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<h1>Source code for MMTK.Visualization</h1><div class="highlight"><pre>
<span class="c"># This module contains interfaces to external visualization programs</span>
<span class="c"># and a visualization base class</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Visualization of chemical objects, including animation</span>
<span class="sd">This module provides visualization of chemical objects and animated</span>
<span class="sd">visualization of normal modes and sequences of configurations, including</span>
<span class="sd">trajectories. Visualization depends on external visualization programs.</span>
<span class="sd">On Unix systems, these programs are defined by environment variables.</span>
<span class="sd">Under Windows NT, the system definitions for files with extension</span>
<span class="sd">"pdb" and "wrl" are used.</span>
<span class="sd">A viewer for PDB files can be defined by the environment variable</span>
<span class="sd">'PDBVIEWER'. For showing a PDB file, MMTK will execute a command</span>
<span class="sd">consisting of the value of this variable followed by a space</span>
<span class="sd">and the name of the PDB file.</span>
<span class="sd">A viewer for VRML files can be defined by the environment variable</span>
<span class="sd">'VRMLVIEWER'. For showing a VRML file, MMTK will execute a command</span>
<span class="sd">consisting of the value of this variable followed by a space</span>
<span class="sd">and the name of the VRML file.</span>
<span class="sd">Since there is no standard for launching viewers for animation,</span>
<span class="sd">MMTK supports only two programs: VMD and XMol. MMTK detects</span>
<span class="sd">these programs by inspecting the value of the environment variable</span>
<span class="sd">'PDBVIEWER'. This value must be the file name of the executable,</span>
<span class="sd">and must give "vmd" or "xmol" after stripping off an optional</span>
<span class="sd">directory specification.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Units</span><span class="p">,</span> <span class="n">Utility</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="kn">import</span> <span class="nn">subprocess</span><span class="o">,</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">tempfile</span><span class="o">,</span> <span class="nn">os</span>
<span class="c">#</span>
<span class="c"># If you want temporary files in a non-standard directory, make</span>
<span class="c"># its name the value of this variable:</span>
<span class="c">#</span>
<span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="c">#</span>
<span class="c"># Identify OS</span>
<span class="c">#</span>
<span class="n">running_on_windows</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span> <span class="o">==</span> <span class="s">'win32'</span>
<span class="n">running_on_macosx</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'darwin'</span><span class="p">)</span>
<span class="n">running_on_linux</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'linux'</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Get visualization program names</span>
<span class="c">#</span>
<span class="n">viewer</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pdbviewer</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s">'PDBVIEWER'</span><span class="p">]</span>
<span class="n">prog</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">pdbviewer</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">viewer</span><span class="p">[</span><span class="s">'pdb'</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">pdbviewer</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="n">vrmlviewer</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s">'VRMLVIEWER'</span><span class="p">]</span>
<span class="n">prog</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">vrmlviewer</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">viewer</span><span class="p">[</span><span class="s">'vrml'</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">vrmlviewer</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> <span class="k">pass</span>
<div class="viewcode-block" id="definePDBViewer"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.definePDBViewer">[docs]</a><span class="k">def</span> <span class="nf">definePDBViewer</span><span class="p">(</span><span class="n">progname</span><span class="p">,</span> <span class="n">exec_path</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Define the program used to view PDB files.</span>
<span class="sd"> :param progname: the canonical name of the PDB viewer. If it is</span>
<span class="sd"> a known one (one of "vmd", "xmol", "imol"),</span>
<span class="sd"> special features such as animation may be</span>
<span class="sd"> available.</span>
<span class="sd"> :type progname: str</span>
<span class="sd"> :param exec_path: the path to the executable program</span>
<span class="sd"> :type exec_path: str</span>
<span class="sd"> """</span>
<span class="n">viewer</span><span class="p">[</span><span class="s">'pdb'</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">progname</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span> <span class="n">exec_path</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="defineVRMLiewer"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.defineVRMLiewer">[docs]</a><span class="k">def</span> <span class="nf">defineVRMLiewer</span><span class="p">(</span><span class="n">progname</span><span class="p">,</span> <span class="n">exec_path</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Define the program used to view VRML files.</span>
<span class="sd"> :param progname: the canonical name of the VRML viewer</span>
<span class="sd"> :type progname: str</span>
<span class="sd"> :param exec_path: the path to the executable program</span>
<span class="sd"> :type exec_path: str</span>
<span class="sd"> """</span>
<span class="n">viewer</span><span class="p">[</span><span class="s">'vrml'</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">progname</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span> <span class="n">exec_path</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Visualization base class. Defines methods for general visualization</span>
