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<h1>Source code for MMTK.Solvation</h1><div class="highlight"><pre>
<span class="c"># This module contains code for solvation.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Solvation of solute molecules</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">ChemicalObjects</span><span class="p">,</span> <span class="n">Units</span><span class="p">,</span> <span class="n">Universe</span>
<span class="kn">from</span> <span class="nn">MMTK.MolecularSurface</span> <span class="kn">import</span> <span class="n">surfaceAndVolume</span>
<span class="kn">from</span> <span class="nn">MMTK.Minimization</span> <span class="kn">import</span> <span class="n">SteepestDescentMinimizer</span>
<span class="kn">from</span> <span class="nn">MMTK.Dynamics</span> <span class="kn">import</span> <span class="n">VelocityVerletIntegrator</span><span class="p">,</span> <span class="n">VelocityScaler</span><span class="p">,</span> \
<span class="n">TranslationRemover</span><span class="p">,</span> <span class="n">RotationRemover</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">TrajectoryOutput</span><span class="p">,</span> <span class="n">SnapshotGenerator</span><span class="p">,</span> \
<span class="n">StandardLogOutput</span>
<span class="kn">import</span> <span class="nn">copy</span>
<span class="c">#</span>
<span class="c"># Calculate the number of solvent molecules</span>
<span class="c">#</span>
<div class="viewcode-block" id="numberOfSolventMolecules"><a class="viewcode-back" href="../../modules.html#MMTK.Solvation.numberOfSolventMolecules">[docs]</a><span class="k">def</span> <span class="nf">numberOfSolventMolecules</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">solvent</span><span class="p">,</span> <span class="n">density</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: a finite universe</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param solvent: a molecule, or the name of a molecule in the database</span>
<span class="sd"> :type solvent: :class:`~MMTK.ChemicalObjects.Molecule` or str</span>
<span class="sd"> :param density: the density of the solvent (amu/nm**3)</span>
<span class="sd"> :type density: float</span>
<span class="sd"> :returns: the number of solvent molecules that must be added to the</span>
<span class="sd"> universe, in addition to whatever it already contains,</span>
<span class="sd"> to obtain the given solvent density.</span>
<span class="sd"> :rtype: int</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">solvent</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">solvent</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="p">(</span><span class="n">solvent</span><span class="p">)</span>
<span class="n">cell_volume</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">()</span>
<span class="k">if</span> <span class="n">cell_volume</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">"universe volume is undefined"</span><span class="p">)</span>
<span class="n">solute_volume</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">universe</span><span class="o">.</span><span class="n">_objects</span><span class="p">:</span>
<span class="n">solute_volume</span> <span class="o">=</span> <span class="n">solute_volume</span> <span class="o">+</span> <span class="n">surfaceAndVolume</span><span class="p">(</span><span class="n">o</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="n">density</span><span class="o">*</span><span class="p">(</span><span class="n">cell_volume</span><span class="o">-</span><span class="n">solute_volume</span><span class="p">)</span><span class="o">/</span><span class="n">solvent</span><span class="o">.</span><span class="n">mass</span><span class="p">()))</span>
<span class="c">#</span>
<span class="c"># Add solvent to a universe containing solute molecules.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="addSolvent"><a class="viewcode-back" href="../../modules.html#MMTK.Solvation.addSolvent">[docs]</a><span class="k">def</span> <span class="nf">addSolvent</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">solvent</span><span class="p">,</span> <span class="n">density</span><span class="p">,</span> <span class="n">scale_factor</span><span class="o">=</span><span class="mf">4.</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Scales up the universe and adds as many solvent molecules</span>
<span class="sd"> as are necessary to obtain the specified solvent density,</span>
<span class="sd"> taking account of the solute molecules that are already present</span>
<span class="sd"> in the universe. The molecules are placed at random positions</span>
<span class="sd"> in the scaled-up universe, but without overlaps between</span>
<span class="sd"> any two molecules.</span>
<span class="sd"> :param universe: a finite universe</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param solvent: a molecule, or the name of a molecule in the database</span>
<span class="sd"> :type solvent: :class:`~MMTK.ChemicalObjects.Molecule` or str</span>
<span class="sd"> :param density: the density of the solvent (amu/nm**3)</span>
<span class="sd"> :type density: float</span>
<span class="sd"> :param scale_factor: the factor by which the initial universe is</span>
<span class="sd"> expanded before adding the solvent molecules</span>
<span class="sd"> :type scale_factor: float</span>
<span class="sd"> """</span>
