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<div class="section" id="extract-a-subset-from-a-trajectory">
<h1>Extract a subset from a trajectory<a class="headerlink" href="#extract-a-subset-from-a-trajectory" 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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44</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># This program reads a trajecory for a solvated protein and</span>
<span class="c"># extracts just the protein data, which it stores in a new</span>
<span class="c"># trajectory. This trajectory is smaller and easier to analyze</span>
<span class="c"># or visualize.</span>
<span class="c">#</span>
<span class="c"># Note: You cannot run this example without having a suitable</span>
<span class="c"># trajectory file, whose name you should put in place of</span>
<span class="c"># "full_trajectory.nc" below.</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.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">TrajectoryOutput</span><span class="p">,</span> <span class="n">SnapshotGenerator</span>
<span class="c"># Open the input trajectory.</span>
<span class="n">full</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'full_trajectory.nc'</span><span class="p">)</span>
<span class="c"># Collect the items you want to keep. Here we keep everything but</span>
<span class="c"># water molecules.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">full</span><span class="o">.</span><span class="n">universe</span>
<span class="n">keep</span> <span class="o">=</span> <span class="n">Collection</span><span class="p">()</span>
<span class="k">for</span> <span class="nb">object</span> <span class="ow">in</span> <span class="n">universe</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">is_water</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'water'</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">is_water</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">is_water</span><span class="p">:</span>
<span class="n">keep</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="c"># Open the new trajectory for just the interesting objects.</span>
<span class="n">subset</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">keep</span><span class="p">,</span> <span class="s">'subset_trajectory.nc'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="c"># Make a snapshot generator for saving.</span>
<span class="n">snapshot</span> <span class="o">=</span> <span class="n">SnapshotGenerator</span><span class="p">(</span><span class="n">universe</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">subset</span><span class="p">,</span> <span class="bp">None</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"># Loop over all steps and save them to the new trajectory.</span>
<span class="k">for</span> <span class="n">configuration</span> <span class="ow">in</span> <span class="n">full</span><span class="o">.</span><span class="n">configuration</span><span class="p">:</span>
<span class="n">universe</span><span class="o">.</span><span class="n">setConfiguration</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="c"># Close both trajectories.</span>
<span class="n">full</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">subset</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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