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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module Vector'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.Vector%27-module.html">Module Bio.PDB.Vector'</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) 2004, 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 class="py-name">array</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 class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Variable Bio.Affy.CelFile.arccos=Bio.Affy.CelFile-module.html#arccos,Variable Bio.LogisticRegression.arccos=Bio.LogisticRegression-module.html#arccos,Variable Bio.MarkovModel.arccos=Bio.MarkovModel-module.html#arccos,Variable Bio.MaxEntropy.arccos=Bio.MaxEntropy-module.html#arccos,Variable Bio.NaiveBayes.arccos=Bio.NaiveBayes-module.html#arccos,Variable Bio.PDB.Vector'.arccos=Bio.PDB.Vector%27-module.html#arccos,Variable Bio.Statistics.lowess.arccos=Bio.Statistics.lowess-module.html#arccos,Variable Bio.distance.arccos=Bio.distance-module.html#arccos,Variable Bio.kNN.arccos=Bio.kNN-module.html#arccos"><a title="Bio.Affy.CelFile.arccos
Bio.LogisticRegression.arccos
Bio.MarkovModel.arccos
Bio.MaxEntropy.arccos
Bio.NaiveBayes.arccos
Bio.PDB.Vector'.arccos
Bio.Statistics.lowess.arccos
Bio.distance.arccos
Bio.kNN.arccos" class="py-name" href="#" onclick="return doclink('link-2', 'arccos', 'link-2');">arccos</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 id="link-3" class="py-name" targets="Variable Bio.Affy.CelFile.cos=Bio.Affy.CelFile-module.html#cos,Variable Bio.LogisticRegression.cos=Bio.LogisticRegression-module.html#cos,Variable Bio.MarkovModel.cos=Bio.MarkovModel-module.html#cos,Variable Bio.MaxEntropy.cos=Bio.MaxEntropy-module.html#cos,Variable Bio.NaiveBayes.cos=Bio.NaiveBayes-module.html#cos,Variable Bio.PDB.Vector'.cos=Bio.PDB.Vector%27-module.html#cos,Variable Bio.Statistics.lowess.cos=Bio.Statistics.lowess-module.html#cos,Variable Bio.distance.cos=Bio.distance-module.html#cos,Variable Bio.kNN.cos=Bio.kNN-module.html#cos"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-3', 'cos', 'link-3');">cos</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.Affy.CelFile.sin=Bio.Affy.CelFile-module.html#sin,Variable Bio.LogisticRegression.sin=Bio.LogisticRegression-module.html#sin,Variable Bio.MarkovModel.sin=Bio.MarkovModel-module.html#sin,Variable Bio.MaxEntropy.sin=Bio.MaxEntropy-module.html#sin,Variable Bio.NaiveBayes.sin=Bio.NaiveBayes-module.html#sin,Variable Bio.PDB.Vector'.sin=Bio.PDB.Vector%27-module.html#sin,Variable Bio.Statistics.lowess.sin=Bio.Statistics.lowess-module.html#sin,Variable Bio.distance.sin=Bio.distance-module.html#sin,Variable Bio.kNN.sin=Bio.kNN-module.html#sin"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-4', 'sin', 'link-4');">sin</a></tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.trace()=Bio.Nexus.Nodes.Chain-class.html#trace"><a title="Bio.Nexus.Nodes.Chain.trace" class="py-name" href="#" onclick="return doclink('link-5', 'trace', 'link-5');">trace</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt class="py-name">acos</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</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">determinant</tt><tt class="py-op">,</tt> <tt class="py-name">eigenvectors</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">MLab</tt> <tt class="py-keyword">import</tt> <tt class="py-name">eye</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Variable Bio.Affy.CelFile.pi=Bio.Affy.CelFile-module.html#pi,Variable Bio.LogisticRegression.pi=Bio.LogisticRegression-module.html#pi,Variable Bio.MarkovModel.pi=Bio.MarkovModel-module.html#pi,Variable Bio.MaxEntropy.pi=Bio.MaxEntropy-module.html#pi,Variable Bio.NaiveBayes.pi=Bio.NaiveBayes-module.html#pi,Variable Bio.PDB.Vector'.pi=Bio.PDB.Vector%27-module.html#pi,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#pi,Variable Bio.Statistics.lowess.pi=Bio.Statistics.lowess-module.html#pi,Variable Bio.distance.pi=Bio.distance-module.html#pi,Variable Bio.kNN.pi=Bio.kNN-module.html#pi"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-6', 'pi', 'link-6');">pi</a></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="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt id="link-7" 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-7', '__doc__', 'link-7');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"Vector class, including rotation-related functions."</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="m2rotaxis"></a><div id="m2rotaxis-def"><a name="L17"></a><tt class="py-lineno"> 17</tt> <a class="py-toggle" href="#" id="m2rotaxis-toggle" onclick="return toggle('m2rotaxis');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#m2rotaxis">m2rotaxis</a><tt class="py-op">(</tt><tt class="py-param">m</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="m2rotaxis-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="m2rotaxis-expanded"><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"> Return angles, axis pair that corresponds to rotation matrix m.</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-comment"># Angle always between 0 and pi</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Sense of rotation is defined by axis orientation</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="Bio.Nexus.Nodes.Chain.trace" class="py-name" href="#" onclick="return doclink('link-8', 'trace', 'link-5');">trace</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt id="link-9" class="py-name" targets="Method Bio.PDB.Vector'.Vector.angle()=Bio.PDB.Vector%27.Vector-class.html#angle"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-9', 'angle', 'link-9');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">acos</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-10" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-10', 'angle', 'link-9');">angle</a></tt><tt class="py-op"><</tt><tt class="py-number">1e-15</tt><tt class="py-op">:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-comment"># Angle is 0</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Class Bio.PDB.Vector'.Vector=Bio.PDB.Vector%27.Vector-class.html"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-11', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-12" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-12', 'angle', 'link-9');">angle</a></tt><tt class="py-op"><</tt><tt id="link-13" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-13', 'pi', 'link-6');">pi</a></tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-comment"># Angle is smaller than pi</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-14" 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-14', 'x', 'link-14');">x</a></tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">2</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-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</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-name">m</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">z</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-number">0</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">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt id="link-15" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-15', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-16', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">z</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">axis</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.normalize=Bio.EUtils.DTDs.LinkOut.normalize-class.html,Method Bio.PDB.Vector'.Vector.normalize()=Bio.PDB.Vector%27.Vector-class.html#normalize,Method Bio.config.FormatRegistry.FormatRegistry.normalize()=Bio.config.FormatRegistry.FormatRegistry-class.html#normalize,Function Martel.test.test_RecordReader2.normalize()=Martel.test.test_RecordReader2-module.html#normalize"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-17', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-18" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-18', 'angle', 'link-9');">angle</a></tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-comment"># Angle is pi - special case!