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<div class="section" id="importing-a-trajectory-in-dcd-format">
<h1>Importing a trajectory in DCD format<a class="headerlink" href="#importing-a-trajectory-in-dcd-format" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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33</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Conversion of a DCD trajectory (CHARMM/XPlor) to MMTK's trajectory format.</span>
<span class="c">#</span>
<span class="c"># Note: In order to create the files "rotation.dcd" and "rotation.pdb" which</span>
<span class="c"># are read by this example, you must run the example dcd_export.py.</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span>
<span class="kn">from</span> <span class="nn">MMTK.PDB</span> <span class="kn">import</span> <span class="n">PDBConfiguration</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">TrajectoryOutput</span>
<span class="kn">from</span> <span class="nn">MMTK.DCD</span> <span class="kn">import</span> <span class="n">DCDReader</span>
<span class="c"># Create the universe.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="c"># Create all objects from the PDB file. The PDB file *must* match the</span>
<span class="c"># the DCD file (same atom order), and you *must* create all objects</span>
<span class="c"># defined in the PDB file, otherwise interpretation of the DCD file</span>
<span class="c"># is not possible.</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">PDBConfiguration</span><span class="p">(</span><span class="s">'rotation.pdb'</span><span class="p">)</span>
<span class="n">chain</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">peptide_chains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">createPeptideChain</span><span class="p">(</span><span class="n">c_terminus</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">Protein</span><span class="p">([</span><span class="n">chain</span><span class="p">]))</span>
<span class="c"># Create the trajectory object for output.</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">"rotation_from_dcd.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span> <span class="s">"Converted from DCD"</span><span class="p">)</span>
<span class="c"># Create a DCD reader that reads all configurations.</span>
<span class="n">dcd_reader</span> <span class="o">=</span> <span class="n">DCDReader</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">dcd_file</span> <span class="o">=</span> <span class="s">'rotation.dcd'</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TrajectoryOutput</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">)])</span>
<span class="c"># Run the reader...</span>
<span class="n">dcd_reader</span><span class="p">()</span>
<span class="c"># ... and close the output trajectory.</span>
<span class="n">t</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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