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Module HSExposure
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.HSExposure-module.html">Module Bio.PDB.HSExposure</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># 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"># 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"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Half-sphere exposure and coordination number calculation."""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</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">math</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Affy.CelFile.pi=Bio.Affy.CelFile-module.html#pi,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#pi"><a title="Bio.Affy.CelFile.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi" class="py-name" href="#" onclick="return doclink('link-0', 'pi', 'link-0');">pi</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-2', 'PDB', 'link-2');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.PDB.AbstractPropertyMap=Bio.PDB.AbstractPropertyMap-module.html,Class Bio.PDB.AbstractPropertyMap.AbstractPropertyMap=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html"><a title="Bio.PDB.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap" class="py-name" href="#" onclick="return doclink('link-3', 'AbstractPropertyMap', 'link-3');">AbstractPropertyMap</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name"><a title="Bio.PDB.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap" class="py-name" href="#" onclick="return doclink('link-4', 'AbstractPropertyMap', 'link-3');">AbstractPropertyMap</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-5', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-6', 'PDB', 'link-2');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-7', 'PDBParser', 'link-7');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-8', 'PDBParser', 'link-7');">PDBParser</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-10', 'PDB', 'link-2');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Module Bio.PDB.Polypeptide=Bio.PDB.Polypeptide-module.html,Class Bio.PDB.Polypeptide.Polypeptide=Bio.PDB.Polypeptide.Polypeptide-class.html"><a title="Bio.PDB.Polypeptide
Bio.PDB.Polypeptide.Polypeptide" class="py-name" href="#" onclick="return doclink('link-11', 'Polypeptide', 'link-11');">Polypeptide</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Class Bio.PDB.Polypeptide.CaPPBuilder=Bio.PDB.Polypeptide.CaPPBuilder-class.html"><a title="Bio.PDB.Polypeptide.CaPPBuilder" class="py-name" href="#" onclick="return doclink('link-12', 'CaPPBuilder', 'link-12');">CaPPBuilder</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name" targets="Function Bio.PDB.Polypeptide.is_aa()=Bio.PDB.Polypeptide-module.html#is_aa"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-13', 'is_aa', 'link-13');">is_aa</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-14" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-14', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-15', 'PDB', 'link-2');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'Vector', 'link-16');">Vector</a></tt> <tt class="py-keyword">import</tt> <tt id="link-17" class="py-name" targets="Function Bio.PDB.Vector'.rotaxis()=Bio.PDB.Vector%27-module.html#rotaxis"><a title="Bio.PDB.Vector'.rotaxis" class="py-name" href="#" onclick="return doclink('link-17', 'rotaxis', 'link-17');">rotaxis</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="_AbstractHSExposure"></a><div id="_AbstractHSExposure-def"><a name="L17"></a><tt class="py-lineno"> 17</tt> <a class="py-toggle" href="#" id="_AbstractHSExposure-toggle" onclick="return toggle('_AbstractHSExposure');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.HSExposure._AbstractHSExposure-class.html">_AbstractHSExposure</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractPropertyMap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_AbstractHSExposure-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_AbstractHSExposure-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"> Abstract class to calculate Half-Sphere Exposure (HSE).</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> The HSE can be calculated based on the CA-CB vector, or the pseudo CB-CA</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> vector based on three consecutive CA atoms. This is done by two separate </tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> subclasses. </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_AbstractHSExposure.__init__"></a><div id="_AbstractHSExposure.__init__-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="_AbstractHSExposure.__init__-toggle" onclick="return toggle('_AbstractHSExposure.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure._AbstractHSExposure-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">model</tt><tt class="py-op">,</tt> <tt class="py-param">radius</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">,</tt> <tt class="py-param">hse_up_key</tt><tt class="py-op">,</tt> <tt class="py-param">hse_down_key</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-param">angle_key</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="_AbstractHSExposure.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_AbstractHSExposure.__init__-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> @param model: model</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> @param radius: HSE radius</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> @param offset: number of flanking residues that are ignored in the calculation</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> of the number of neighbors</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> @type offset: int</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> @param hse_up_key: key used to store HSEup in the entity.xtra attribute</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> @type hse_up_key: string</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> @param hse_down_key: key used to store HSEdown in the entity.xtra attribute</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> @type hse_down_key: string</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> @param angle_key: key used to store the angle between CA-CB and CA-pCB in </tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> the entity.xtra attribute</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> @type angle_key: string</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">offset</tt><tt class="py-op">>=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-comment"># For PyMOL visualization</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ca_cb_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-18" class="py-name"><a title="Bio.PDB.Polypeptide.CaPPBuilder" class="py-name" href="#" onclick="return doclink('link-18', 'CaPPBuilder', 'link-12');">CaPPBuilder</a></tt><tt class="py-op">(</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">ppl</tt><tt class="py-op">=</tt><tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.PDB.Polypeptide._PPBuilder.build_peptides()=Bio.PDB.Polypeptide._PPBuilder-class.html#build_peptides"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-19', 'build_peptides', 'link-19');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">hse_map</tt><tt class="py-op">=</tt><tt