</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">m00</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</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">m11</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-number">1</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">m22</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m00</tt><tt class="py-op">></tt><tt class="py-name">m11</tt> <tt class="py-keyword">and</tt> <tt class="py-name">m00</tt><tt class="py-op">></tt><tt class="py-name">m22</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-19', 'x', 'link-14');">x</a></tt><tt class="py-op">=</tt><tt id="link-20" 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-20', 'sqrt', 'link-1');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">m00</tt><tt class="py-op">-</tt><tt class="py-name">m11</tt><tt class="py-op">-</tt><tt class="py-name">m22</tt><tt class="py-op">+</tt><tt class="py-number">0.5</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">y</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</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-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-14');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">z</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</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-number">2</tt><tt class="py-op">*</tt><tt id="link-22" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-22', 'x', 'link-14');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">m11</tt><tt class="py-op">></tt><tt class="py-name">m00</tt> <tt class="py-keyword">and</tt> <tt class="py-name">m11</tt><tt class="py-op">></tt><tt class="py-name">m22</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">=</tt><tt id="link-23" 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-23', 'sqrt', 'link-1');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">m11</tt><tt class="py-op">-</tt><tt class="py-name">m00</tt><tt class="py-op">-</tt><tt class="py-name">m22</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-14');">x</a></tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</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-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">z</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-number">2</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">z</tt><tt class="py-op">=</tt><tt id="link-25" 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-25', 'sqrt', 'link-1');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">m22</tt><tt class="py-op">-</tt><tt class="py-name">m00</tt><tt class="py-op">-</tt><tt class="py-name">m11</tt><tt class="py-op">+</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-14');">x</a></tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">[</tt><tt class="py-number">0</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-number">2</tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">y</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-number">2</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">z</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">axis</tt><tt class="py-op">=</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-27', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">axis</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-29', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-30" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-30', 'pi', 'link-6');">pi</a></tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt> </tt>
</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="vector_to_axis"></a><div id="vector_to_axis-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="vector_to_axis-toggle" onclick="return toggle('vector_to_axis');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#vector_to_axis">vector_to_axis</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">,</tt> <tt class="py-param">point</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="vector_to_axis-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="vector_to_axis-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> Returns the vector between a point and</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> the closest point on a line (ie. the perpendicular</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> projection of the point on the line).</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> @type line: L{Vector}</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> @param line: vector defining a line</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> @type point: L{Vector}</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> @param point: vector defining the point</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.PDB.Vector'.Vector.normalized()=Bio.PDB.Vector%27.Vector-class.html#normalized"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-31', 'normalized', 'link-31');">normalized</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">np</tt><tt class="py-op">=</tt><tt id="link-32" class="py-name" targets="Variable Bio.LocusLink.locus_format.point=Bio.LocusLink.locus_format-module.html#point"><a title="Bio.LocusLink.locus_format.point" class="py-name" href="#" onclick="return doclink('link-32', 'point', 'link-32');">point</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.PDB.Vector'.Vector.norm()=Bio.PDB.Vector%27.Vector-class.html#norm"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-33', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-34" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-34', 'angle', 'link-9');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-35', 'angle', 'link-9');">angle</a></tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.LocusLink.locus_format.point" class="py-name" href="#" onclick="return doclink('link-36', 'point', 'link-32');">point</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-keyword">return</tt> <tt id="link-37" class="py-name"><a title="Bio.LocusLink.locus_format.point" class="py-name" href="#" onclick="return doclink('link-37', 'point', 'link-32');">point</a></tt><tt class="py-op">-</tt><tt class="py-name">line</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">*</tt><tt id="link-38" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-38', 'cos', 'link-3');">cos</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-39', 'angle', 'link-9');">angle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><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>
