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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SVDSuperimposer-module.html">Package SVDSuperimposer</a> ::
Module SVDSuperimposer'
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<h1 class="epydoc">Source Code for <a href="Bio.SVDSuperimposer.SVDSuperimposer%27-module.html">Module Bio.SVDSuperimposer.SVDSuperimposer'</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@vub.ac.be)</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 class="py-name">matrixmultiply</tt><tt class="py-op">,</tt> <tt class="py-name">transpose</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-0', 'sum', 'link-0');">sum</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Variable Bio.Affy.CelFile.sqrt=Bio.Affy.CelFile-module.html#sqrt,Variable Bio.LogisticRegression.sqrt=Bio.LogisticRegression-module.html#sqrt,Variable Bio.MarkovModel.sqrt=Bio.MarkovModel-module.html#sqrt,Variable Bio.MaxEntropy.sqrt=Bio.MaxEntropy-module.html#sqrt,Variable Bio.NaiveBayes.sqrt=Bio.NaiveBayes-module.html#sqrt,Variable Bio.PDB.ResidueDepth'.sqrt=Bio.PDB.ResidueDepth%27-module.html#sqrt,Variable Bio.PDB.Vector'.sqrt=Bio.PDB.Vector%27-module.html#sqrt,Variable Bio.SVDSuperimposer.SVDSuperimposer'.sqrt=Bio.SVDSuperimposer.SVDSuperimposer%27-module.html#sqrt,Variable Bio.SVDSuperimposer.sqrt=Bio.SVDSuperimposer-module.html#sqrt,Variable Bio.Statistics.lowess.sqrt=Bio.Statistics.lowess-module.html#sqrt,Variable Bio.distance.sqrt=Bio.distance-module.html#sqrt,Variable Bio.kNN.sqrt=Bio.kNN-module.html#sqrt"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-1', 'sqrt', 'link-1');">sqrt</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">LinearAlgebra</tt> <tt class="py-keyword">import</tt> <tt class="py-name">singular_value_decomposition</tt><tt class="py-op">,</tt> <tt class="py-name">determinant</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer"></a><div id="SVDSuperimposer-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="SVDSuperimposer-toggle" onclick="return toggle('SVDSuperimposer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html">SVDSuperimposer</a><tt class="py-op">:</tt> </tt>
</div><div id="SVDSuperimposer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SVDSuperimposer-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"> SVDSuperimposer finds the best rotation and translation to put</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> two point sets on top of each other (minimizing the RMSD). This is </tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> eg. useful to superimpose crystal structures. </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> SVD stands for Singular Value Decomposition, which is used to calculate</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> the superposition.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> Reference:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> Matrix computations, 2nd ed. Golub, G. & Van Loan, CF., The Johns </tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> Hopkins University Press, Baltimore, 1989</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SVDSuperimposer.__init__"></a><div id="SVDSuperimposer.__init__-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.__init__-toggle" onclick="return toggle('SVDSuperimposer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-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="SVDSuperimposer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.__init__-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._clear()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#_clear"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._clear" class="py-name" href="#" onclick="return doclink('link-2', '_clear', 'link-2');">_clear</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-comment"># Private methods</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="SVDSuperimposer._clear"></a><div id="SVDSuperimposer._clear-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="SVDSuperimposer._clear-toggle" onclick="return toggle('SVDSuperimposer._clear');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#_clear">_clear</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="SVDSuperimposer._clear-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer._clear-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">transformed_coords</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tran</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</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>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">init_rms</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer._rms"></a><div id="SVDSuperimposer._rms-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="SVDSuperimposer._rms-toggle" onclick="return toggle('SVDSuperimposer._rms');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#_rms">_rms</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">coords1</tt><tt class="py-op">,</tt> <tt class="py-param">coords2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SVDSuperimposer._rms-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer._rms-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-docstring">"Return rms deviations between coords1 and coords2."</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">diff</tt><tt class="py-op">=</tt><tt class="py-name">coords1</tt><tt class="py-op">-</tt><tt class="py-name">coords2</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-name">coords1</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-3" class="py-name"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-3', 'sqrt', 'link-1');">sqrt</a></tt><tt class="py-op">(</tt><tt id="link-4" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-4', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-5', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">diff</tt><tt class="py-op">*</tt><tt class="py-name">diff</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-comment"># Public methods</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="SVDSuperimposer.set"></a><div id="SVDSuperimposer.set-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.set-toggle" onclick="return toggle('SVDSuperimposer.set');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#set">set</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reference_coords</tt><tt class="py-op">,</tt> <tt class="py-param">coords</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SVDSuperimposer.set-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.set-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> Set the coordinates to be superimposed.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> coords will be put on top of reference_coords.</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-docstring"> o reference_coords: an NxDIM array</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> o coords: an NxDIM array</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> DIM is the dimension of the points, N is the number</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> of points to be superimposed.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment"># clear everything from previous runs</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._clear" class="py-name" href="#" onclick="return doclink('link-6', '_clear', 'link-2');">_clear</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment"># store cordinates</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt><tt class="py-op">=</tt><tt class="py-name">reference_coords</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt><tt class="py-op">=</tt><tt class="py-name">coords</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">reference_coords</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">m</tt><tt class="py-op">=</tt><tt class="py-name">coords</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">!=</tt><tt class="py-name">m</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"Coordinate number/dimension mismatch."</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer.run"></a><div id="SVDSuperimposer.run-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.run-toggle" onclick="return toggle('SVDSuperimposer.run');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#run">run</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="SVDSuperimposer.run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.run-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-docstring">"Superimpose the coordinate sets."</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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">coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"No coordinates set."</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">coords</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">reference_coords</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># center on centroid</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">av1</tt><tt class="py-op">=</tt><tt id="link-7" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-7', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">coords</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">n</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">av2</tt><tt class="py-op">=</tt><tt id="link-8" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-8', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">reference_coords</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">n</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">coords</tt><tt class="py-op">=</tt><tt class="py-name">coords</tt><tt class="py-op">-</tt><tt class="py-name">av1</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">reference_coords</tt><tt class="py-op">=</tt><tt class="py-name">reference_coords</tt><tt class="py-op">-</tt><tt class="py-name">av2</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment"># correlation matrix</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">coords</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">reference_coords</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">u</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-9', 'd', 'link-9');">d</a></tt><tt class="py-op">,</tt> <tt class="py-name">vt</tt><tt class="py-op">=</tt><tt class="py-name">singular_value_decomposition</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">vt</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">u</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-comment"># check if we have found a reflection</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">determinant</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">vt</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">vt</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">vt</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">u</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tran</tt><tt class="py-op">=</tt><tt class="py-name">av2</tt><tt class="py-op">-</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">av1</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer.get_transformed"></a><div id="SVDSuperimposer.get_transformed-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.get_transformed-toggle" onclick="return toggle('SVDSuperimposer.get_transformed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#get_transformed">get_transformed</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="SVDSuperimposer.get_transformed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.get_transformed-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-docstring">"Get the transformed coordinate set."