<span class="c"># tasks.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="Viewable"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.Viewable">[docs]</a><span class="k">class</span> <span class="nc">Viewable</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Any viewable chemical object</span>
<span class="sd"> This is a mix-in class that defines a general</span>
<span class="sd"> visualization method for all viewable objects, i.e. chemical</span>
<span class="sd"> objects (atoms, molecules, etc.), collections, and universes.</span>
<span class="sd"> """</span>
<div class="viewcode-block" id="Viewable.graphicsObjects"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.Viewable.graphicsObjects">[docs]</a> <span class="k">def</span> <span class="nf">graphicsObjects</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="sd">"""</span>
<span class="sd"> :keyword configuration: the configuration in which the objects</span>
<span class="sd"> are drawn (default: the current configuration)</span>
<span class="sd"> :type configuration: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :keyword model: the graphical representation to be used (one of</span>
<span class="sd"> "wireframe", "tube", "ball_and_stick", "vdw" and</span>
<span class="sd"> "vdw_and_stick"). The vdw models use balls</span>
<span class="sd"> with the radii taken from the atom objects.</span>
<span class="sd"> Default is "wireframe".</span>
<span class="sd"> :type model: str</span>
<span class="sd"> :keyword ball_radius: the radius of the balls representing the atoms</span>
<span class="sd"> in a ball_and_stick model, default: 0.03</span>
<span class="sd"> This is also used in vdw and vdw_and_stick when</span>
<span class="sd"> an atom does not supply a radius.</span>
<span class="sd"> :type ball_radius: float</span>
<span class="sd"> :keyword stick_radius: the radius of the sticks representing the bonds</span>
<span class="sd"> in a ball_and_stick, vdw_and_stick or tube model.</span>
<span class="sd"> Default: 0.02 for the tube model, 0.01 for the</span>
<span class="sd"> ball_and_stick and vdw_and_stick models</span>
<span class="sd"> :type stick_radius: float</span>
<span class="sd"> :keyword graphics_module: the module in which the elementary graphics</span>
<span class="sd"> objects are defined</span>
<span class="sd"> (default: Scientific.Visualization.VRML)</span>
<span class="sd"> :type graphics_module: module</span>
<span class="sd"> :keyword color_values: a color value for each atom which defines</span>
<span class="sd"> the color via the color scale object specified</span>
<span class="sd"> by the option color_scale. If no value is</span>
<span class="sd"> given, the atoms' colors are taken from the</span>
<span class="sd"> attribute 'color' of each atom object (default</span>
<span class="sd"> values for each chemical element are provided</span>
<span class="sd"> in the chemical database).</span>
<span class="sd"> :type color_values: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> :keyword color_scale: an object that returns a color object (as defined</span>
<span class="sd"> in the module Scientific.Visualization.Color)</span>
<span class="sd"> when called with a number argument. Suitable</span>
<span class="sd"> objects are defined by</span>
<span class="sd"> Scientific.Visualization.Color.ColorScale and</span>
<span class="sd"> Scientific.Visualization.Color.SymmetricColorScale.</span>
<span class="sd"> The object is used only when the option</span>
<span class="sd"> color_values is specified as well. The default</span>
<span class="sd"> is a blue-to-red color scale that covers the</span>
<span class="sd"> range of the values given in color_values.</span>
<span class="sd"> :type color_scale: callable</span>
<span class="sd"> :keyword color: a color name predefined in the module</span>
<span class="sd"> Scientific.Visualization.Color. The corresponding</span>
<span class="sd"> color is applied to all graphics objects that are</span>
<span class="sd"> returned.</span>
<span class="sd"> :returns: a list of graphics objects that represent</span>
<span class="sd"> the object for which the method is called.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'model'</span><span class="p">,</span> <span class="s">'wireframe'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'tube'</span><span class="p">:</span>
<span class="n">model</span> <span class="o">=</span> <span class="s">'ball_and_stick'</span>
<span class="n">radius</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'stick_radius'</span><span class="p">,</span> <span class="mf">0.02</span><span class="p">)</span>
<span class="n">options</span><span class="p">[</span><span class="s">'stick_radius'</span><span class="p">]</span> <span class="o">=</span> <span class="n">radius</span>
<span class="n">options</span><span class="p">[</span><span class="s">'ball_radius'</span><span class="p">]</span> <span class="o">=</span> <span class="n">radius</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">module</span> <span class="o">=</span> <span class="n">options</span><span class="p">[</span><span class="s">'graphics_module'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">Scientific.Visualization</span> <span class="kn">import</span> <span class="n">VRML</span>
<span class="n">module</span> <span class="o">=</span> <span class="n">VRML</span>
<span class="n">color</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">color_values</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color_values'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color_values</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">lower</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">minimum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">color_values</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">upper</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">maximum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">color_values</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">options</span><span class="p">[</span><span class="s">'color_scale'</span><span class="p">]</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">ColorScale</span><span class="p">((</span><span class="n">lower</span><span class="p">,</span> <span class="n">upper</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">distance_fn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span><span class="o">.</span><span class="n">distanceVector</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Universe</span>