<a name="rotaxis2m"></a><div id="rotaxis2m-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="rotaxis2m-toggle" onclick="return toggle('rotaxis2m');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#rotaxis2m">rotaxis2m</a><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">vector</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rotaxis2m-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rotaxis2m-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> Calculate a left multiplying rotation matrix that rotates</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> theta rad around vector.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> Example: </tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> >>> m=rotaxis(pi, Vector(1,0,0))</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> >>> rotated_vector=any_vector.left_multiply(m)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> @type theta: float</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> @param theta: the rotation angle</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> @type vector: L{Vector}</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> @param vector: the rotation axis</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> @return: The rotation matrix, a 3x3 Numeric array.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">vector</tt><tt class="py-op">=</tt><tt class="py-name">vector</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-40', 'copy', 'link-40');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">vector</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-41', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt id="link-42" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-42', 'cos', 'link-3');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt id="link-43" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-43', 's', 'link-43');">s</a></tt><tt class="py-op">=</tt><tt id="link-44" class="py-name"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-44', 'sin', 'link-4');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">t</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">c</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-45', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">=</tt><tt class="py-name">vector</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.PDB.Vector'.Vector.get_array()=Bio.PDB.Vector%27.Vector-class.html#get_array"><a title="Bio.PDB.Vector'.Vector.get_array" class="py-name" href="#" onclick="return doclink('link-46', 'get_array', 'link-46');">get_array</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">rot</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-number">3</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="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># 1st row</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">t</tt><tt class="py-op">*</tt><tt id="link-47" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-47', 'x', 'link-14');">x</a></tt><tt class="py-op">*</tt><tt id="link-48" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-48', 'x', 'link-14');">x</a></tt><tt class="py-op">+</tt><tt class="py-name">c</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">0</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">t</tt><tt class="py-op">*</tt><tt id="link-49" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-49', 'x', 'link-14');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">-</tt><tt id="link-50" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-50', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt class="py-name">z</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">0</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-name">t</tt><tt class="py-op">*</tt><tt id="link-51" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-51', 'x', 'link-14');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">+</tt><tt id="link-52" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-52', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt class="py-name">y</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># 2nd row</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">t</tt><tt class="py-op">*</tt><tt id="link-53" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-53', 'x', 'link-14');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">+</tt><tt id="link-54" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-54', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt class="py-name">z</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">1</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">t</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">+</tt><tt class="py-name">c</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">1</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-name">t</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">-</tt><tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt id="link-56" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-56', 'x', 'link-14');">x</a></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-comment"># 3rd row</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">t</tt><tt class="py-op">*</tt><tt id="link-57" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-57', 'x', 'link-14');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">-</tt><tt id="link-58" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-58', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt class="py-name">y</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">2</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">t</tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">+</tt><tt id="link-59" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-59', 's', 'link-43');">s</a></tt><tt class="py-op">*</tt><tt id="link-60" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-60', 'x', 'link-14');">x</a></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">[</tt><tt class="py-number">2</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-name">t</tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">*</tt><tt class="py-name">z</tt><tt class="py-op">+</tt><tt class="py-name">c</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rot</tt> </tt>