class="py-op">{</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">hse_list</tt><tt class="py-op">=</tt><tt class="py-op">[</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">hse_keys</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp1</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppl</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">for</tt> <tt id="link-20" 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-20', 'i', 'link-20');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-21" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-21', 'range', 'link-21');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-20');">i</a></tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">r1</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">r1</tt><tt class="py-op">=</tt><tt class="py-name">pp1</tt><tt class="py-op">[</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-20');">i</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">r2</tt><tt class="py-op">=</tt><tt class="py-name">pp1</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-20');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-20');">i</a></tt><tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp1</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="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">r3</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">r3</tt><tt class="py-op">=</tt><tt class="py-name">pp1</tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-20');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># This method is provided by the subclasses to calculate HSE</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.PDB.HSExposure.HSExposureCA._get_cb()=Bio.PDB.HSExposure.HSExposureCA-class.html#_get_cb,Method Bio.PDB.HSExposure.HSExposureCB._get_cb()=Bio.PDB.HSExposure.HSExposureCB-class.html#_get_cb,Method Bio.PDB.HSExposure._AbstractHSExposure._get_cb()=Bio.PDB.HSExposure._AbstractHSExposure-class.html#_get_cb"><a title="Bio.PDB.HSExposure.HSExposureCA._get_cb
Bio.PDB.HSExposure.HSExposureCB._get_cb
Bio.PDB.HSExposure._AbstractHSExposure._get_cb" class="py-name" href="#" onclick="return doclink('link-27', '_get_cb', 'link-27');">_get_cb</a></tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt class="py-name">r2</tt><tt class="py-op">,</tt> <tt class="py-name">r3</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># Missing atoms, or i==0, or i==len(pp1)-1</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">pcb</tt><tt class="py-op">,</tt> <tt id="link-28" 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-28', 'angle', 'link-28');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">result</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">hse_u</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">hse_d</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">ca2</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_vector()=Bio.PDB.Atom.Atom-class.html#get_vector"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-29', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppl</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-30" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-30', 'range', 'link-21');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pp1</tt> <tt class="py-keyword">is</tt> <tt class="py-name">pp2</tt> <tt class="py-keyword">and</tt> <tt id="link-31" 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-31', 'abs', 'link-31');">abs</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-20');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">)</tt><tt class="py-op"><=</tt><tt class="py-name">offset</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment"># neighboring residues in the chain are ignored </tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">ro</tt><tt class="py-op">=</tt><tt class="py-name">pp2</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-33" class="py-name"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-33', 'is_aa', 'link-13');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">ro</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ro</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.PDB.Chain.Chain.has_id()=Bio.PDB.Chain.Chain-class.html#has_id,Method Bio.PDB.Entity.Entity.has_id()=Bio.PDB.Entity.Entity-class.html#has_id"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-34', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CA'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">cao</tt><tt class="py-op">=</tt><tt class="py-name">ro</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-35', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">d</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">cao</tt><tt class="py-op">-</tt><tt class="py-name">ca2</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'norm', 'link-36');">norm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-name">radius</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-37', 'angle', 'link-28');">angle</a></tt><tt class="py-op">(</tt><tt class="py-name">pcb</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi" class="py-name" href="#" onclick="return doclink('link-38', 'pi', 'link-0');">pi</a></tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">hse_u</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">hse_d</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">res_id</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Nexus.Nodes.Node.get_id()=Bio.Nexus.Nodes.Node-class.html#get_id,Method Bio.PDB.Atom.Atom.get_id()=Bio.PDB.Atom.Atom-class.html#get_id,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_id()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_id,Method Bio.PDB.Entity.Entity.get_id()=Bio.PDB.Entity.Entity-class.html#get_id,Method Bio.PDB.FragmentMapper'.Fragment.get_id()=Bio.PDB.FragmentMapper%27.Fragment-class.html#get_id"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-39', 'get_id', 'link-39');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt id="link-40" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.chain_id=Bio.FSSP.fssp_rec.align-class.html#chain_id"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-40', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_parent()=Bio.PDB.Atom.Atom-class.html#get_parent,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_parent()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_parent,Method Bio.PDB.Entity.Entity.get_parent()=Bio.PDB.Entity.Entity-class.html#get_parent"><a title="Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-41', 'get_parent', 'link-41');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-42', 'get_id', 'link-39');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># Fill the 3 data structures</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">hse_map</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-43', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">res_id</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">hse_u</tt><tt class="py-op">,</tt> <tt class="py-name">hse_d</tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-44', 'angle', 'link-28');">angle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">hse_list</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-45', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">hse_u</tt><tt class="py-op">,</tt> <tt class="py-name">hse_d</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-46', 'angle', 'link-28');">angle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">hse_keys</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-47', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-48', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">res_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># Add to xtra</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-name">hse_up_key</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">hse_u</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-name">hse_down_key</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">hse_d</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">angle_key</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">r2</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-name">angle_key</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-49', 'angle', 'link-28');">angle</a></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-50" class="py-name"><a title="Bio.PDB.