<span class="n">distance_fn</span> <span class="o">=</span> <span class="n">Universe</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span><span class="o">.</span><span class="n">distanceVector</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">_atomColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">color</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">color</span>
<span class="n">color_values</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color_values'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color_values</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">atom</span><span class="o">.</span><span class="n">color</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">scale</span> <span class="o">=</span> <span class="n">options</span><span class="p">[</span><span class="s">'color_scale'</span><span class="p">]</span>
<span class="k">return</span> <span class="n">scale</span><span class="p">(</span><span class="n">color_values</span><span class="p">[</span><span class="n">atom</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># View anything viewable.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="view"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.view">[docs]</a><span class="k">def</span> <span class="nf">view</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="o">*</span><span class="n">parameters</span><span class="p">):</span>
<span class="s">"Equivalent to object.view(parameters)."</span>
<span class="nb">object</span><span class="o">.</span><span class="n">view</span><span class="p">(</span><span class="o">*</span><span class="n">parameters</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Display an object or a collection of objects using an external</span>
<span class="c"># viewing program.</span>
<span class="c">#</span></div>
<span class="k">def</span> <span class="nf">genericViewConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">format</span> <span class="o">=</span> <span class="s">'pdb'</span><span class="p">,</span>
<span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="n">viewer_format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">viewer_format</span> <span class="o">==</span> <span class="s">'pdb'</span><span class="p">:</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">filename</span> <span class="o">+</span> <span class="s">'.pdb'</span>
<span class="k">elif</span> <span class="n">viewer_format</span> <span class="o">==</span> <span class="s">'vrml'</span><span class="p">:</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">filename</span> <span class="o">+</span> <span class="s">'.wrl'</span>
<span class="k">if</span> <span class="n">running_on_windows</span><span class="p">:</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">startfile</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="k">except</span> <span class="n">win32api</span><span class="o">.</span><span class="n">error</span><span class="p">,</span> <span class="n">error_number</span><span class="p">:</span>
<span class="c">#Looking for error 31, SE_ERR_NOASSOC, in particular</span>
<span class="n">file_type</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">error_number</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">==</span><span class="mi">31</span><span class="p">:</span>
<span class="k">print</span> <span class="p">(</span><span class="s">'There is no program associated with .</span><span class="si">%s</span><span class="s"> files,'</span> <span class="o">+</span> \
<span class="s">' please install a suitable viewer'</span><span class="p">)</span> <span class="o">%</span> <span class="n">file_type</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">print</span> <span class="s">'Unexpected error attempting to open .</span><span class="si">%s</span><span class="s"> file'</span> <span class="o">%</span> <span class="n">file_type</span>
<span class="k">print</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_value</span>
<span class="k">elif</span> <span class="n">viewer</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">viewer_format</span><span class="p">):</span>
<span class="c"># On Unix-like systems, give priority to a user-specified viewer.</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">fork</span><span class="p">()</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">pipe</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">popen</span><span class="p">(</span><span class="n">viewer</span><span class="p">[</span><span class="n">format</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">' '</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> \
<span class="s">' 1> /dev/null 2>&1'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="n">pipe</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">_exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">running_on_macosx</span><span class="p">:</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">call</span><span class="p">([</span><span class="s">"/usr/bin/open"</span><span class="p">,</span> <span class="n">filename</span><span class="p">])</span>
<span class="k">elif</span> <span class="n">running_on_linux</span><span class="p">:</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">call</span><span class="p">([</span><span class="s">"xdg-open"</span><span class="p">,</span> <span class="n">filename</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">'No viewer for </span><span class="si">%s</span><span class="s"> defined.'</span> <span class="o">%</span> <span class="n">viewer_format</span><span class="p">)</span>
<span class="k">return</span>