<span class="c"># Calculate number of solvent molecules and universe size</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">solvent</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">solvent</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="p">(</span><span class="n">solvent</span><span class="p">)</span>
<span class="n">cell_volume</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">()</span>
<span class="k">if</span> <span class="n">cell_volume</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">"universe volume is undefined"</span><span class="p">)</span>
<span class="n">solute</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">_objects</span><span class="p">)</span>
<span class="n">solute_volume</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="n">excluded_regions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">solute</span><span class="p">:</span>
<span class="n">solute_volume</span> <span class="o">=</span> <span class="n">solute_volume</span> <span class="o">+</span> <span class="n">surfaceAndVolume</span><span class="p">(</span><span class="n">o</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">excluded_regions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">boundingSphere</span><span class="p">())</span>
<span class="n">n_solvent</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="n">density</span><span class="o">*</span><span class="p">(</span><span class="n">cell_volume</span><span class="o">-</span><span class="n">solute_volume</span><span class="p">)</span><span class="o">/</span><span class="n">solvent</span><span class="o">.</span><span class="n">mass</span><span class="p">()))</span>
<span class="n">solvent_volume</span> <span class="o">=</span> <span class="n">n_solvent</span><span class="o">*</span><span class="n">solvent</span><span class="o">.</span><span class="n">mass</span><span class="p">()</span><span class="o">/</span><span class="n">density</span>
<span class="n">cell_volume</span> <span class="o">=</span> <span class="n">solvent_volume</span> <span class="o">+</span> <span class="n">solute_volume</span>
<span class="n">universe</span><span class="o">.</span><span class="n">translateBy</span><span class="p">(</span><span class="o">-</span><span class="n">solute</span><span class="o">.</span><span class="n">position</span><span class="p">())</span>
<span class="n">universe</span><span class="o">.</span><span class="n">scaleSize</span><span class="p">((</span><span class="n">cell_volume</span><span class="o">/</span><span class="n">universe</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">())</span><span class="o">**</span><span class="p">(</span><span class="mf">1.</span><span class="o">/</span><span class="mf">3.</span><span class="p">))</span>
<span class="c"># Scale up the universe and add solvent molecules at random positions</span>
<span class="n">universe</span><span class="o">.</span><span class="n">scaleSize</span><span class="p">(</span><span class="n">scale_factor</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span> <span class="o">=</span> <span class="n">scale_factor</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_solvent</span><span class="p">):</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">solvent</span><span class="p">)</span>
<span class="n">m</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">randomPoint</span><span class="p">())</span>
<span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">boundingSphere</span><span class="p">()</span>
<span class="n">collision</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">for</span> <span class="n">region</span> <span class="ow">in</span> <span class="n">excluded_regions</span><span class="p">:</span>
<span class="k">if</span> <span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">center</span><span class="o">-</span><span class="n">region</span><span class="o">.</span><span class="n">center</span><span class="p">)</span><span class="o">.</span><span class="n">length</span><span class="p">()</span> <span class="o"><</span> <span class="n">s</span><span class="o">.</span><span class="n">radius</span><span class="o">+</span><span class="n">region</span><span class="o">.</span><span class="n">radius</span><span class="p">:</span>
<span class="n">collision</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">collision</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">m</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">randomPoint</span><span class="p">())</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">excluded_regions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Shrink the universe to its final size</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="shrinkUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Solvation.shrinkUniverse">[docs]</a><span class="k">def</span> <span class="nf">shrinkUniverse</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="mf">300.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span><span class="p">,</span> <span class="n">trajectory</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
<span class="n">scale_factor</span><span class="o">=</span><span class="mf">0.95</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Shrinks the universe, which must have been scaled up by</span>
<span class="sd"> :class:`~MMTK.Solvation.addSolvent`, back to its original size.</span>
<span class="sd"> The compression is performed in small steps, in between which</span>
<span class="sd"> some energy minimization and molecular dynamics steps are executed.</span>