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap" class="py-name" href="#" onclick="return doclink('link-50', 'AbstractPropertyMap', 'link-3');">AbstractPropertyMap</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Affy.CelFile.CelScanner.__init__()=Bio.Affy.CelFile.CelScanner-class.html#__init__,Method Bio.Affy.CelFile.Record.__init__()=Bio.Affy.CelFile.Record-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__()=Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html#__init__,Method Bio.Align.Applications._Dialign.DialignCommandline.__init__()=Bio.Align.Applications._Dialign.DialignCommandline-class.html#__init__,Method Bio.Align.Applications._Mafft.MafftCommandline.__init__()=Bio.Align.Applications._Mafft.MafftCommandline-class.html#__init__,Method Bio.Align.Applications._Muscle.MuscleCommandline.__init__()=Bio.Align.Applications._Muscle.MuscleCommandline-class.html#__init__,Method Bio.Align.Applications._Prank.PrankCommandline.__init__()=Bio.Align.Applications._Prank.PrankCommandline-class.html#__init__,Method Bio.Align.Applications._Probcons.ProbconsCommandline.__init__()=Bio.Align.Applications._Probcons.ProbconsCommandline-class.html#__init__,Method Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__()=Bio.Align.Applications._TCoffee.TCoffeeCommandline-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.Align.MultipleSeqAlignment.__init__()=Bio.Align.MultipleSeqAlignment-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method 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Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-51', '__init__', 'link-51');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">hse_map</tt><tt class="py-op">,</tt> <tt class="py-name">hse_keys</tt><tt class="py-op">,</tt> <tt class="py-name">hse_list</tt><tt class="py-op">)</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="_AbstractHSExposure._get_cb"></a><div id="_AbstractHSExposure._get_cb-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="_AbstractHSExposure._get_cb-toggle" onclick="return toggle('_AbstractHSExposure._get_cb');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure._AbstractHSExposure-class.html#_get_cb">_get_cb</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r1</tt><tt class="py-op">,</tt> <tt class="py-param">r2</tt><tt class="py-op">,</tt> <tt class="py-param">r3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_AbstractHSExposure._get_cb-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_AbstractHSExposure._get_cb-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-docstring">"""This method is provided by the subclasses to calculate HSE."""</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">NotImplemented</tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="_AbstractHSExposure._get_gly_cb_vector"></a><div id="_AbstractHSExposure._get_gly_cb_vector-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="_AbstractHSExposure._get_gly_cb_vector-toggle" onclick="return toggle('_AbstractHSExposure._get_gly_cb_vector');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure._AbstractHSExposure-class.html#_get_gly_cb_vector">_get_gly_cb_vector</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_AbstractHSExposure._get_gly_cb_vector-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_AbstractHSExposure._get_gly_cb_vector-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> Return a pseudo CB vector for a Gly residue.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> The pseudoCB vector is centered at the origin.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> CB coord=N coord rotated over -120 degrees </tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> along the CA-C axis.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">n_v</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt class="py-string">"N"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-52', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">c_v</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-53', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">ca_v</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-54', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment"># center at origin</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">n_v</tt><tt class="py-op">=</tt><tt class="py-name">n_v</tt><tt class="py-op">-</tt><tt class="py-name">ca_v</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">c_v</tt><tt class="py-op">=</tt><tt class="py-name">c_v</tt><tt class="py-op">-</tt><tt class="py-name">ca_v</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># rotation around c-ca over -120 deg</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">rot</tt><tt class="py-op">=</tt><tt id="link-55" class="py-name"><a title="Bio.PDB.Vector'.rotaxis" class="py-name" href="#" onclick="return doclink('link-55', 'rotaxis', 'link-17');">rotaxis</a></tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt id="link-56" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi" class="py-name" href="#" onclick="return doclink('link-56', 'pi', 'link-0');">pi</a></tt><tt class="py-op">*</tt><tt class="py-number">120.0</tt><tt class="py-op">/</tt><tt class="py-number">180.0</tt><tt class="py-op">,</tt> <tt class="py-name">c_v</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">cb_at_origin_v</tt><tt class="py-op">=</tt><tt class="py-name">n_v</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'left_multiply', 'link-57');">left_multiply</a></tt><tt class="py-op">(</tt><tt class="py-name">rot</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-comment"># move back to ca position</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">cb_v</tt><tt class="py-op">=</tt><tt class="py-name">cb_at_origin_v</tt><tt class="py-op">+</tt><tt class="py-name">ca_v</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment"># This is for PyMol visualization</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ca_cb_list</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-58', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">ca_v</tt><tt class="py-op">,</tt> <tt class="py-name">cb_v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cb_at_origin_v</tt> </tt>