<span class="k">def</span> <span class="nf">viewConfiguration</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">pdbviewer</span><span class="p">,</span> <span class="n">exec_path</span> <span class="o">=</span> <span class="n">viewer</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'pdb'</span><span class="p">,</span> <span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">))</span>
<span class="n">function</span> <span class="o">=</span> <span class="p">{</span><span class="s">'vmd'</span><span class="p">:</span> <span class="n">viewConfigurationVMD</span><span class="p">,</span>
<span class="s">'xmol'</span><span class="p">:</span> <span class="n">viewConfigurationXMol</span><span class="p">,</span>
<span class="s">'imol'</span><span class="p">:</span> <span class="n">viewConfigurationIMol</span><span class="p">}</span> \
<span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pdbviewer</span><span class="p">,</span><span class="n">genericViewConfiguration</span><span class="p">)</span>
<span class="n">function</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Normal mode and trajectory animation</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">viewSequence</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Launches an animation using an external viewer.</span>
<span class="sd"> :param object: the object for which the animation is displayed.</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param conf_list: a sequence of configurations that define the animation</span>
<span class="sd"> :type conf_list: sequence</span>
<span class="sd"> :param periodic: if True, turn animation into a loop</span>
<span class="sd"> :param label: an optional text string that some interfaces</span>
<span class="sd"> use to pass a description of the object to the</span>
<span class="sd"> visualization system.</span>
<span class="sd"> :type label: str</span>
<span class="sd"> """</span>
<span class="n">pdbviewer</span><span class="p">,</span> <span class="n">exec_path</span> <span class="o">=</span> <span class="n">viewer</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'pdb'</span><span class="p">,</span> <span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">))</span>
<span class="n">function</span> <span class="o">=</span> <span class="p">{</span><span class="s">'vmd'</span><span class="p">:</span> <span class="n">viewSequenceVMD</span><span class="p">,</span>
<span class="s">'xmol'</span><span class="p">:</span> <span class="n">viewSequenceXMol</span><span class="p">,</span>
<span class="s">'imol'</span><span class="p">:</span> <span class="n">viewSequenceIMol</span><span class="p">,</span>
<span class="bp">None</span><span class="p">:</span> <span class="bp">None</span><span class="p">}[</span><span class="n">pdbviewer</span><span class="p">]</span>
<span class="k">if</span> <span class="n">function</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">'No viewer with animation feature defined.'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">function</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
<div class="viewcode-block" id="viewTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.viewTrajectory">[docs]</a><span class="k">def</span> <span class="nf">viewTrajectory</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">subset</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Launches an animation based on a trajectory using an external viewer.</span>
<span class="sd"> :param trajectory: the trajectory</span>
<span class="sd"> :type trajectory: :class:`~MMTK.Trajectory.Trajectory`</span>
<span class="sd"> :param first: the first trajectory step to be used</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the first trajectory step NOT to be used</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the distance between two consecutive steps shown</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> :param subset: the subset of the universe that is shown</span>
<span class="sd"> (default: the whole universe)</span>
<span class="sd"> :type subset: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param label: an optional text string that some interfaces</span>
<span class="sd"> use to pass a description of the object to the</span>
<span class="sd"> visualization system.</span>
<span class="sd"> :type label: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="s">''</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">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="n">trajectory</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">last</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="k">elif</span> <span class="n">last</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">last</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="o">+</span> <span class="n">last</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="k">if</span> <span class="n">subset</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">subset</span> <span class="o">=</span> <span class="n">universe</span>
<span class="n">viewSequence</span><span class="p">(</span><span class="n">subset</span><span class="p">,</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">configuration</span><span class="p">[</span><span class="n">first</span><span class="p">:</span><span class="n">last</span><span class="p">:</span><span class="n">skip</span><span class="p">],</span> <span class="n">label</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">viewMode</span><span class="p">(</span><span class="n">mode</span><span class="p">,</span> <span class="n">factor</span><span class="o">=</span><span class="mf">1.</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">mode</span><span class="o">.</span><span class="n">universe</span>
<span class="k">if</span> <span class="n">subset</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">subset</span> <span class="o">=</span> <span class="n">universe</span>
<span class="n">conf</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">viewSequence</span><span class="p">(</span><span class="n">subset</span><span class="p">,</span> <span class="p">[</span><span class="n">conf</span><span class="p">,</span> <span class="n">conf</span><span class="o">+</span><span class="n">factor</span><span class="o">*</span><span class="n">mode</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">conf</span><span class="o">-</span><span class="n">factor</span><span class="o">*</span><span class="n">mode</span><span class="p">],</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">label</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># XMol support</span>
