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<h1>Source code for MMTK.XML</h1><div class="highlight"><pre>
<span class="c"># XML I/O</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">XML format for describing molecular systems</span>
<span class="sd">Note: this format is not used by any other program at the moment. It should</span>
<span class="sd">be considered experimental and subject to change.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">import</span> <span class="nn">MMTK</span>
<span class="kn">from</span> <span class="nn">MMTK.MoleculeFactory</span> <span class="kn">import</span> <span class="n">MoleculeFactory</span>
<span class="kn">from</span> <span class="nn">xml.etree.ElementTree</span> <span class="kn">import</span> <span class="n">iterparse</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<div class="viewcode-block" id="XMLMoleculeFactory"><a class="viewcode-back" href="../../modules.html#MMTK.XML.XMLMoleculeFactory">[docs]</a><span class="k">class</span> <span class="nc">XMLMoleculeFactory</span><span class="p">(</span><span class="n">MoleculeFactory</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> XML molecule factory</span>
<span class="sd"> </span>
<span class="sd"> An XML molecule factory reads an XML specification of a molecular</span>
<span class="sd"> system and builds the molecule objects and universe described</span>
<span class="sd"> therein. The universe can be obtained through the attribute</span>
<span class="sd"> *universe*.</span>
<span class="sd"> </span>
<span class="sd"> :param file: the name of an XML file, or a file object</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
<span class="n">MoleculeFactory</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">for</span> <span class="n">event</span><span class="p">,</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">iterparse</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
<span class="n">tag</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">tag</span>
<span class="n">ob_id</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'id'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">tag</span> <span class="o">==</span> <span class="s">'molecule'</span> <span class="ow">and</span> <span class="n">ob_id</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeGroup</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="n">element</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">tag</span> <span class="o">==</span> <span class="s">'templates'</span><span class="p">:</span>
<span class="n">element</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">tag</span> <span class="o">==</span> <span class="s">'universe'</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeUniverse</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">makeGroup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
<span class="n">group</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'id'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">createGroup</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
<span class="k">for</span> <span class="n">molecule_element</span> <span class="ow">in</span> <span class="n">element</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">'molecule'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addSubgroup</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="n">molecule_element</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'title'</span><span class="p">,</span> <span class="s">''</span><span class="p">),</span>
<span class="n">molecule_element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'ref'</span><span class="p">])</span>
<span class="n">atom_array</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s">'atomArray'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">atom_array</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom_element</span> <span class="ow">in</span> <span class="n">atom_array</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addAtom</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="n">atom_element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'title'</span><span class="p">],</span>
<span class="n">atom_element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'elementType'</span><span class="p">])</span>
<span class="n">bond_array</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s">'bondArray'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">bond_array</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">for</span> <span class="n">bond_element</span> <span class="ow">in</span> <span class="n">bond_array</span><span class="p">:</span>
<span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span> <span class="o">=</span> <span class="n">bond_element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'atomRefs2'</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">atom1</span> <span class="o">=</span> <span class="s">'.'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">atom1</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">':'</span><span class="p">))</span>
<span class="n">atom2</span> <span class="o">=</span> <span class="s">'.'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">atom2</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">':'</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addBond</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">makeUniverse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
<span class="n">topology</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'topology'</span><span class="p">,</span> <span class="s">'infinite'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">topology</span> <span class="o">==</span> <span class="s">'infinite'</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">topology</span> <span class="o">==</span> <span class="s">'periodic3d'</span><span class="p">:</span>
<span class="n">cellshape</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'cellshape'</span><span class="p">]</span>
<span class="k">if</span> <span class="n">cellshape</span> <span class="o">==</span> <span class="s">'orthorhombic'</span><span class="p">:</span>
<span class="n">cellsize</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'cellsize'</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">units</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'units'</span><span class="p">,</span> <span class="s">'units:nm'</span><span class="p">)</span>
<span class="n">factor</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">MMTK</span><span class="o">.</span><span class="n">Units</span><span class="p">,</span> <span class="n">units</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">':'</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">OrthorhombicPeriodicUniverse</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span>
<span class="p">[</span><span class="n">factor</span><span class="o">*</span><span class="nb">float</span><span class="p">(</span><span class="n">size</span><span class="p">)</span> <span class="k">for</span> <span class="n">size</span> <span class="ow">in</span> <span class="n">cellsize</span><span class="p">]))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"cell shape </span><span class="si">%s</span><span class="s"> not implemented"</span> <span class="o">%</span> <span class="n">cellshape</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"topology </span><span class="si">%s</span><span class="s"> not implemented"</span> <span class="o">%</span> <span class="n">topology</span><span class="p">)</span>
<span class="n">atom_index</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">subelement</span> <span class="ow">in</span> <span class="n">element</span><span class="p">:</span>
<span class="k">if</span> <span class="n">subelement</span><span class="o">.</span><span class="n">tag</span> <span class="o">==</span> <span class="s">'molecule'</span><span class="p">:</span>
<span class="n">molecule</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">retrieveMolecule</span><span class="p">(</span><span class="n">subelement</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'ref'</span><span class="p">])</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">molecule</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">atom</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">atom_index</span>
<span class="n">atom_index</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">molecule</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">subelement</span><span class="o">.</span><span class="n">tag</span> <span class="o">==</span> <span class="s">'atom'</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">Atom</span><span class="p">(</span><span class="n">subelement</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'elementType'</span><span class="p">])</span>
<span class="n">atom</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">atom_index</span>
<span class="n">atom_index</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="n">configuration</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">configuration</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s">'atomArray'</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">array</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'x3'</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
<span class="n">y</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">array</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'y3'</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
<span class="n">z</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">array</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s">'z3'</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
<span class="n">units</span> <span class="o">=</span> <span class="n">array</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'units'</span><span class="p">,</span> <span class="s">'units:nm'</span><span class="p">)</span>
<span class="n">factor</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">MMTK</span><span class="o">.</span><span class="n">Units</span><span class="p">,</span> <span class="n">units</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">':'</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span>
<span class="n">array</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span>
<span class="n">array</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span>
<span class="n">array</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span>
<span class="n">N</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">array</span><span class="p">,</span> <span class="n">factor</span><span class="p">,</span> <span class="n">array</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span></div>
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