</div><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-name">rotaxis</tt><tt class="py-op">=</tt><tt id="link-61" class="py-name" targets="Function Bio.PDB.Vector'.rotaxis2m()=Bio.PDB.Vector%27-module.html#rotaxis2m"><a title="Bio.PDB.Vector'.rotaxis2m" class="py-name" href="#" onclick="return doclink('link-61', 'rotaxis2m', 'link-61');">rotaxis2m</a></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="refmat"></a><div id="refmat-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="refmat-toggle" onclick="return toggle('refmat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#refmat">refmat</a><tt class="py-op">(</tt><tt class="py-param">p</tt><tt class="py-op">,</tt><tt class="py-param">q</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="refmat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="refmat-expanded"><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> Return a (left multiplying) matrix that mirrors p onto q.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> >>> mirror=refmat(p,q)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> >>> qq=p.left_multiply(mirror)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> >>> print q, qq # q and qq should be the same</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> @type p,q: L{Vector}</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> @return: The mirror operation, a 3x3 Numeric array. </tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-62', 'normalize', 'link-17');">normalize</a></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-name">q</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-63', 'normalize', 'link-17');">normalize</a></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-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">-</tt><tt class="py-name">q</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-64', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-number">1e-5</tt><tt class="py-op">:</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">eye</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">pq</tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">-</tt><tt class="py-name">q</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">pq</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-65', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">b</tt><tt class="py-op">=</tt><tt class="py-name">pq</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.PDB.Vector'.Vector.get_array" class="py-name" href="#" onclick="return doclink('link-66', 'get_array', 'link-46');">get_array</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 class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">shape</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-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt id="link-67" 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-67', 'i', 'link-67');">i</a></tt><tt class="py-op">=</tt><tt class="py-name">eye</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">ref</tt><tt class="py-op">=</tt><tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-67');">i</a></tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">,</tt> <tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ref</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="rotmat"></a><div id="rotmat-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="rotmat-toggle" onclick="return toggle('rotmat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#rotmat">rotmat</a><tt class="py-op">(</tt><tt class="py-param">p</tt><tt class="py-op">,</tt><tt class="py-param">q</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rotmat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rotmat-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> Return a (left multiplying) matrix that rotates p onto q.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> >>> r=rotmat(p,q)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> >>> print q, p.left_multiply(r)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> @param p: moving vector</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> @type p: L{Vector}</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> @param q: fixed vector</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> @type q: L{Vector}</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> @return: rotation matrix that rotates p onto q</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: 3x3 Numeric array</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">=</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt id="link-69" class="py-name" targets="Function Bio.PDB.Vector'.refmat()=Bio.PDB.Vector%27-module.html#refmat"><a title="Bio.PDB.Vector'.refmat" class="py-name" href="#" onclick="return doclink('link-69', 'refmat', 'link-69');">refmat</a></tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-70" class="py-name"><a title="Bio.PDB.Vector'.refmat" class="py-name" href="#" onclick="return doclink('link-70', 'refmat', 'link-69');">refmat</a></tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rot</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="calc_angle"></a><div id="calc_angle-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="calc_angle-toggle" onclick="return toggle('calc_angle');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#calc_angle">calc_angle</a><tt class="py-op">(</tt><tt class="py-param">v1</tt><tt class="py-op">,</tt> <tt class="py-param">v2</tt><tt class="py-op">,</tt> <tt class="py-param">v3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="calc_angle-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="calc_angle-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Calculate the angle between 3 vectors</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> representing 3 connected points.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> @param v1, v2, v3: the tree points that define the angle</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> @type v1, v2, v3: L{Vector}</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> @return: angle</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: float</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">v1</tt><tt class="py-op">=</tt><tt class="py-name">v1</tt><tt class="py-op">-</tt><tt class="py-name">v2</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">v3</tt><tt class="py-op">=</tt><tt class="py-name">v3</tt><tt class="py-op">-</tt><tt class="py-name">v2</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-71', 'angle', 'link-9');">angle</a></tt><tt class="py-op">(</tt><tt class="py-name">v3</tt><tt class="py-op">)</tt> </tt>