<span class="c"># </span>
<span class="c">#</span>
<span class="c"># Animation with XMol.</span>
<span class="c">#</span>
<span class="n">viewConfigurationXMol</span> <span class="o">=</span> <span class="n">viewConfiguration</span>
<span class="k">def</span> <span class="nf">viewSequenceXMol</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">file_list</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">conf</span> <span class="ow">in</span> <span class="n">conf_list</span><span class="p">:</span>
<span class="nb">file</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">file_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="s">'pdb'</span><span class="p">)</span>
<span class="n">bigfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">call</span><span class="p">([</span><span class="s">'cat'</span><span class="p">]</span> <span class="o">+</span> <span class="n">file_list</span> <span class="o">+</span> <span class="p">[</span><span class="s">'>'</span><span class="p">,</span> <span class="n">bigfile</span><span class="p">])</span>
<span class="k">for</span> <span class="nb">file</span> <span class="ow">in</span> <span class="n">file_list</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">fork</span><span class="p">()</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">pipe</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">popen</span><span class="p">(</span><span class="s">'xmol -readFormat pdb '</span> <span class="o">+</span> <span class="n">bigfile</span> <span class="o">+</span> \
<span class="s">' 1> /dev/null 2>&1'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="n">pipe</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">bigfile</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">_exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># VMD support</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c"># View configuration</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">isCalpha</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">isProtein</span><span class="p">,</span> <span class="n">isPeptideChain</span>
<span class="kn">from</span> <span class="nn">MMTK.Universe</span> <span class="kn">import</span> <span class="n">isUniverse</span>
<span class="kn">from</span> <span class="nn">MMTK.Collections</span> <span class="kn">import</span> <span class="n">isCollection</span>
<span class="k">if</span> <span class="n">isProtein</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">chain_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">chain_list</span> <span class="o">=</span> <span class="p">[</span><span class="nb">object</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">isUniverse</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> <span class="ow">or</span> <span class="n">isCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">chain_list</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="nb">object</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isProtein</span><span class="p">(</span><span class="n">element</span><span class="p">):</span>
<span class="n">chain_list</span> <span class="o">=</span> <span class="n">chain_list</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="n">element</span><span class="p">):</span>
<span class="n">chain_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">chain_list</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">if</span> <span class="n">chain</span><span class="o">.</span><span class="n">model</span> <span class="o">!=</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">viewConfigurationVMD</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">format</span> <span class="o">=</span> <span class="s">'pdb'</span><span class="p">,</span>
<span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Universe</span>
<span class="n">format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">if</span> <span class="n">format</span> <span class="o">!=</span> <span class="s">'pdb'</span><span class="p">:</span>
<span class="k">return</span> <span class="n">genericViewConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">filename_tcl</span> <span class="o">=</span> <span class="n">filename</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span>
<span class="n">script</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">script_tcl</span> <span class="o">=</span> <span class="n">script</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">script</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'mol load pdb '</span> <span class="o">+</span> <span class="n">filename_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">isCalpha</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'mol modstyle 0 all trace</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'color Name 1 white</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'color Name 2 white</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'color Name 3 white</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">Universe</span><span class="o">.</span><span class="n">isUniverse</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="c"># add a box around periodic universes</span>
<span class="n">basis</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">basisVectors</span><span class="p">()</span>
<span class="k">if</span> <span class="n">basis</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">v3</span> <span class="o">=</span> <span class="n">basis</span>
<span class="n">p</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">)</span>
<span class="k">for</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span> <span class="ow">in</span> <span class="p">[(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">),</span>
<span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span>
<span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span>