</div></div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="HSExposureCA"></a><div id="HSExposureCA-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="HSExposureCA-toggle" onclick="return toggle('HSExposureCA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCA-class.html">HSExposureCA</a><tt class="py-op">(</tt><tt class="py-base-class">_AbstractHSExposure</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HSExposureCA-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> Class to calculate HSE based on the approximate CA-CB vectors,</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> using three consecutive CA positions.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="HSExposureCA.__init__"></a><div id="HSExposureCA.__init__-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="HSExposureCA.__init__-toggle" onclick="return toggle('HSExposureCA.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCA-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">model</tt><tt class="py-op">,</tt> <tt class="py-param">radius</tt><tt class="py-op">=</tt><tt class="py-number">12</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCA.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HSExposureCA.__init__-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> @param model: the model that contains the residues</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<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"> @param radius: radius of the sphere (centred at the CA atom)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> @param offset: number of flanking residues that are ignored in the calculation of the number of neighbors</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> @type offset: int</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 id="link-59" class="py-name" targets="Class Bio.PDB.HSExposure._AbstractHSExposure=Bio.PDB.HSExposure._AbstractHSExposure-class.html"><a title="Bio.PDB.HSExposure._AbstractHSExposure" class="py-name" href="#" onclick="return doclink('link-59', '_AbstractHSExposure', 'link-59');">_AbstractHSExposure</a></tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Affy.CelFile.CelScanner.__init__
Bio.Affy.CelFile.Record.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__
Bio.Align.Applications._Dialign.DialignCommandline.__init__
Bio.Align.Applications._Mafft.MafftCommandline.__init__
Bio.Align.Applications._Muscle.MuscleCommandline.__init__
Bio.Align.Applications._Prank.PrankCommandline.__init__
Bio.Align.Applications._Probcons.ProbconsCommandline.__init__
Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__
Bio.Align.Generic.Alignment.__init__
Bio.Align.MultipleSeqAlignment.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationError.__init__
Bio.Application._AbstractParameter.__init__
Bio.Application._Argument.__init__
Bio.Application._Option.__init__
Bio.Application._Switch.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.BlastpgpCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.Applications.NcbiblastformatterCommandline.__init__
Bio.Blast.Applications.NcbiblastnCommandline.__init__
Bio.Blast.Applications.NcbiblastpCommandline.__init__
Bio.Blast.Applications.NcbiblastxCommandline.__init__
Bio.Blast.Applications.NcbipsiblastCommandline.__init__
Bio.Blast.Applications.NcbirpsblastCommandline.__init__
Bio.Blast.Applications.NcbirpstblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastxCommandline.__init__
Bio.Blast.Applications.RpsBlastCommandline.__init__
Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__
Bio.Blast.Applications._BlastCommandLine.__init__
Bio.Blast.Applications._NcbibaseblastCommandline.__init__
Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__
Bio.Blast.Applications._NcbiblastCommandline.__init__
Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Compass._Scanner.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.Hetero.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.Emboss.Applications.DiffseqCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FConsenseCommandline.__init__
Bio.Emboss.Applications.FDNADistCommandline.__init__
Bio.Emboss.Applications.FDNAParsCommandline.__init__
Bio.Emboss.Applications.FNeighborCommandline.__init__
Bio.Emboss.Applications.FProtDistCommandline.__init__
Bio.Emboss.Applications.FProtParsCommandline.__init__
Bio.Emboss.Applications.FSeqBootCommandline.__init__
Bio.Emboss.Applications.FTreeDistCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.IepCommandline.__init__
Bio.Emboss.Applications.NeedleCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.SeqmatchallCommandline.__init__
Bio.Emboss.Applications.SeqretCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Applications._EmbossCommandLine.__init__
Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__
Bio.Emboss.Primer3.Primers.__init__
Bio.Emboss.Primer3.Record.__init__
Bio.Emboss.PrimerSearch.Amplifier.__init__
Bio.Emboss.PrimerSearch.InputRecord.__init__
Bio.Emboss.PrimerSearch.OutputRecord.__init__
Bio.Entrez.Parser.CorruptedXMLError.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.NotXMLError.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Entrez.Parser.ValidationError.__init__
Bio.ExPASy.Enzyme.Record.__init__
Bio.ExPASy.Prodoc.Record.__init__
Bio.ExPASy.Prodoc.Reference.__init__
Bio.ExPASy.Prosite.Record.__init__
Bio.ExPASy.ScanProsite.ContentHandler.__init__
Bio.ExPASy.ScanProsite.Parser.__init__
Bio.ExPASy.ScanProsite.Record.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
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Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
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Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__
Bio.Graphics.GenomeDiagram._Feature.Feature.__init__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__
Bio.Graphics.GenomeDiagram._Track.Track.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__
Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__
Bio.Motif.Parsers.AlignAce.Record.__init__
Bio.Motif.Parsers.MAST.Record.__init__
Bio.Motif.Parsers.MEME.MEMEInstance.__init__
Bio.Motif.Parsers.MEME.MEMEMotif.__init__
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Bio.Motif.Thresholds.ScoreDistribution.__init__
Bio.Motif._Motif.Motif.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
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Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
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Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
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Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
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Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
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Bio.Nexus.Nexus.StepMatrix.__init__
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Bio.Nexus.Trees.NodeData.__init__
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Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
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Bio.PDB.DSSP'.DSSP.__init__
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Bio.PDB.Entity.Entity.__init__
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Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
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Bio.PDB.Residue.DisorderedResidue.__init__
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Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