</div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="calc_dihedral"></a><div id="calc_dihedral-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="calc_dihedral-toggle" onclick="return toggle('calc_dihedral');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'-module.html#calc_dihedral">calc_dihedral</a><tt class="py-op">(</tt><tt class="py-param">v1</tt><tt class="py-op">,</tt> <tt class="py-param">v2</tt><tt class="py-op">,</tt> <tt class="py-param">v3</tt><tt class="py-op">,</tt> <tt class="py-param">v4</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="calc_dihedral-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="calc_dihedral-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> Calculate the dihedral angle between 4 vectors</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> representing 4 connected points. The angle is in</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> ]-pi, pi].</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> @param v1, v2, v3, v4: the four points that define the dihedral angle</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> @type v1, v2, v3, v4: L{Vector}</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">ab</tt><tt class="py-op">=</tt><tt class="py-name">v1</tt><tt class="py-op">-</tt><tt class="py-name">v2</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">cb</tt><tt class="py-op">=</tt><tt class="py-name">v3</tt><tt class="py-op">-</tt><tt class="py-name">v2</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt id="link-72" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-72', 'db', 'link-72');">db</a></tt><tt class="py-op">=</tt><tt class="py-name">v4</tt><tt class="py-op">-</tt><tt class="py-name">v3</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">u</tt><tt class="py-op">=</tt><tt class="py-name">ab</tt><tt class="py-op">**</tt><tt class="py-name">cb</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-73" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-73', 'v', 'link-73');">v</a></tt><tt class="py-op">=</tt><tt id="link-74" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-74', 'db', 'link-72');">db</a></tt><tt class="py-op">**</tt><tt class="py-name">cb</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">w</tt><tt class="py-op">=</tt><tt class="py-name">u</tt><tt class="py-op">**</tt><tt id="link-75" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-75', 'v', 'link-73');">v</a></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-76', 'angle', 'link-9');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">u</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-77', 'angle', 'link-9');">angle</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-78', 'v', 'link-73');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-comment"># Determine sign of angle</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cb</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-79', 'angle', 'link-9');">angle</a></tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">0.001</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-80', 'angle', 'link-9');">angle</a></tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt id="link-81" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-81', 'angle', 'link-9');">angle</a></tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ZeroDivisionError</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-comment"># dihedral=pi</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-82" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-82', 'angle', 'link-9');">angle</a></tt> </tt>
</div><a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> </tt>
<a name="Vector"></a><div id="Vector-def"><a name="L204"></a><tt class="py-lineno">204</tt> <a class="py-toggle" href="#" id="Vector-toggle" onclick="return toggle('Vector');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html">Vector</a><tt class="py-op">:</tt> </tt>
</div><div id="Vector-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Vector-expanded"><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-docstring">"3D vector"</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="Vector.__init__"></a><div id="Vector.__init__-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="Vector.__init__-toggle" onclick="return toggle('Vector.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">z</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__init__-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">y</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">z</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># Array, list, tuple...</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-83', 'x', 'link-14');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"Vector: x is not a list/tuple/array of 3 numbers"</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-84', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment"># Three numbers</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</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">_ar</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-85', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">z</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="Vector.__repr__"></a><div id="Vector.__repr__-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="Vector.__repr__-toggle" onclick="return toggle('Vector.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__repr__">__repr__</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="Vector.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__repr__-expanded"><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-86', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<Vector %.2f, %.2f, %.2f>"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-87" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-87', 'x', 'link-14');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> </tt>
</div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
<a name="Vector.__neg__"></a><div id="Vector.__neg__-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="Vector.__neg__-toggle" onclick="return toggle('Vector.__neg__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__neg__">__neg__</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="Vector.__neg__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__neg__-expanded"><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector(-x, -y, -z)"</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">a</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">_ar</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-88" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-88', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="Vector.__add__"></a><div id="Vector.__add__-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="Vector.__add__-toggle" onclick="return toggle('Vector.__add__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__add__">__add__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__add__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__add__-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector+other Vector or scalar"</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt id="link-89" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-89', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">+</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">+</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-90" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-90', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="Vector.__sub__"></a><div id="Vector.__sub__-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="Vector.__sub__-toggle" onclick="return toggle('Vector.__sub__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__sub__">__sub__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__sub__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__sub__-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector-other Vector or scalar"</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-91', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">-</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">-</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-92" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-92', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="Vector.