htdocs update (master)

Author: DiamondLightSource-build-server

_modules/dxtbx/model/crystal.html

@@ -45,6 +45,7 @@
   <h1>Source code for dxtbx.model.crystal</h1><div class="highlight"><pre>
 <span></span><span class="kn">from</span><span class="w"> </span><span class="nn">__future__</span><span class="w"> </span><span class="kn">import</span> <span class="n">annotations</span>
 
+<span class="kn">import</span><span class="w"> </span><span class="nn">iotbx.phil</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">cctbx.sgtbx</span><span class="w"> </span><span class="kn">import</span> <span class="n">space_group</span> <span class="k">as</span> <span class="n">SG</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">scitbx</span><span class="w"> </span><span class="kn">import</span> <span class="n">matrix</span>
 
@@ -61,6 +62,25 @@ <h1>Source code for dxtbx.model.crystal</h1><div class="highlight"><pre>
         <span class="n">MosaicCrystalSauter2014</span><span class="p">,</span>
     <span class="p">)</span>
 
+<span class="n">crystal_phil_scope</span> <span class="o">=</span> <span class="n">iotbx</span><span class="o">.</span><span class="n">phil</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">  crystal</span>
+<span class="sd">    .expert_level = 1</span>
+<span class="sd">    .short_caption = &quot;Crystal overrides&quot;</span>
+<span class="sd">  {</span>
+<span class="sd">    unit_cell = None</span>
+<span class="sd">      .type = unit_cell</span>
+
+<span class="sd">    A_matrix = None</span>
+<span class="sd">      .type = floats(size=9)</span>
+<span class="sd">      .help = &quot;The crystal setting A=UB matrix. If set, this will override the unit cell.&quot;</span>
+
+<span class="sd">    space_group = None</span>
+<span class="sd">      .type = space_group</span>
+<span class="sd">  }</span>
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="p">)</span>
+
 
 <div class="viewcode-block" id="CrystalFactory">
 <a class="viewcode-back" href="../../../documentation/library_reference/dxtbx/crystal.html#dxtbx.model.crystal.CrystalFactory">[docs]</a>
@@ -178,6 +198,41 @@ <h1>Source code for dxtbx.model.crystal</h1><div class="highlight"><pre>
         <span class="n">_c</span> <span class="o">=</span> <span class="n">rotate_mosflm_to_imgCIF</span> <span class="o">*</span> <span class="n">c</span>
 
         <span class="k">return</span> <span class="n">Crystal</span><span class="p">(</span><span class="n">_a</span><span class="p">,</span> <span class="n">_b</span><span class="p">,</span> <span class="n">_c</span><span class="p">,</span> <span class="n">space_group</span><span class="o">=</span><span class="n">space_group</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="CrystalFactory.from_phil">
+<a class="viewcode-back" href="../../../documentation/library_reference/dxtbx/crystal.html#dxtbx.model.crystal.CrystalFactory.from_phil">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">from_phil</span><span class="p">(</span>
+        <span class="n">params</span><span class="p">:</span> <span class="n">iotbx</span><span class="o">.</span><span class="n">phil</span><span class="o">.</span><span class="n">scope_extract</span><span class="p">,</span>
+        <span class="n">reference</span><span class="p">:</span> <span class="n">Crystal</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Crystal</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Convert the phil parameters into a crystal model</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">all_params</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">unit_cell</span><span class="p">,</span>
+            <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">A_matrix</span><span class="p">,</span>
+            <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">space_group</span><span class="p">,</span>
+        <span class="p">]</span>
+        <span class="k">if</span> <span class="n">all_params</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">all_params</span><span class="p">):</span>
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">reference</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">crystal</span> <span class="o">=</span> <span class="n">Crystal</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span> <span class="s2">&quot;P1&quot;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">crystal</span> <span class="o">=</span> <span class="n">reference</span>
+            <span class="n">crystal</span><span class="o">.</span><span class="n">reset_scan_points</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">unit_cell</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">crystal</span><span class="o">.</span><span class="n">set_unit_cell</span><span class="p">(</span><span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">unit_cell</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">A_matrix</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">crystal</span><span class="o">.</span><span class="n">set_A</span><span class="p">(</span><span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">A_matrix</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">space_group</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">crystal</span><span class="o">.</span><span class="n">set_space_group</span><span class="p">(</span><span class="n">params</span><span class="o">.</span><span class="n">crystal</span><span class="o">.</span><span class="n">space_group</span><span class="o">.</span><span class="n">group</span><span class="p">())</span>
+
+        <span class="k">return</span> <span class="n">crystal</span></div>
 </div>
 
 </pre></div>

documentation/library_reference/dxtbx/crystal.html

@@ -420,6 +420,12 @@ <h1>dxtbx.model.crystal<a class="headerlink" href="#dxtbx-model-crystal" title="
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="dxtbx.model.crystal.CrystalFactory.from_phil">
+<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_phil</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">iotbx.phil.scope_extract</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#dxtbx.model.Crystal" title="dxtbx.model.Crystal"><span class="pre">Crystal</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.13)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#dxtbx.model.Crystal" title="dxtbx.model.Crystal"><span class="pre">Crystal</span></a></span></span><a class="reference internal" href="../../../_modules/dxtbx/model/crystal.html#CrystalFactory.from_phil"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#dxtbx.model.crystal.CrystalFactory.from_phil" title="Link to this definition">¶</a></dt>
+<dd><p>Convert the phil parameters into a crystal model</p>
+</dd></dl>
+
 </dd></dl>
 
 </section>

genindex.html

@@ -1506,6 +1506,8 @@ <h2 id="F">F</h2>
 
       <ul>
         <li><a href="documentation/library_reference/dxtbx/beam.html#dxtbx.model.beam.BeamFactory.from_phil">(dxtbx.model.beam.BeamFactory static method)</a>
+</li>
+        <li><a href="documentation/library_reference/dxtbx/crystal.html#dxtbx.model.crystal.CrystalFactory.from_phil">(dxtbx.model.crystal.CrystalFactory static method)</a>
 </li>
         <li><a href="documentation/library_reference/dxtbx/detector.html#dxtbx.model.detector.DetectorFactory.from_phil">(dxtbx.model.detector.DetectorFactory static method)</a>
 </li>