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Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
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Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
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Bio.Sequencing.Ace.ct.__init__
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Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-60', '__init__', 'link-51');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-string">'EXP_HSE_A_U'</tt><tt class="py-op">,</tt> <tt class="py-string">'EXP_HSE_A_D'</tt><tt class="py-op">,</tt> <tt class="py-string">'EXP_CB_PCB_ANGLE'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="HSExposureCA._get_cb"></a><div id="HSExposureCA._get_cb-def"><a name="L155"></a><tt class="py-lineno">155</tt> <a class="py-toggle" href="#" id="HSExposureCA._get_cb-toggle" onclick="return toggle('HSExposureCA._get_cb');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCA-class.html#_get_cb">_get_cb</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r1</tt><tt class="py-op">,</tt> <tt class="py-param">r2</tt><tt class="py-op">,</tt> <tt class="py-param">r3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCA._get_cb-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HSExposureCA._get_cb-expanded"><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> Calculate the approximate CA-CB direction for a central</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> CA atom based on the two flanking CA positions, and the angle</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> with the real CA-CB vector. </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-docstring"> The CA-CB vector is centered at the origin.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> @param r1, r2, r3: three consecutive residues</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> @type r1, r2, r3: L{Residue}</tt> </tt>
<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-keyword">if</tt> <tt class="py-name">r1</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">r3</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">ca1</tt><tt class="py-op">=</tt><tt class="py-name">r1</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-61', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">ca2</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-62', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">ca3</tt><tt class="py-op">=</tt><tt class="py-name">r3</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-63', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-comment"># center</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">d1</tt><tt class="py-op">=</tt><tt class="py-name">ca2</tt><tt class="py-op">-</tt><tt class="py-name">ca1</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">d3</tt><tt class="py-op">=</tt><tt class="py-name">ca2</tt><tt class="py-op">-</tt><tt class="py-name">ca3</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">d1</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.PDB.Vector'.Vector.normalize()=Bio.PDB.Vector%27.Vector-class.html#normalize"><a title="Bio.PDB.Vector'.Vector.normalize" class="py-name" href="#" onclick="return doclink('link-64', 'normalize', 'link-64');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">d3</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalize" class="py-name" href="#" onclick="return doclink('link-65', 'normalize', 'link-64');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># bisection</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">b</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">d1</tt><tt class="py-op">+</tt><tt class="py-name">d3</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">b</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalize" class="py-name" href="#" onclick="return doclink('link-66', 'normalize', 'link-64');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment"># Add to ca_cb_list for drawing</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ca_cb_list</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-67', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">ca2</tt><tt class="py-op">,</tt> <tt class="py-name">b</tt><tt class="py-op">+</tt><tt class="py-name">ca2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-68', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CB'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">cb</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CB'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-69', 'get_vector', 'link-29');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">cb_ca</tt><tt class="py-op">=</tt><tt class="py-name">cb</tt><tt class="py-op">-</tt><tt class="py-name">ca2</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">cb_ca</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalize" class="py-name" href="#" onclick="return doclink('link-70', 'normalize', 'link-64');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <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-28');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">cb_ca</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-72', 'angle', 'link-28');">angle</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.PDB.Residue.Residue.get_resname()=Bio.PDB.Residue.Residue-class.html#get_resname"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-73', 'get_resname', 'link-73');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-string">'GLY'</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">cb_ca</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Method Bio.PDB.HSExposure._AbstractHSExposure._get_gly_cb_vector()=Bio.PDB.HSExposure._AbstractHSExposure-class.html#_get_gly_cb_vector"><a title="Bio.PDB.HSExposure._AbstractHSExposure._get_gly_cb_vector" class="py-name" href="#" onclick="return doclink('link-74', '_get_gly_cb_vector', 'link-74');">_get_gly_cb_vector</a></tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cb_ca</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-75', 'angle', 'link-28');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</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-28');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">cb_ca</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-28');">angle</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.PDB.Vector'.Vector.angle" class="py-name" href="#" onclick="return doclink('link-78', 'angle', 'link-28');">angle</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-comment"># vector b is centered at the origin!</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">b</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-28');">angle</a></tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="HSExposureCA.pcb_vectors_pymol"></a><div id="HSExposureCA.pcb_vectors_pymol-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="HSExposureCA.pcb_vectors_pymol-toggle" onclick="return toggle('HSExposureCA.pcb_vectors_pymol');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCA-class.html#pcb_vectors_pymol">pcb_vectors_pymol</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">=</tt><tt class="py-string">"hs_exp.py"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCA.pcb_vectors_pymol-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HSExposureCA.pcb_vectors_pymol-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> Write a PyMol script that visualizes the pseudo CB-CA directions </tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> at the CA coordinates.