__mul__"></a><div id="Vector.__mul__-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="Vector.__mul__-toggle" onclick="return toggle('Vector.__mul__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__mul__">__mul__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__mul__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__mul__-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector.Vector (dot product)"</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-93" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-93', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">*</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="Vector.__div__"></a><div id="Vector.__div__-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="Vector.__div__-toggle" onclick="return toggle('Vector.__div__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__div__">__div__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__div__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__div__-expanded"><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector(coords/a)"</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">/</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-94', 'x', 'link-14');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-95" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-95', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="Vector.__pow__"></a><div id="Vector.__pow__-def"><a name="L251"></a><tt class="py-lineno">251</tt> <a class="py-toggle" href="#" id="Vector.__pow__-toggle" onclick="return toggle('Vector.__pow__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__pow__">__pow__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__pow__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__pow__-expanded"><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-docstring">"Return VectorxVector (cross product) or Vectorxscalar"</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt id="link-96" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-96', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt id="link-97" 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-97', 'd', 'link-97');">d</a></tt><tt class="py-op">,</tt><tt id="link-98" class="py-name" targets="Variable Bio.Affy.CelFile.e=Bio.Affy.CelFile-module.html#e,Variable Bio.LogisticRegression.e=Bio.LogisticRegression-module.html#e,Variable Bio.MarkovModel.e=Bio.MarkovModel-module.html#e,Variable Bio.MaxEntropy.e=Bio.MaxEntropy-module.html#e,Variable Bio.NaiveBayes.e=Bio.NaiveBayes-module.html#e,Variable Bio.Statistics.lowess.e=Bio.Statistics.lowess-module.html#e,Variable Bio.distance.e=Bio.distance-module.html#e,Variable Bio.kNN.e=Bio.kNN-module.html#e"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-98', 'e', 'link-98');">e</a></tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">=</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">c1</tt><tt class="py-op">=</tt><tt class="py-name">determinant</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-name">b</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-99', 'e', 'link-98');">e</a></tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">c2</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">determinant</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-name">a</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-100', 'd', 'link-97');">d</a></tt><tt class="py-op">,</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">c3</tt><tt class="py-op">=</tt><tt class="py-name">determinant</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-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-101', 'd', 'link-97');">d</a></tt><tt class="py-op">,</tt><tt id="link-102" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-102', 'e', 'link-98');">e</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-103" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-103', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">c1</tt><tt class="py-op">,</tt><tt class="py-name">c2</tt><tt class="py-op">,</tt><tt class="py-name">c3</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">*</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-104" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-104', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="Vector.__getitem__"></a><div id="Vector.__getitem__-def"><a name="L264"></a><tt class="py-lineno">264</tt> <a class="py-toggle" href="#" id="Vector.__getitem__-toggle" onclick="return toggle('Vector.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__getitem__-expanded"><a name="L265"></a><tt class="py-lineno">265</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">_ar</tt><tt class="py-op">[</tt><tt id="link-105" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-105', 'i', 'link-67');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="Vector.__setitem__"></a><div id="Vector.__setitem__-def"><a name="L267"></a><tt class="py-lineno">267</tt> <a class="py-toggle" href="#" id="Vector.__setitem__-toggle" onclick="return toggle('Vector.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.__setitem__-expanded"><a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">[</tt><tt id="link-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-67');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-107" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-107', 'value', 'link-107');">value</a></tt> </tt>
</div><a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> </tt>
<a name="Vector.norm"></a><div id="Vector.norm-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="Vector.norm-toggle" onclick="return toggle('Vector.norm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#norm">norm</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="Vector.norm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.norm-expanded"><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-docstring">"Return vector norm"</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-108" 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-108', 'sqrt', 'link-1');">sqrt</a></tt><tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-109', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="Vector.normsq"></a><div id="Vector.normsq-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="Vector.normsq-toggle" onclick="return toggle('Vector.normsq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#normsq">normsq</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="Vector.normsq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.normsq-expanded"><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-docstring">"Return square of vector norm"</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-110" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-110', 'abs', 'link-110');">abs</a></tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-111', 'sum', 'link-0');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="Vector.normalize"></a><div id="Vector.normalize-def"><a name="L278"></a><tt class="py-lineno">278</tt> <a class="py-toggle" href="#" id="Vector.normalize-toggle" onclick="return toggle('Vector.normalize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#normalize">normalize</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="Vector.normalize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.normalize-expanded"><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-docstring">"Normalize the Vector"</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-112', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