<span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span>
<span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">),</span> <span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">)]:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'graphics 0 line {</span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s">} {</span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s">}</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span>
<span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">p1</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="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p2</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="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">filename_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span> <span class="o">!=</span> <span class="s">'win32'</span><span class="p">:</span>
<span class="c"># Under Windows, it seems to be impossible to delete</span>
<span class="c"># the script file while it is still in use. For the moment</span>
<span class="c"># we just don't delete it at all.</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">script_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">([</span><span class="n">viewer</span><span class="p">[</span><span class="s">'pdb'</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="s">'-nt'</span><span class="p">,</span> <span class="s">'-e'</span><span class="p">,</span> <span class="n">script</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># Animate sequence</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">viewSequenceVMD</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">script</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">script_tcl</span> <span class="o">=</span> <span class="n">script</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span>
<span class="n">np</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">numberOfPoints</span><span class="p">()</span>
<span class="n">universe</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">np</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="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">conf_list</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">DCD</span>
<span class="n">pdbfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">pdbfile_tcl</span> <span class="o">=</span> <span class="n">pdbfile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span>
<span class="n">dcdfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">dcdfile_tcl</span> <span class="o">=</span> <span class="n">dcdfile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="n">DCD</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">pdbfile</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">DCD</span><span class="o">.</span><span class="n">writeDCD</span><span class="p">(</span><span class="n">conf_list</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="n">dcdfile</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="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">script</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'mol load pdb '</span> <span class="o">+</span> <span class="n">pdbfile_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">isCalpha</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'mol modstyle 0 all trace</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate read dcd '</span> <span class="o">+</span> <span class="n">dcdfile_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">periodic</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate style loop</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate style once</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate forward</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">pdbfile_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">dcdfile_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span> <span class="o">!=</span> <span class="s">'win32'</span><span class="p">:</span>
<span class="c"># Under Windows, it seems to be impossible to delete</span>
<span class="c"># the script file while it is still in use. For the moment</span>
<span class="c"># we just don't delete it at all.</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">script_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">file_list</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">conf</span> <span class="ow">in</span> <span class="n">conf_list</span><span class="p">:</span>
<span class="nb">file</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span>
<span class="n">file_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="s">'pdb'</span><span class="p">)</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">script</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'mol load pdb '</span> <span class="o">+</span> <span class="n">file_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">conf</span> <span class="ow">in</span> <span class="n">file_list</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate read pdb '</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">periodic</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate style loop</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate style once</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'animate forward</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">conf</span> <span class="ow">in</span> <span class="n">file_list</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">'</span><span class="se">\\</span><span class="s">'</span><span class="p">,</span> <span class="s">'</span><span class="se">\\\\</span><span class="s">'</span><span class="p">)</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span> <span class="o">!=</span> <span class="s">'win32'</span><span class="p">:</span>
<span class="c"># Under Windows, it seems to be impossible to delete</span>
<span class="c"># the script file while it is still in use. For the moment</span>