</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> @param filename: the name of the pymol script file</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> @type filename: string</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ca_cb_list</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Nothing to draw."</tt><tt class="py-op">,</tt> <tt class="py-name">RuntimeWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-80', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"from pymol.cgo import *\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-81', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"from pymol import cmd\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-82', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"obj=[\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-83', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"BEGIN, LINES,\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-84', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"COLOR, %.2f, %.2f, %.2f,\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">ca</tt><tt class="py-op">,</tt> <tt class="py-name">cb</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ca_cb_list</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-85" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-85', 'x', 'link-85');">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">ca</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'get_array', 'link-86');">get_array</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
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<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-89', 'x', 'link-85');">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">cb</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.PDB.Vector'.Vector.get_array" class="py-name" href="#" onclick="return doclink('link-90', 'get_array', 'link-86');">get_array</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.AlignIO.write
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Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-91', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"VERTEX, %.2f, %.2f, %.2f,\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-92', 'x', 'link-85');">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>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.AlignIO.write
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Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-93', 'write', 'link-80');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"END]\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.AlignIO.write
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<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
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</div></div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="HSExposureCB"></a><div id="HSExposureCB-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="HSExposureCB-toggle" onclick="return toggle('HSExposureCB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCB-class.html">HSExposureCB</a><tt class="py-op">(</tt><tt class="py-base-class">_AbstractHSExposure</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HSExposureCB-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> Class to calculate HSE based on the real CA-CB vectors.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="HSExposureCB.__init__"></a><div id="HSExposureCB.__init__-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="HSExposureCB.__init__-toggle" onclick="return toggle('HSExposureCB.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCB-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">model</tt><tt class="py-op">,</tt> <tt class="py-param">radius</tt><tt class="py-op">=</tt><tt class="py-number">12</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCB.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HSExposureCB.__init__-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> @param model: the model that contains the residues</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> @param radius: radius of the sphere (centred at the CA atom)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> @param offset: number of flanking residues that are ignored in the calculation of the number of neighbors</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> @type offset: int</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="Bio.PDB.HSExposure._AbstractHSExposure" class="py-name" href="#" onclick="return doclink('link-96', '_AbstractHSExposure', 'link-59');">_AbstractHSExposure</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
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Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-97', '__init__', 'link-51');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">,</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-string">'EXP_HSE_B_U'</tt><tt class="py-op">,</tt> <tt class="py-string">'EXP_HSE_B_D'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="HSExposureCB._get_cb"></a><div id="HSExposureCB._get_cb-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="HSExposureCB._get_cb-toggle" onclick="return toggle('HSExposureCB._get_cb');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.HSExposureCB-class.html#_get_cb">_get_cb</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r1</tt><tt class="py-op">,</tt> <tt class="py-param">r2</tt><tt class="py-op">,</tt> <tt class="py-param">r3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HSExposureCB._get_cb-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HSExposureCB._get_cb-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> Method to calculate CB-CA vector.</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> @param r1, r2, r3: three consecutive residues (only r2 is used)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> @type r1, r2, r3: L{Residue}</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-98', 'get_resname', 'link-73');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-string">'GLY'</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.PDB.HSExposure._AbstractHSExposure._get_gly_cb_vector" class="py-name" href="#" onclick="return doclink('link-99', '_get_gly_cb_vector', 'link-74');">_get_gly_cb_vector</a></tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-100', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CB'</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-101', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CA'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">vcb</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CB'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-102', 'get_vector', 'link-29');">get_vector</a></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">vca</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-103', 'get_vector', 'link-29');">get_vector</a></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-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">vcb</tt><tt class="py-op">-</tt><tt class="py-name">vca</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="ExposureCN"></a><div id="ExposureCN-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="ExposureCN-toggle" onclick="return toggle('ExposureCN');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.ExposureCN-class.html">ExposureCN</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractPropertyMap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExposureCN-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExposureCN-expanded"><a name="ExposureCN.