<a name="Vector.normalized"></a><div id="Vector.normalized-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="Vector.normalized-toggle" onclick="return toggle('Vector.normalized');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#normalized">normalized</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="Vector.normalized-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.normalized-expanded"><a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-docstring">"Return a normalized copy of the Vector"</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-113', 'v', 'link-73');">v</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-114', 'copy', 'link-40');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-115', 'v', 'link-73');">v</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-116', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-117" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-117', 'v', 'link-73');">v</a></tt> </tt>
</div><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="Vector.angle"></a><div id="Vector.angle-def"><a name="L288"></a><tt class="py-lineno">288</tt> <a class="py-toggle" href="#" id="Vector.angle-toggle" onclick="return toggle('Vector.angle');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#angle">angle</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.angle-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.angle-expanded"><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-docstring">"Return angle between two vectors"</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt id="link-118" class="py-name" targets="Variable Bio.PDB.Polypeptide.n1=Bio.PDB.Polypeptide-module.html#n1"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-118', 'n1', 'link-118');">n1</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-119', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">n2</tt><tt class="py-op">=</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-120', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">c</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">other</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-121', 'n1', 'link-118');">n1</a></tt><tt class="py-op">*</tt><tt class="py-name">n2</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-comment"># Take care of roundoff errors</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-122" class="py-name"><a title="Bio.Affy.CelFile.arccos
Bio.LogisticRegression.arccos
Bio.MarkovModel.arccos
Bio.MaxEntropy.arccos
Bio.NaiveBayes.arccos
Bio.PDB.Vector'.arccos
Bio.Statistics.lowess.arccos
Bio.distance.arccos
Bio.kNN.arccos" class="py-name" href="#" onclick="return doclink('link-122', 'arccos', 'link-2');">arccos</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
</div><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="Vector.get_array"></a><div id="Vector.get_array-def"><a name="L298"></a><tt class="py-lineno">298</tt> <a class="py-toggle" href="#" id="Vector.get_array-toggle" onclick="return toggle('Vector.get_array');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#get_array">get_array</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="Vector.get_array-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.get_array-expanded"><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-docstring">"Return (a copy of) the array of coordinates"</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt> </tt>
</div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="Vector.left_multiply"></a><div id="Vector.left_multiply-def"><a name="L302"></a><tt class="py-lineno">302</tt> <a class="py-toggle" href="#" id="Vector.left_multiply-toggle" onclick="return toggle('Vector.left_multiply');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#left_multiply">left_multiply</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.left_multiply-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.left_multiply-expanded"><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector=Matrix x Vector"</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">matrixmultiply</tt><tt class="py-op">(</tt><tt id="link-123" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.matrix()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#matrix,Variable Bio.MetaTool.metatool_format.matrix=Bio.MetaTool.metatool_format-module.html#matrix,Method Bio.Prosite._RecordConsumer.matrix()=Bio.Prosite._RecordConsumer-class.html#matrix"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-123', 'matrix', 'link-123');">matrix</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-124" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-124', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="Vector.right_multiply"></a><div id="Vector.right_multiply-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="Vector.right_multiply-toggle" onclick="return toggle('Vector.right_multiply');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#right_multiply">right_multiply</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Vector.right_multiply-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.right_multiply-expanded"><a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-docstring">"Return Vector=Vector x Matrix"</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <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">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">,</tt> <tt id="link-125" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-125', 'matrix', 'link-123');">matrix</a></tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-126" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-126', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="Vector.copy"></a><div id="Vector.copy-def"><a name="L312"></a><tt class="py-lineno">312</tt> <a class="py-toggle" href="#" id="Vector.copy-toggle" onclick="return toggle('Vector.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Vector'.Vector-class.html#copy">copy</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="Vector.