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<a href="Bio-module.html">Package Bio</a> ::
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Module Superimposer'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.Superimposer%27-module.html">Module Bio.PDB.Superimposer'</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Affy.CelFile.Float0=Bio.Affy.CelFile-module.html#Float0,Variable Bio.LogisticRegression.Float0=Bio.LogisticRegression-module.html#Float0,Variable Bio.MarkovModel.Float0=Bio.MarkovModel-module.html#Float0,Variable Bio.MaxEntropy.Float0=Bio.MaxEntropy-module.html#Float0,Variable Bio.NaiveBayes.Float0=Bio.NaiveBayes-module.html#Float0,Variable Bio.PDB.FragmentMapper'.Float0=Bio.PDB.FragmentMapper%27-module.html#Float0,Variable Bio.PDB.PDBParser'.Float0=Bio.PDB.PDBParser%27-module.html#Float0,Variable Bio.PDB.Superimposer'.Float0=Bio.PDB.Superimposer%27-module.html#Float0,Variable Bio.Statistics.lowess.Float0=Bio.Statistics.lowess-module.html#Float0,Variable Bio.distance.Float0=Bio.distance-module.html#Float0,Variable Bio.kNN.Float0=Bio.kNN-module.html#Float0"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-0', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.SVDSuperimposer=Bio.SVDSuperimposer-module.html,Class Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-2', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-3', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-5', 'PDB', 'link-5');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Module Bio.PDB.PDBExceptions=Bio.PDB.PDBExceptions-module.html"><a title="Bio.PDB.PDBExceptions" class="py-name" href="#" onclick="return doclink('link-6', 'PDBExceptions', 'link-6');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Variable Bio.PDB.DSSP'.PDBException=Bio.PDB.DSSP%27-module.html#PDBException,Variable Bio.PDB.PDBExceptions.PDBException=Bio.PDB.PDBExceptions-module.html#PDBException,Variable Bio.PDB.Superimposer'.PDBException=Bio.PDB.Superimposer%27-module.html#PDBException"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-7', 'PDBException', 'link-7');">PDBException</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-8" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-8', '__doc__', 'link-8');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"Superimpose two structures."</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="Superimposer"></a><div id="Superimposer-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="Superimposer-toggle" onclick="return toggle('Superimposer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Superimposer'.Superimposer-class.html">Superimposer</a><tt class="py-op">:</tt> </tt>
</div><div id="Superimposer-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Superimposer-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> Rotate/translate one set of atoms on top of another,</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> thereby minimizing the RMSD.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Superimposer.__init__"></a><div id="Superimposer.__init__-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="Superimposer.__init__-toggle" onclick="return toggle('Superimposer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Superimposer'.Superimposer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Superimposer.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Superimposer.__init__-expanded"><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotran</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rms</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
</div><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> </tt>
<a name="Superimposer.set_atoms"></a><div id="Superimposer.set_atoms-def"><a name="L24"></a><tt class="py-lineno">24</tt> <a class="py-toggle" href="#" id="Superimposer.set_atoms-toggle" onclick="return toggle('Superimposer.set_atoms');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Superimposer'.Superimposer-class.html#set_atoms">set_atoms</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fixed</tt><tt class="py-op">,</tt> <tt class="py-param">moving</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Superimposer.set_atoms-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Superimposer.set_atoms-expanded"><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> Put (translate/rotate) the atoms in fixed on the atoms in </tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> moving, in such a way that the RMSD is minimized.</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> @param fixed: list of (fixed) atoms</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> @param moving: list of (moving) atoms </tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> @type fixed,moving: [L{Atom}, L{Atom},...]</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fixed</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">moving</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-9" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-9', 'PDBException', 'link-7');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Fixed and moving atom lists differ in size"</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fixed</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">fixed_coord</tt><tt class="py-op">=</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">moving_coord</tt><tt class="py-op">=</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-10" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-10', 'i', 'link-10');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fixed</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">fixed_coord</tt><tt class="py-op">[</tt><tt id="link-11" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-11', 'i', 'link-10');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">fixed</tt><tt class="py-op">[</tt><tt id="link-12" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-12', 'i', 'link-10');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_coord()=Bio.PDB.Atom.Atom-class.html#get_coord"><a title="Bio.PDB.Atom.Atom.get_coord" class="py-name" href="#" onclick="return doclink('link-13', 'get_coord', 'link-13');">get_coord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">moving_coord</tt><tt class="py-op">[</tt><tt id="link-14" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-14', 'i', 'link-10');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">moving</tt><tt class="py-op">[</tt><tt id="link-15" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-15', 'i', 'link-10');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Atom.Atom.get_coord" class="py-name" href="#" onclick="return doclink('link-16', 'get_coord', 'link-13');">get_coord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">=</tt><tt id="link-17" class="py-name"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-17', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set,Method Bio.config.DBRegistry.DBObject.set()=Bio.config.DBRegistry.DBObject-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-18', 'set', 'link-18');">set</a></tt><tt class="py-op">(</tt><tt class="py-name">fixed_coord</tt><tt class="py-op">,</tt> <tt class="py-name">moving_coord</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.AlignAce.Applications.AlignAceCommandline.run()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#run,Method Bio.AlignAce.Applications.CompareAceCommandline.run()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#run,Method Bio.Entrez.Parser.DataHandler.run()=Bio.Entrez.Parser.DataHandler-class.html#run,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#run,Method Martel.setup.my_install.run()=Martel.setup.my_install-class.html#run,Method Martel.setup.run_install_tests.run()=Martel.setup.run_install_tests-class.html#run,Method Martel.setup.run_local_tests.run()=Martel.setup.run_local_tests-class.html#run"><a title="Bio.AlignAce.Applications.AlignAceCommandline.run