</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</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">coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"No coordinates set."</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</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">rot</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"Nothing superimposed yet."</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</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">transformed_coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">transformed_coords</tt><tt class="py-op">=</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tran</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">transformed_coords</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer.get_rotran"></a><div id="SVDSuperimposer.get_rotran-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.get_rotran-toggle" onclick="return toggle('SVDSuperimposer.get_rotran');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#get_rotran">get_rotran</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="SVDSuperimposer.get_rotran-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.get_rotran-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-docstring">"Right multiplying rotation matrix and translation."</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</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">rot</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"Nothing superimposed yet."</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rot</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tran</tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer.get_init_rms"></a><div id="SVDSuperimposer.get_init_rms-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.get_init_rms-toggle" onclick="return toggle('SVDSuperimposer.get_init_rms');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#get_init_rms">get_init_rms</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="SVDSuperimposer.get_init_rms-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.get_init_rms-expanded"><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-docstring">"Root mean square deviation of untransformed coordinates."</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</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">coords</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> <tt class="py-string">"No coordinates set yet."</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</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">init_rms</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">init_rms</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._rms()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#_rms"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._rms" class="py-name" href="#" onclick="return doclink('link-10', '_rms', 'link-10');">_rms</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">init_rms</tt> </tt>
</div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="SVDSuperimposer.get_rms"></a><div id="SVDSuperimposer.get_rms-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="SVDSuperimposer.get_rms-toggle" onclick="return toggle('SVDSuperimposer.get_rms');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer-class.html#get_rms">get_rms</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="SVDSuperimposer.get_rms-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SVDSuperimposer.get_rms-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-docstring">"Root mean square deviation of superimposed coordinates."</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</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">rms</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">transformed_coords</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_transformed()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#get_transformed"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_transformed" class="py-name" href="#" onclick="return doclink('link-11', 'get_transformed', 'link-11');">get_transformed</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</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">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer._rms" class="py-name" href="#" onclick="return doclink('link-12', '_rms', 'link-10');">_rms</a></tt><tt class="py-op">(</tt><tt class="py-name">transformed_coords</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reference_coords</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rms</tt> </tt>
</div></div><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</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="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</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="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># start with two coordinate sets (Nx3 arrays - Float0)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt id="link-13" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-13', 'x', 'link-13');">x</a></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-op">[</tt><tt class="py-number">51.65</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1.90</tt><tt class="py-op">,</tt> <tt class="py-number">50.07</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">50.40</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1.23</tt><tt class="py-op">,</tt> <tt class="py-number">50.65</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">50.68</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">0.04</tt><tt class="py-op">,</tt> <tt class="py-number">51.54</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">50.22</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">0.02</tt><tt class="py-op">,</tt> <tt class="py-number">52.85</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-14" 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-14', 'Float0', 'link-14');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">y</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-op">[</tt><tt class="py-number">51.30</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">2.99</tt><tt class="py-op">,</tt> <tt class="py-number">46.54</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">51.09</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1.88</tt><tt class="py-op">,</tt> <tt class="py-number">47.58</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">52.36</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1.20</tt><tt class="py-op">,</tt> <tt class="py-number">48.03</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-number">52.71</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1.18</tt><tt class="py-op">,</tt> <tt class="py-number">49.38</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-15" 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-15', 'Float0', 'link-14');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment"># start!</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sup</tt><tt class="py-op">=</tt><tt id="link-16" 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-16', 'SVDSuperimposer', 'link-16');">SVDSuperimposer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-comment"># set the coords</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># y will be rotated and translated on x</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'set', 'link-17');">set</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-18', 'x', 'link-13');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-comment"># do the lsq fit</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-comment"></tt> <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="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-comment"># get the rmsd</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-comment"></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="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-comment"># get rotation (right multiplying!) and the translation</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"></tt> <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">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>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-comment"># rotate y on x</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">y_on_x1</tt><tt class="py-op">=</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">rot</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">tran</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment"># same thing</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">y_on_x2</tt><tt class="py-op">=</tt><tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_transformed" class="py-name" href="#" onclick="return doclink('link-22', 'get_transformed', 'link-11');">get_transformed</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">y_on_x1</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">y_on_x2</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt> <tt class="py-name">rms</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt><script type="text/javascript">
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