__init__"></a><div id="ExposureCN.__init__-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="ExposureCN.__init__-toggle" onclick="return toggle('ExposureCN.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.HSExposure.ExposureCN-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">model</tt><tt class="py-op">,</tt> <tt class="py-param">radius</tt><tt class="py-op">=</tt><tt class="py-number">12.0</tt><tt class="py-op">,</tt> <tt class="py-param">offset</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExposureCN.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExposureCN.__init__-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> A residue's exposure is defined as the number of CA atoms around </tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> that residues CA atom. A dictionary is returned that uses a L{Residue}</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> object as key, and the residue exposure as corresponding value.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"> @param model: the model that contains the residues</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> @param radius: radius of the sphere (centred at the CA atom)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"> @param offset: number of flanking residues that are ignored in the calculation of the number of neighbors</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"> @type offset: int</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">offset</tt><tt class="py-op">>=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-104" class="py-name"><a title="Bio.PDB.Polypeptide.CaPPBuilder" class="py-name" href="#" onclick="return doclink('link-104', 'CaPPBuilder', 'link-12');">CaPPBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">=</tt><tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-105', 'build_peptides', 'link-19');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">fs_map</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">fs_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">fs_keys</tt><tt class="py-op">=</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 class="py-keyword">for</tt> <tt class="py-name">pp1</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppl</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">for</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-20');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-107" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-107', 'range', 'link-21');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">fs</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">r1</tt><tt class="py-op">=</tt><tt class="py-name">pp1</tt><tt class="py-op">[</tt><tt id="link-108" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-108', 'i', 'link-20');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-109" class="py-name"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-109', 'is_aa', 'link-13');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-110', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CA'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">ca1</tt><tt class="py-op">=</tt><tt class="py-name">r1</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppl</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-111" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-111', 'range', 'link-21');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pp1</tt> <tt class="py-keyword">is</tt> <tt class="py-name">pp2</tt> <tt class="py-keyword">and</tt> <tt id="link-112" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-112', 'abs', 'link-31');">abs</a></tt><tt class="py-op">(</tt><tt id="link-113" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-113', 'i', 'link-20');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">)</tt><tt class="py-op"><=</tt><tt class="py-name">offset</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">r2</tt><tt class="py-op">=</tt><tt class="py-name">pp2</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-114" class="py-name"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-114', 'is_aa', 'link-13');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-115', 'has_id', 'link-34');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'CA'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">ca2</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">d</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">ca2</tt><tt class="py-op">-</tt><tt class="py-name">ca1</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">d</tt><tt class="py-op"><</tt><tt class="py-name">radius</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">fs</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">res_id</tt><tt class="py-op">=</tt><tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-116', 'get_id', 'link-39');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt id="link-117" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-117', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">=</tt><tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-118', 'get_parent', 'link-41');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-119', 'get_id', 'link-39');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-comment"># Fill the 3 data structures</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">fs_map</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-120" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-120', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">res_id</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">fs</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">fs_list</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-121', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">fs_keys</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-122', 'append', 'link-45');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-123', 'chain_id', 'link-40');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">res_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-comment"># Add to xtra</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">r1</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">'EXP_CN'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">fs</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Bio.PDB.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap" class="py-name" href="#" onclick="return doclink('link-124', 'AbstractPropertyMap', 'link-3');">AbstractPropertyMap</a></tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Affy.CelFile.CelScanner.__init__
Bio.Affy.CelFile.Record.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__
Bio.Align.Applications._Dialign.DialignCommandline.__init__
Bio.Align.Applications._Mafft.MafftCommandline.__init__
Bio.Align.Applications._Muscle.MuscleCommandline.__init__
Bio.Align.Applications._Prank.PrankCommandline.__init__
Bio.Align.Applications._Probcons.ProbconsCommandline.__init__
Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__
Bio.Align.Generic.Alignment.__init__
