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  <div class="section" id="calculating-atomic-fluctuations-from-a-trajectory">
<h1>Calculating atomic fluctuations from a trajectory<a class="headerlink" href="#calculating-atomic-fluctuations-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"># Calculate atomic fluctuations from a trajectory.</span>
<span class="c">#</span>
<span class="c"># The trajectory file contains a protein. The fluctuations are calculated</span>
<span class="c"># for all atoms, and then the average over the C-alpha atoms is determined.</span>
<span class="c"># Note that calculating the fluctuations for only the C-alpha atoms is</span>
<span class="c"># more complicated and no faster.</span>
<span class="c">#</span>
<span class="c"># This example illustrates:</span>
<span class="c"># 1) Reading trajectory files</span>
<span class="c"># 2) Selecting parts of a system</span>
<span class="c"># 3) Calculating trajectory averages</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="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span>

<span class="c"># Open the trajectory, use every tenth step</span>
<span class="n">trajectory</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">&#39;lysozyme.nc&#39;</span><span class="p">)[::</span><span class="mi">10</span><span class="p">]</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">universe</span>

<span class="c"># Calculate the average conformation</span>
<span class="n">average</span> <span class="o">=</span> <span class="n">ParticleVector</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="k">for</span> <span class="n">step</span> <span class="ow">in</span> <span class="n">trajectory</span><span class="p">:</span>
    <span class="n">average</span> <span class="o">+=</span> <span class="n">step</span><span class="p">[</span><span class="s">&#39;configuration&#39;</span><span class="p">]</span>
<span class="n">average</span> <span class="o">/=</span> <span class="nb">len</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span>

<span class="c"># Calculate the fluctiations for all atoms</span>
<span class="n">fluctuations</span> <span class="o">=</span> <span class="n">ParticleScalar</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="k">for</span> <span class="n">step</span> <span class="ow">in</span> <span class="n">trajectory</span><span class="p">:</span>
    <span class="n">d</span> <span class="o">=</span> <span class="n">step</span><span class="p">[</span><span class="s">&#39;configuration&#39;</span><span class="p">]</span><span class="o">-</span><span class="n">average</span>
    <span class="n">fluctuations</span> <span class="o">+=</span> <span class="n">d</span><span class="o">*</span><span class="n">d</span>
<span class="n">fluctuations</span> <span class="o">/=</span> <span class="nb">len</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span>

<span class="c"># Collect the C-alpha atoms</span>
<span class="n">calphas</span> <span class="o">=</span> <span class="n">Collection</span><span class="p">()</span>
<span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">universe</span><span class="o">.</span><span class="n">objectList</span><span class="p">(</span><span class="n">Protein</span><span class="p">):</span>
    <span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">protein</span><span class="p">:</span>
        <span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">chain</span><span class="p">:</span>
            <span class="n">calphas</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">residue</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">)</span>

<span class="c"># Average over the C-alpha atoms</span>
<span class="n">calpha_mask</span> <span class="o">=</span> <span class="n">calphas</span><span class="o">.</span><span class="n">booleanMask</span><span class="p">()</span>
<span class="k">print</span> <span class="p">(</span><span class="n">fluctuations</span><span class="o">*</span><span class="n">calpha_mask</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span><span class="o">/</span><span class="n">calphas</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
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