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<div class="section" id="assembling-a-trajectory-step-by-step">
<h1>Assembling a trajectory step by step<a class="headerlink" href="#assembling-a-trajectory-step-by-step" 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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30</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># "Manual" creation of a trajectory using the snapshot generator.</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.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">SnapshotGenerator</span><span class="p">,</span> <span class="n">TrajectoryOutput</span>
<span class="c"># Construct system</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">universe</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s">'bala1'</span><span class="p">)</span>
<span class="c"># Transformation to be applied between the steps</span>
<span class="n">transformation</span> <span class="o">=</span> <span class="n">Rotation</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">1.</span><span class="p">),</span> <span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="c"># Create trajectory</span>
<span class="n">trajectory</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.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span> <span class="s">"A rotating molecule"</span><span class="p">)</span>
<span class="c"># Create the snapshot generator</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">trajectory</span><span class="p">,</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"># Perform rotations and write the configurations</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">20</span><span class="p">):</span>
<span class="n">universe</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">applyTransformation</span><span class="p">(</span><span class="n">transformation</span><span class="p">)</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="c"># Close trajectory</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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