517,7 +2517,7 @@ <h3>Parameters:<a class="headerlink" href="#id1" title="Link to this heading">¶
 
 <dl class="py method">
 <dt class="sig sig-object py" id="iotbx.map_model_manager.map_model_manager.set_log">
-<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_model_manager.map_model_manager.set_log" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_model_manager.map_model_manager.set_log" title="Link to this definition">¶</a></dt>
 <dd><p>Set output log file</p>
 </dd></dl>
 
@@ -2716,7 +2716,7 @@ <h3>Parameters:<a class="headerlink" href="#id1" title="Link to this heading">¶
 
 <dl class="py method">
 <dt class="sig sig-object py" id="iotbx.map_model_manager.map_model_manager.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">log=&lt;colorama.ansitowin32.StreamWrapper</span> <span class="pre">object&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#iotbx.map_model_manager.map_model_manager.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">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="#iotbx.map_model_manager.map_model_manager.show_summary" title="Link to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
@@ -2999,7 +2999,7 @@ <h3>Parameters:<a class="headerlink" href="#id1" title="Link to this heading">¶
 
 <dl class="py method">
 <dt class="sig sig-object py" id="iotbx.map_model_manager.match_map_model_ncs.set_log">
-<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_model_manager.match_map_model_ncs.set_log" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">set_log</span></span><span class="sig-paren">(</span><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="#iotbx.map_model_manager.match_map_model_ncs.set_log" title="Link to this definition">¶</a></dt>
 <dd><p>Set output log file</p>
 </dd></dl>