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<h1>Source code for MMTK.DCD</h1><div class="highlight"><pre>
<span class="c"># This module implements a DCD reader/writer</span>
<span class="c">#</span>
<span class="c"># Written by Lutz Ehrlich</span>
<span class="c"># Adapted to MMTK conventions by Konrad Hinsen</span>
<span class="sd">"""</span>
<span class="sd">Reading and writing of DCD trajectory files</span>
<span class="sd">The DCD format for trajectories is used by CHARMM, X-Plor,</span>
<span class="sd">and NAMD. It can be read by various visualization programs.</span>
<span class="sd">The DCD format is defined as a binary (unformatted) Fortran</span>
<span class="sd">format and is therefore platform-dependent.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">import</span> <span class="nn">MMTK_DCD</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">PDB</span><span class="p">,</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">Units</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<div class="viewcode-block" id="DCDReader"><a class="viewcode-back" href="../../modules.html#MMTK.DCD.DCDReader">[docs]</a><span class="k">class</span> <span class="nc">DCDReader</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryGenerator</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reader for DCD trajectories (CHARMM/X-Plor/NAMD)</span>
<span class="sd"> A DCDReader reads a DCD trajectory and "plays back" the</span>
<span class="sd"> data as if it were generated directly by an integrator.</span>
<span class="sd"> The universe for which the DCD file is read must be</span>
<span class="sd"> perfectly compatible with the data in the file, including</span>
<span class="sd"> an identical internal atom numbering. This can be guaranteed</span>
<span class="sd"> only if the universe was created from a PDB file that is</span>
<span class="sd"> compatible with the DCD file without leaving out any</span>
<span class="sd"> part of the system.</span>
<span class="sd"> Reading is started by calling the reader object.</span>
<span class="sd"> The following data categories and variables are available for</span>
<span class="sd"> output:</span>
<span class="sd"> * category "time": time</span>
<span class="sd"> * category "configuration": configuration</span>
<span class="sd"> """</span>
<span class="n">default_options</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">available_data</span> <span class="o">=</span> <span class="p">[</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'time'</span><span class="p">]</span>
<span class="n">restart_data</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the information from the</span>
<span class="sd"> trajectory file is read</span>
<span class="sd"> :param options: keyword options</span>
<span class="sd"> :keyword dcd_file: the name of the DCD trajecory file to be read</span>
<span class="sd"> :keyword actions: a list of actions to be executed periodically</span>
<span class="sd"> (default is none)</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryGenerator</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setCallOptions</span><span class="p">(</span><span class="n">options</span><span class="p">)</span>
<span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">MMTK_DCD</span><span class="o">.</span><span class="n">readDCD</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="n">configuration</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">getActions</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'dcd_file'</span><span class="p">))</span>
</div>
<span class="k">def</span> <span class="nf">writeDCD</span><span class="p">(</span><span class="n">vector_list</span><span class="p">,</span> <span class="n">dcd_file_name</span><span class="p">,</span> <span class="n">factor</span><span class="p">,</span> <span class="n">atom_order</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
<span class="n">delta_t</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">conf_flag</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">vector_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">universe</span>
<span class="n">natoms</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">numberOfPoints</span><span class="p">()</span>
<span class="k">if</span> <span class="n">atom_order</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atom_order</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">arrayrange</span><span class="p">(</span><span class="n">natoms</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom_order</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">atom_order</span><span class="p">)</span>
<span class="n">i_start</span> <span class="o">=</span> <span class="mi">0</span> <span class="c"># always start at frame 0</span>
<span class="n">n_savc</span> <span class="o">=</span> <span class="mi">1</span> <span class="c"># save every frame</span>
<span class="n">fd</span> <span class="o">=</span> <span class="n">MMTK_DCD</span><span class="o">.</span><span class="n">writeOpenDCD</span><span class="p">(</span><span class="n">dcd_file_name</span><span class="p">,</span> <span class="n">natoms</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector_list</span><span class="p">),</span>
<span class="n">i_start</span><span class="p">,</span> <span class="n">n_savc</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">)</span>
<span class="k">for</span> <span class="n">vector</span> <span class="ow">in</span> <span class="n">vector_list</span><span class="p">:</span>
<span class="k">if</span> <span class="n">conf_flag</span><span class="p">:</span>