Bio.AlignAce.Applications.CompareAceCommandline.run
Bio.Entrez.Parser.DataHandler.run
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run
Martel.setup.my_install.run
Martel.setup.run_install_tests.run
Martel.setup.run_local_tests.run" class="py-name" href="#" onclick="return doclink('link-19', 'run', 'link-19');">run</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rms</tt><tt class="py-op">=</tt><tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rms()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#get_rms"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rms" class="py-name" href="#" onclick="return doclink('link-20', 'get_rms', 'link-20');">get_rms</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotran</tt><tt class="py-op">=</tt><tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rotran()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#get_rotran"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rotran" class="py-name" href="#" onclick="return doclink('link-21', 'get_rotran', 'link-21');">get_rotran</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="Superimposer.apply"></a><div id="Superimposer.apply-def"><a name="L47"></a><tt class="py-lineno">47</tt> <a class="py-toggle" href="#" id="Superimposer.apply-toggle" onclick="return toggle('Superimposer.apply');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Superimposer'.Superimposer-class.html#apply">apply</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">atom_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Superimposer.apply-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Superimposer.apply-expanded"><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-docstring"> Rotate/translate a list of atoms.</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotran</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-22" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-22', 'PDBException', 'link-7');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"No transformation has been calculated yet"</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">,</tt> <tt class="py-name">tran</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rotran</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">rot</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-23', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">tran</tt><tt class="py-op">=</tt><tt class="py-name">tran</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-24', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">atom</tt> <tt class="py-keyword">in</tt> <tt class="py-name">atom_list</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.PDB.Atom.Atom.transform()=Bio.PDB.Atom.Atom-class.html#transform"><a title="Bio.PDB.Atom.Atom.transform" class="py-name" href="#" onclick="return doclink('link-25', 'transform', 'link-25');">transform</a></tt><tt class="py-op">(</tt><tt class="py-name">rot</tt><tt class="py-op">,</tt> <tt class="py-name">tran</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-26" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-26', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-27', 'PDB', 'link-5');">PDB</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-28" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-28', 'PDBParser', 'link-28');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt id="link-29" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-29', 's1', 'link-29');">s1</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser.get_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure,Method Bio.PDB.PDBParser'.PDBParser.get_structure()=Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure,Method Bio.PDB.StructureBuilder.StructureBuilder.get_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-30', 'get_structure', 'link-30');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"FIXED"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-name">fixed</tt><tt class="py-op">=</tt><tt id="link-31" class="py-name" targets="Package Bio.GA.Selection=Bio.GA.Selection-module.html,Module Bio.PDB.Selection=Bio.PDB.Selection-module.html"><a title="Bio.GA.Selection
Bio.PDB.Selection" class="py-name" href="#" onclick="return doclink('link-31', 'Selection', 'link-31');">Selection</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Function Bio.PDB.Selection.unfold_entities()=Bio.PDB.Selection-module.html#unfold_entities"><a title="Bio.PDB.Selection.unfold_entities" class="py-name" href="#" onclick="return doclink('link-32', 'unfold_entities', 'link-32');">unfold_entities</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-33', 's1', 'link-29');">s1</a></tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt id="link-34" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-34', 's2', 'link-34');">s2</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-35', 'get_structure', 'link-30');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"MOVING"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-name">moving</tt><tt class="py-op">=</tt><tt id="link-36" class="py-name"><a title="Bio.GA.Selection
Bio.PDB.Selection" class="py-name" href="#" onclick="return doclink('link-36', 'Selection', 'link-31');">Selection</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Selection.unfold_entities" class="py-name" href="#" onclick="return doclink('link-37', 'unfold_entities', 'link-32');">unfold_entities</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-38', 's2', 'link-34');">s2</a></tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">identity</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-39', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-name">tran</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-number">2.0</tt><tt class="py-op">,</tt> <tt class="py-number">3.0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-40', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">atom</tt> <tt class="py-keyword">in</tt> <tt class="py-name">moving</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Atom.Atom.transform" class="py-name" href="#" onclick="return doclink('link-41', 'transform', 'link-25');">transform</a></tt><tt class="py-op">(</tt><tt class="py-name">rot</tt><tt class="py-op">,</tt> <tt class="py-name">tran</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">=</tt><tt id="link-42" class="py-name" targets="Class Bio.PDB.Superimposer'.Superimposer=Bio.PDB.Superimposer%27.Superimposer-class.html"><a title="Bio.PDB.Superimposer'.Superimposer" class="py-name" href="#" onclick="return doclink('link-42', 'Superimposer', 'link-42');">Superimposer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.PDB.Superimposer'.Superimposer.set_atoms()=Bio.PDB.Superimposer%27.Superimposer-class.html#set_atoms"><a title="Bio.PDB.Superimposer'.Superimposer.set_atoms" class="py-name" href="#" onclick="return doclink('link-43', 'set_atoms', 'link-43');">set_atoms</a></tt><tt class="py-op">(</tt><tt class="py-name">fixed</tt><tt class="py-op">,</tt> <tt class="py-name">moving</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt class="py-name">rotran</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt class="py-name">rms</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.PDB.Superimposer'.Superimposer.apply()=Bio.PDB.Superimposer%27.Superimposer-class.html#apply"><a title="Bio.PDB.Superimposer'.Superimposer.apply" class="py-name" href="#" onclick="return doclink('link-44', 'apply', 'link-44');">apply</a></tt><tt class="py-op">(</tt><tt class="py-name">moving</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> </tt><script type="text/javascript">
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