<span class="c"># we just don't delete it at all.</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'file delete '</span> <span class="o">+</span> <span class="n">script_tcl</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">([</span><span class="n">viewer</span><span class="p">[</span><span class="s">'pdb'</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="s">'-nt'</span><span class="p">,</span> <span class="s">'-e'</span><span class="p">,</span> <span class="n">script</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># iMol support</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c"># View configuration</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">viewConfigurationIMol</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">format</span> <span class="o">=</span> <span class="s">'pdb'</span><span class="p">,</span>
<span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">format</span> <span class="o">=</span> <span class="n">format</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">if</span> <span class="n">format</span> <span class="o">!=</span> <span class="s">'pdb'</span><span class="p">:</span>
<span class="k">return</span> <span class="n">genericViewConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span> <span class="o">+</span> <span class="s">'.pdb'</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="nb">object</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">call</span><span class="p">([</span><span class="s">'open'</span><span class="p">,</span> <span class="s">'-a'</span><span class="p">,</span> <span class="n">prog</span><span class="p">,</span> <span class="n">filename</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># Animate sequence</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">viewSequenceIMol</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">PDB</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempdir</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mktemp</span><span class="p">()</span> <span class="o">+</span> <span class="s">'.pdb'</span>
<span class="nb">file</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">filename</span><span class="p">)</span>
<span class="k">for</span> <span class="n">conf</span> <span class="ow">in</span> <span class="n">conf_list</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">nextModel</span><span class="p">()</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">tempfile</span><span class="o">.</span><span class="n">tempdir</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">subprocess</span><span class="o">.</span><span class="n">call</span><span class="p">([</span><span class="s">'open'</span><span class="p">,</span> <span class="s">'-a'</span><span class="p">,</span> <span class="n">prog</span><span class="p">,</span> <span class="n">filename</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># PyMOL support</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">PyMOL</span>
<span class="k">if</span> <span class="n">PyMOL</span><span class="o">.</span><span class="n">in_pymol</span><span class="p">:</span>
<span class="n">_representation</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">viewConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">configuration</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">format</span> <span class="o">=</span> <span class="s">'pdb'</span><span class="p">,</span>
<span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">global</span> <span class="n">_representation</span>
<span class="k">if</span> <span class="n">label</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">label</span> <span class="o">=</span> <span class="s">"MMTK Object"</span>
<span class="k">if</span> <span class="n">_representation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">_representation</span><span class="o">.</span><span class="n">remove</span><span class="p">()</span>
<span class="n">_representation</span> <span class="o">=</span> <span class="n">PyMOL</span><span class="o">.</span><span class="n">Representation</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
<span class="n">_representation</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<div class="viewcode-block" id="viewSequence"><a class="viewcode-back" href="../../modules.html#MMTK.Visualization.viewSequence">[docs]</a> <span class="k">def</span> <span class="nf">viewSequence</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">conf_list</span><span class="p">,</span> <span class="n">periodic</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">global</span> <span class="n">_representation</span>
<span class="k">if</span> <span class="n">label</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">label</span> <span class="o">=</span> <span class="s">"MMTK Object"</span>
<span class="k">if</span> <span class="n">_representation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">_representation</span><span class="o">.</span><span class="n">remove</span><span class="p">()</span>
<span class="n">_representation</span> <span class="o">=</span> <span class="n">PyMOL</span><span class="o">.</span><span class="n">Representation</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">label</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">_representation</span><span class="o">.</span><span class="n">movie</span><span class="p">(</span><span class="n">conf_list</span><span class="p">)</span>
</div>
<span class="n">genericViewMode</span> <span class="o">=</span> <span class="n">viewMode</span>
<span class="k">def</span> <span class="nf">viewMode</span><span class="p">(</span><span class="n">mode</span><span class="p">,</span> <span class="n">factor</span><span class="o">=</span><span class="mf">1.</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymol</span> <span class="kn">import</span> <span class="n">cmd</span>
<span class="n">cmd</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">"movie_delay"</span><span class="p">,</span><span class="s">"200"</span><span class="p">,</span><span class="n">log</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">genericViewMode</span><span class="p">(</span><span class="n">mode</span><span class="p">,</span> <span class="n">factor</span><span class="p">,</span> <span class="n">subset</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
</pre></div>
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