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Vector.copy-expanded"><a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-docstring">"Return a deep copy of the Vector"</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-127" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-127', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ar</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</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="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt id="link-128" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-128', 'pi', 'link-6');">pi</a></tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">RandomArray</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</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="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">v1</tt><tt class="py-op">=</tt><tt id="link-129" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-129', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">v2</tt><tt class="py-op">=</tt><tt id="link-130" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-130', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">v3</tt><tt class="py-op">=</tt><tt id="link-131" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-131', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-name">v4</tt><tt class="py-op">=</tt><tt id="link-132" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-132', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-name">v4</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-133', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v4</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-134" class="py-name" targets="Function Bio.PDB.Vector'.calc_angle()=Bio.PDB.Vector%27-module.html#calc_angle"><a title="Bio.PDB.Vector'.calc_angle" class="py-name" href="#" onclick="return doclink('link-134', 'calc_angle', 'link-134');">calc_angle</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">dih</tt><tt class="py-op">=</tt><tt id="link-135" class="py-name" targets="Function Bio.PDB.Vector'.calc_dihedral()=Bio.PDB.Vector%27-module.html#calc_dihedral"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-135', 'calc_dihedral', 'link-135');">calc_dihedral</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">,</tt> <tt class="py-name">v4</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment"># Test dihedral sign</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">dih</tt><tt class="py-op">></tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"DIHEDRAL "</tt><tt class="py-op">,</tt> <tt class="py-name">dih</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">ref</tt><tt class="py-op">=</tt><tt id="link-136" class="py-name"><a title="Bio.PDB.Vector'.refmat" class="py-name" href="#" onclick="return doclink('link-136', 'refmat', 'link-69');">refmat</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">=</tt><tt id="link-137" class="py-name" targets="Function Bio.PDB.Vector'.rotmat()=Bio.PDB.Vector%27-module.html#rotmat"><a title="Bio.PDB.Vector'.rotmat" class="py-name" href="#" onclick="return doclink('link-137', 'rotmat', 'link-137');">rotmat</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v3</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Method Bio.PDB.Vector'.Vector.left_multiply()=Bio.PDB.Vector%27.Vector-class.html#left_multiply"><a title="Bio.PDB.Vector'.Vector.left_multiply" class="py-name" href="#" onclick="return doclink('link-138', 'left_multiply', 'link-138');">left_multiply</a></tt><tt class="py-op">(</tt><tt class="py-name">ref</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.PDB.Vector'.Vector.left_multiply" class="py-name" href="#" onclick="return doclink('link-139', 'left_multiply', 'link-138');">left_multiply</a></tt><tt class="py-op">(</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Method Bio.PDB.Vector'.Vector.right_multiply()=Bio.PDB.Vector%27.Vector-class.html#right_multiply"><a title="Bio.PDB.Vector'.Vector.right_multiply" class="py-name" href="#" onclick="return doclink('link-140', 'right_multiply', 'link-140');">right_multiply</a></tt><tt class="py-op">(</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-comment"># -</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">-</tt><tt class="py-name">v2</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-comment"># +</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">+</tt><tt class="py-name">v2</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">+</tt><tt class="py-number">3</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-comment"># *</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">*</tt><tt class="py-name">v2</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-comment"># /</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-comment"># **</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">**</tt><tt class="py-name">v2</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-comment"># norm</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-141', 'norm', 'link-33');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-comment"># norm squared</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name" targets="Method Bio.PDB.Vector'.Vector.normsq()=Bio.PDB.Vector%27.Vector-class.html#normsq"><a title="Bio.PDB.Vector'.Vector.normsq" class="py-name" href="#" onclick="return doclink('link-142', 'normsq', 'link-142');">normsq</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-comment"># setitem</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">v1</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-number">10</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-comment"># getitem</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-name">v1</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"ROT"</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt id="link-143" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-143', 'angle', 'link-9');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt id="link-144" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-144', 'pi', 'link-6');">pi</a></tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt id="link-145" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-145', 'Vector', 'link-11');">Vector</a></tt><tt class="py-op">(</tt><tt class="py-name">random</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">random</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="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">axis</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-146', 'normalize', 'link-17');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">m</tt><tt class="py-op">=</tt><tt class="py-name">rotaxis</tt><tt class="py-op">(</tt><tt id="link-147" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-147', 'angle', 'link-9');">angle</a></tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">cangle</tt><tt class="py-op">,</tt> <tt class="py-name">caxis</tt><tt class="py-op">=</tt><tt id="link-148" class="py-name" targets="Function Bio.PDB.Vector'.m2rotaxis()=Bio.PDB.Vector%27-module.html#m2rotaxis"><a title="Bio.PDB.Vector'.m2rotaxis" class="py-name" href="#" onclick="return doclink('link-148', 'm2rotaxis', 'link-148');">m2rotaxis</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-149" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-149', 'angle', 'link-9');">angle</a></tt><tt class="py-op">-</tt><tt class="py-name">cangle</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">axis</tt><tt class="py-op">-</tt><tt class="py-name">caxis</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt><script type="text/javascript">
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