Bio.Align.MultipleSeqAlignment.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationError.__init__
Bio.Application._AbstractParameter.__init__
Bio.Application._Argument.__init__
Bio.Application._Option.__init__
Bio.Application._Switch.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.BlastpgpCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.Applications.NcbiblastformatterCommandline.__init__
Bio.Blast.Applications.NcbiblastnCommandline.__init__
Bio.Blast.Applications.NcbiblastpCommandline.__init__
Bio.Blast.Applications.NcbiblastxCommandline.__init__
Bio.Blast.Applications.NcbipsiblastCommandline.__init__
Bio.Blast.Applications.NcbirpsblastCommandline.__init__
Bio.Blast.Applications.NcbirpstblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastxCommandline.__init__
Bio.Blast.Applications.RpsBlastCommandline.__init__
Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__
Bio.Blast.Applications._BlastCommandLine.__init__
Bio.Blast.Applications._NcbibaseblastCommandline.__init__
Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__
Bio.Blast.Applications._NcbiblastCommandline.__init__
Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Compass._Scanner.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.Hetero.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.Emboss.Applications.DiffseqCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FConsenseCommandline.__init__
Bio.Emboss.Applications.FDNADistCommandline.__init__
Bio.Emboss.Applications.FDNAParsCommandline.__init__
Bio.Emboss.Applications.FNeighborCommandline.__init__
Bio.Emboss.Applications.FProtDistCommandline.__init__
Bio.Emboss.Applications.FProtParsCommandline.__init__
Bio.Emboss.Applications.FSeqBootCommandline.__init__
Bio.Emboss.Applications.FTreeDistCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.IepCommandline.__init__
Bio.Emboss.Applications.NeedleCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.SeqmatchallCommandline.__init__
Bio.Emboss.Applications.SeqretCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Applications._EmbossCommandLine.__init__
Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__
Bio.Emboss.Primer3.Primers.__init__
Bio.Emboss.Primer3.Record.__init__
Bio.Emboss.PrimerSearch.Amplifier.__init__
Bio.Emboss.PrimerSearch.InputRecord.__init__
Bio.Emboss.PrimerSearch.OutputRecord.__init__
Bio.Entrez.Parser.CorruptedXMLError.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.NotXMLError.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Entrez.Parser.ValidationError.__init__
Bio.ExPASy.Enzyme.Record.__init__
Bio.ExPASy.Prodoc.Record.__init__
Bio.ExPASy.Prodoc.Reference.__init__
Bio.ExPASy.Prosite.Record.__init__
Bio.ExPASy.ScanProsite.ContentHandler.__init__
Bio.ExPASy.ScanProsite.Parser.__init__
Bio.ExPASy.ScanProsite.Record.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__
Bio.Graphics.GenomeDiagram._Feature.Feature.__init__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__
Bio.Graphics.GenomeDiagram._Track.Track.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__
Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__
Bio.Motif.Parsers.AlignAce.Record.__init__
Bio.Motif.Parsers.MAST.Record.__init__
Bio.Motif.Parsers.MEME.MEMEInstance.__init__
Bio.Motif.Parsers.MEME.MEMEMotif.__init__
Bio.Motif.Parsers.MEME.MEMERecord.__init__
Bio.Motif.Thresholds.ScoreDistribution.__init__
Bio.Motif._Motif.Motif.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-125', '__init__', 'link-51');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">fs_map</tt><tt class="py-op">,</tt> <tt class="py-name">fs_keys</tt><tt class="py-op">,</tt> <tt class="py-name">fs_list</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
<a name="L314"></a><tt class="py-lineno">314</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="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">import</tt> <tt class="py-name">sys</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-name">p</tt><tt class="py-op">=</tt><tt id="link-126" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-126', 'PDBParser', 'link-7');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser.get_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure,Method Bio.PDB.PDBParser'.PDBParser.get_structure()=Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure,Method Bio.PDB.StructureBuilder.StructureBuilder.get_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-127', 'get_structure', 'link-127');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">'X'</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">model</tt><tt class="py-op">=</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-number">0</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-comment"># Neighbor sphere radius</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">RADIUS</tt><tt class="py-op">=</tt><tt class="py-number">13.0</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">OFFSET</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">hse</tt><tt class="py-op">=</tt><tt id="link-128" class="py-name" targets="Class Bio.PDB.HSExposure.HSExposureCA=Bio.PDB.HSExposure.HSExposureCA-class.html"><a title="Bio.PDB.HSExposure.HSExposureCA" class="py-name" href="#" onclick="return doclink('link-128', 'HSExposureCA', 'link-128');">HSExposureCA</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">=</tt><tt class="py-name">RADIUS</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">=</tt><tt class="py-name">OFFSET</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">hse</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">l</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">print</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-name">hse</tt><tt class="py-op">=</tt><tt id="link-129" class="py-name" targets="Class Bio.PDB.HSExposure.HSExposureCB=Bio.PDB.HSExposure.HSExposureCB-class.html"><a title="Bio.PDB.HSExposure.HSExposureCB" class="py-name" href="#" onclick="return doclink('link-129', 'HSExposureCB', 'link-129');">HSExposureCB</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">=</tt><tt class="py-name">RADIUS</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">=</tt><tt class="py-name">OFFSET</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">hse</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">l</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">hse</tt><tt class="py-op">=</tt><tt id="link-130" class="py-name" targets="Class Bio.PDB.HSExposure.ExposureCN=Bio.PDB.HSExposure.ExposureCN-class.html"><a title="Bio.PDB.HSExposure.ExposureCN" class="py-name" href="#" onclick="return doclink('link-130', 'ExposureCN', 'link-130');">ExposureCN</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">=</tt><tt class="py-name">RADIUS</tt><tt class="py-op">,</tt> <tt class="py-name">offset</tt><tt class="py-op">=</tt><tt class="py-name">OFFSET</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">hse</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">l</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">model</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">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">c</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">'PCB_CB_ANGLE'</tt><tt class="py-op">]</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt><script type="text/javascript">
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