<span class="n">vector</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="bp">None</span><span class="p">,</span> <span class="n">vector</span><span class="p">)</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">factor</span><span class="o">*</span><span class="n">vector</span><span class="o">.</span><span class="n">array</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">take</span><span class="p">(</span><span class="n">array</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">atom_order</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">Float16</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">take</span><span class="p">(</span><span class="n">array</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">atom_order</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">Float16</span><span class="p">)</span>
<span class="n">z</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">take</span><span class="p">(</span><span class="n">array</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">atom_order</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">Float16</span><span class="p">)</span>
<span class="n">MMTK_DCD</span><span class="o">.</span><span class="n">writeDCDStep</span><span class="p">(</span><span class="n">fd</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">)</span>
<span class="n">MMTK_DCD</span><span class="o">.</span><span class="n">writeCloseDCD</span><span class="p">(</span><span class="n">fd</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">writePDB</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">pdb_file_name</span><span class="p">):</span>
<span class="n">offset</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">configuration</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="bp">None</span><span class="p">,</span>
<span class="n">configuration</span><span class="p">)</span>
<span class="n">pdb</span> <span class="o">=</span> <span class="n">PDB</span><span class="o">.</span><span class="n">PDBOutputFile</span><span class="p">(</span><span class="n">pdb_file_name</span><span class="p">,</span> <span class="s">'xplor'</span><span class="p">)</span>
<span class="n">pdb</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="n">pdb</span><span class="o">.</span><span class="n">atom_sequence</span>
<span class="n">pdb</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">sequence</span>
<div class="viewcode-block" id="writeDCDPDB"><a class="viewcode-back" href="../../modules.html#MMTK.DCD.writeDCDPDB">[docs]</a><span class="k">def</span> <span class="nf">writeDCDPDB</span><span class="p">(</span><span class="n">conf_list</span><span class="p">,</span> <span class="n">dcd_file_name</span><span class="p">,</span> <span class="n">pdb_file_name</span><span class="p">,</span> <span class="n">delta_t</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Write a sequence of configurations to a DCD file and generate</span>
<span class="sd"> a compatible PDB file.</span>
<span class="sd"> :param conf_list: the sequence of configurations</span>
<span class="sd"> :type conf_list: sequence of :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :param dcd_file_name: the name of the DCD file</span>
<span class="sd"> :type dcd_file_name: str</span>
<span class="sd"> :param pdb_file_name: the name of the PDB file</span>
<span class="sd"> :type pdb_file_name: str</span>
<span class="sd"> :param delta_t: the time step between two configurations</span>
<span class="sd"> :type delta_t: float</span>
<span class="sd"> """</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">conf_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">universe</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="n">writePDB</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pdb_file_name</span><span class="p">)</span>
<span class="n">indices</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">sequence</span><span class="p">)</span>
<span class="n">writeDCD</span><span class="p">(</span><span class="n">conf_list</span><span class="p">,</span> <span class="n">dcd_file_name</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">Ang</span><span class="p">,</span> <span class="n">indices</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="writeVelocityDCDPDB"><a class="viewcode-back" href="../../modules.html#MMTK.DCD.writeVelocityDCDPDB">[docs]</a><span class="k">def</span> <span class="nf">writeVelocityDCDPDB</span><span class="p">(</span><span class="n">vel_list</span><span class="p">,</span> <span class="n">dcd_file_name</span><span class="p">,</span> <span class="n">pdb_file_name</span><span class="p">,</span> <span class="n">delta_t</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Write a sequence of velocity particle vectors to a DCD file and generate</span>
<span class="sd"> a compatible PDB file.</span>
<span class="sd"> :param vel_list: the sequence of velocity particle vectors</span>
<span class="sd"> :type vel_list: sequence of :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> :param dcd_file_name: the name of the DCD file</span>
<span class="sd"> :type dcd_file_name: str</span>
<span class="sd"> :param pdb_file_name: the name of the PDB file</span>
<span class="sd"> :type pdb_file_name: str</span>
<span class="sd"> :param delta_t: the time step between two velocity sets</span>
<span class="sd"> :type delta_t: float</span>
<span class="sd"> """</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">vel_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">universe</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="n">writePDB</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">(),</span> <span class="n">pdb_file_name</span><span class="p">)</span>
<span class="n">indices</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">sequence</span><span class="p">)</span>
<span class="n">writeDCD</span><span class="p">(</span><span class="n">vel_list</span><span class="p">,</span> <span class="n">dcd_file_name</span><span class="p">,</span> <span class="mf">1.</span><span class="o">/</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">akma_time</span><span class="p">),</span>
<span class="n">indices</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span></div>
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