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<div class="section" id="extract-a-c-alpha-trajectory-from-an-all-atom-trajectory">
<h1>Extract a C-alpha trajectory from an all-atom trajectory<a class="headerlink" href="#extract-a-c-alpha-trajectory-from-an-all-atom-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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86</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># This program reads a trajecory containing one or more proteins</span>
<span class="c"># and extracts a trajectory for a C-alpha model, which it stores in</span>
<span class="c"># a new trajectory. This trajectory is smaller and easier to analyze</span>
<span class="c"># or visualize. Moreover, the global (rigid-body) motion of the</span>
<span class="c"># protein(s) is eliminated from the trajectory.</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="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span><span class="p">,</span> <span class="n">PeptideChain</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="c"># Open the input trajectory.</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">'full_trajectory.nc'</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"># Choose all objects of class "Protein"</span>
<span class="n">proteins</span> <span class="o">=</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="c"># Construct an initial configuration in which the proteins are contiguous.</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">contiguousObjectConfiguration</span><span class="p">(</span><span class="n">proteins</span><span class="p">)</span>
<span class="c"># Construct a C_alpha representation and a mapping from the "real"</span>
<span class="c"># C_alpha atoms to their counterparts in the reduced model.</span>
<span class="n">universe_calpha</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">index</span> <span class="o">=</span> <span class="mi">0</span>
<span class="nb">map</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">:</span>
<span class="n">chains_calpha</span> <span class="o">=</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="n">chains_calpha</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">PeptideChain</span><span class="p">(</span><span class="n">chain</span><span class="o">.</span><span class="n">sequence</span><span class="p">(),</span>
<span class="n">model</span><span class="o">=</span><span class="s">'calpha'</span><span class="p">))</span>
<span class="n">protein_calpha</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">chains_calpha</span><span class="p">)</span>
<span class="n">universe_calpha</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">protein_calpha</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="nb">len</span><span class="p">(</span><span class="n">protein</span><span class="p">)):</span>
<span class="n">chain</span> <span class="o">=</span> <span class="n">protein</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">chain_calpha</span> <span class="o">=</span> <span class="n">protein_calpha</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">chain</span><span class="p">)):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">conf</span><span class="p">[</span><span class="n">chain</span><span class="p">[</span><span class="n">j</span><span class="p">]</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="n">chain_calpha</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
<span class="n">chain_calpha</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">index</span>
<span class="nb">map</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">chain</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">index</span> <span class="o">=</span> <span class="n">index</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">universe_calpha</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="c"># Open the new trajectory for just the interesting objects.</span>
<span class="n">trajectory_calpha</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe_calpha</span><span class="p">,</span> <span class="s">'calpha_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_calpha</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_calpha</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, eliminate rigid-body motion with reference to</span>
<span class="c"># the initial configuration, and save the configurations to the new</span>
<span class="c"># trajectory.</span>
<span class="n">first</span> <span class="o">=</span> <span class="mi">1</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">conf</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">contiguousObjectConfiguration</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span>
<span class="n">step</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">])</span>
<span class="n">conf_calpha</span> <span class="o">=</span> <span class="n">Configuration</span><span class="p">(</span><span class="n">universe_calpha</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">take</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="nb">map</span><span class="p">),</span>
<span class="bp">None</span><span class="p">)</span>
<span class="n">universe_calpha</span><span class="o">.</span><span class="n">setConfiguration</span><span class="p">(</span><span class="n">conf_calpha</span><span class="p">)</span>
<span class="k">if</span> <span class="n">first</span><span class="p">:</span>
<span class="n">initial_conf_calpha</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="n">conf_calpha</span><span class="p">)</span>
<span class="n">first</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">tr</span><span class="p">,</span> <span class="n">rms</span> <span class="o">=</span> <span class="n">universe_calpha</span><span class="o">.</span><span class="n">findTransformation</span><span class="p">(</span><span class="n">initial_conf_calpha</span><span class="p">)</span>
<span class="n">universe_calpha</span><span class="o">.</span><span class="n">applyTransformation</span><span class="p">(</span><span class="n">tr</span><span class="p">)</span>
<span class="k">del</span> <span class="n">step</span><span class="p">[</span><span class="s">'step'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">step</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">del</span> <span class="n">step</span><span class="p">[</span><span class="s">'box_size'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> <span class="k">pass</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">del</span> <span class="n">step</span><span class="p">[</span><span class="s">'velocities'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> <span class="k">pass</span>
<span class="n">snapshot</span><span class="p">(</span><span class="n">data</span> <span class="o">=</span> <span class="n">step</span><span class="p">)</span>
<span class="c"># Close both trajectories.</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">trajectory_calpha</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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