<span class="sd"> The molecular dynamics is run at the given temperature, and</span>
<span class="sd"> an optional trajectory can be specified in which intermediate</span>
<span class="sd"> configurations are stored.</span>
<span class="sd"> :param universe: a finite universe</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param temperature: the temperature at which the Molecular Dynamics</span>
<span class="sd"> steps are run</span>
<span class="sd"> :type temperature: float</span>
<span class="sd"> :param trajectory: the trajectory in which the progress of the</span>
<span class="sd"> shrinking procedure is stored, or a filename</span>
<span class="sd"> :type trajectory: :class:`~MMTK.Trajectory.Trajectory` or str</span>
<span class="sd"> :param scale_factor: the factor by which the universe is scaled</span>
<span class="sd"> at each reduction step</span>
<span class="sd"> :type scale_factor: float</span>
<span class="sd"> """</span>
<span class="c"># Set velocities and initialize trajectory output</span>
<span class="n">universe</span><span class="o">.</span><span class="n">initializeVelocitiesToTemperature</span><span class="p">(</span><span class="n">temperature</span><span class="p">)</span>
<span class="k">if</span> <span class="n">trajectory</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">trajectory</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">trajectory</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span>
<span class="s">"solvation protocol"</span><span class="p">)</span>
<span class="n">close_trajectory</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">close_trajectory</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TrajectoryOutput</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span> <span class="p">[</span><span class="s">"configuration"</span><span class="p">],</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span>
<span class="n">snapshot</span> <span class="o">=</span> <span class="n">SnapshotGenerator</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">actions</span><span class="o">=</span><span class="n">actions</span><span class="p">)</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="c"># Do some minimization and equilibration</span>
<span class="n">minimizer</span> <span class="o">=</span> <span class="n">SteepestDescentMinimizer</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">step_size</span> <span class="o">=</span> <span class="mf">0.05</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">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">VelocityScaler</span><span class="p">(</span><span class="n">temperature</span><span class="p">,</span> <span class="mf">0.01</span><span class="o">*</span><span class="n">temperature</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
<span class="n">TranslationRemover</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">20</span><span class="p">)]</span>
<span class="n">integrator</span> <span class="o">=</span> <span class="n">VelocityVerletIntegrator</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">delta_t</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">fs</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="n">actions</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">):</span>
<span class="n">minimizer</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">40</span><span class="p">)</span>
<span class="n">integrator</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">200</span><span class="p">)</span>
<span class="c"># Scale down the system in small steps</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">while</span> <span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span> <span class="o">></span> <span class="mf">1.</span><span class="p">:</span>
<span class="k">if</span> <span class="n">trajectory</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">%</span> <span class="mi">1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="n">i</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">step_factor</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">scale_factor</span><span class="p">,</span> <span class="mf">1.</span><span class="o">/</span><span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span><span class="p">)</span>
<span class="k">for</span> <span class="nb">object</span> <span class="ow">in</span> <span class="n">universe</span><span class="p">:</span>
<span class="nb">object</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">step_factor</span><span class="o">*</span><span class="nb">object</span><span class="o">.</span><span class="n">position</span><span class="p">())</span>
<span class="n">universe</span><span class="o">.</span><span class="n">scaleSize</span><span class="p">(</span><span class="n">step_factor</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span><span class="o">*</span><span class="n">step_factor</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
<span class="n">minimizer</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">integrator</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">50</span><span class="p">)</span>
<span class="k">del</span> <span class="n">universe</span><span class="o">.</span><span class="n">scale_factor</span>
<span class="k">if</span> <span class="n">trajectory</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="k">if</span> <span class="n">close_trajectory</span><span class="p">:</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
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