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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module Polypeptide
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.Polypeptide-module.html">Module Bio.PDB.Polypeptide</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">"""Polypeptide-related classes (construction and representation).</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Simple example with multiple chains,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.PDB.PDBParser import PDBParser</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.PDB.Polypeptide import PPBuilder</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"> >>> structure = PDBParser().get_structure('2BEG', 'PDB/2BEG.pdb')</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> >>> ppb=PPBuilder()</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> >>> for pp in ppb.build_peptides(structure):</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> LVFFAEDVGSNKGAIIGLMVGGVVIA</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> LVFFAEDVGSNKGAIIGLMVGGVVIA</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> LVFFAEDVGSNKGAIIGLMVGGVVIA</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> LVFFAEDVGSNKGAIIGLMVGGVVIA</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> LVFFAEDVGSNKGAIIGLMVGGVVIA</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">Example with non-standard amino acids using HETATM lines in the PDB file,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">in this case selenomethionine (MSE):</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.PDB.PDBParser import PDBParser</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.PDB.Polypeptide import PPBuilder</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> >>> structure = PDBParser().get_structure('1A8O', 'PDB/1A8O.pdb')</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> >>> ppb=PPBuilder()</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> >>> for pp in ppb.build_peptides(structure):</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> TETLLVQNANPDCKTILKALGPGATLEE</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> TACQG</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">If you want to, you can include non-standard amino acids in the peptides:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> >>> for pp in ppb.build_peptides(structure, aa_only=False):</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()[0], pp[0].get_resname()</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()[-7], pp[-7].get_resname()</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> ... print pp.get_sequence()[-6], pp[-6].get_resname()</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> M MSE</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> M MSE</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> M MSE</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">In this case the selenomethionines (the first and also seventh and sixth from</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring">last residues) have been shown as M (methionine) by the get_sequence method.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Variable Bio.Alphabet.generic_protein=Bio.Alphabet-module.html#generic_protein"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-2', 'generic_protein', 'link-2');">generic_protein</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-4', 'Seq', 'link-4');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-5', 'Seq', 'link-4');">Seq</a></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.SCOP=Bio.SCOP-module.html"><a title="Bio.SCOP" class="py-name" href="#" onclick="return doclink('link-7', 'SCOP', 'link-7');">SCOP</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Module Bio.SCOP.Raf=Bio.SCOP.Raf-module.html"><a title="Bio.SCOP.Raf" class="py-name" href="#" onclick="return doclink('link-8', 'Raf', 'link-8');">Raf</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Variable Bio.PDB.DSSP'.to_one_letter_code=Bio.PDB.DSSP%27-module.html#to_one_letter_code,Variable Bio.PDB.StructureAlignment'.to_one_letter_code=Bio.PDB.StructureAlignment%27-module.html#to_one_letter_code,Variable Bio.SCOP.Raf.to_one_letter_code=Bio.SCOP.Raf-module.html#to_one_letter_code"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.StructureAlignment'.to_one_letter_code
Bio.SCOP.Raf.to_one_letter_code" class="py-name" href="#" onclick="return doclink('link-9', 'to_one_letter_code', 'link-9');">to_one_letter_code</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-11', 'PDB', 'link-11');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Module Bio.PDB.PDBExceptions=Bio.PDB.PDBExceptions-module.html"><a title="Bio.PDB.PDBExceptions" class="py-name" href="#" onclick="return doclink('link-12', 'PDBExceptions', 'link-12');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Class Bio.PDB.PDBExceptions.PDBException=Bio.PDB.PDBExceptions.PDBException-class.html"><a title="Bio.PDB.PDBExceptions.PDBException" class="py-name" href="#" onclick="return doclink('link-13', 'PDBException', 'link-13');">PDBException</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</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-0');">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-11');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Module Bio.PDB.Residue=Bio.PDB.Residue-module.html,Class Bio.PDB.Residue.Residue=Bio.PDB.Residue.Residue-class.html"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-16', 'Residue', 'link-16');">Residue</a></tt> <tt class="py-keyword">import</tt> <tt id="link-17" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-17', 'Residue', 'link-16');">Residue</a></tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name" targets="Class Bio.PDB.Residue.DisorderedResidue=Bio.PDB.Residue.DisorderedResidue-class.html"><a title="Bio.PDB.Residue.DisorderedResidue" class="py-name" href="#" onclick="return doclink('link-18', 'DisorderedResidue', 'link-18');">DisorderedResidue</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-19" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-19', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-20', 'PDB', 'link-11');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'Vector', 'link-21');">Vector</a></tt> <tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Function Bio.PDB.Vector'.calc_dihedral()=Bio.PDB.Vector%27-module.html#calc_dihedral"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-22', 'calc_dihedral', 'link-22');">calc_dihedral</a></tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name" targets="Function Bio.PDB.Vector'.calc_angle()=Bio.PDB.Vector%27-module.html#calc_angle"><a title="Bio.PDB.Vector'.calc_angle" class="py-name" href="#" onclick="return doclink('link-23', 'calc_angle', 'link-23');">calc_angle</a></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable Bio.PDB.Polypeptide.standard_aa_names=Bio.PDB.Polypeptide-module.html#standard_aa_names"><a title="Bio.PDB.Polypeptide.standard_aa_names" class="py-name" href="#" onclick="return doclink('link-24', 'standard_aa_names', 'link-24');">standard_aa_names</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">"ALA"</tt><tt class="py-op">,</tt> <tt class="py-string">"CYS"</tt><tt class="py-op">,</tt> <tt class="py-string">"ASP"</tt><tt class="py-op">,</tt> <tt class="py-string">"GLU"</tt><tt class="py-op">,</tt> <tt class="py-string">"PHE"</tt><tt class="py-op">,</tt> <tt class="py-string">"GLY"</tt><tt class="py-op">,</tt> <tt class="py-string">"HIS"</tt><tt class="py-op">,</tt> <tt class="py-string">"ILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"LYS"</tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">"LEU"</tt><tt class="py-op">,</tt> <tt class="py-string">"MET"</tt><tt class="py-op">,</tt> <tt class="py-string">"ASN"</tt><tt class="py-op">,</tt> <tt class="py-string">"PRO"</tt><tt class="py-op">,</tt> <tt class="py-string">"GLN"</tt><tt class="py-op">,</tt> <tt class="py-string">"ARG"</tt><tt class="py-op">,</tt> <tt class="py-string">"SER"</tt><tt class="py-op">,</tt> <tt class="py-string">"THR"</tt><tt class="py-op">,</tt> <tt class="py-string">"VAL"</tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-string">"TRP"</tt><tt class="py-op">,</tt> <tt class="py-string">"TYR"</tt><tt class="py-op">]</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable Bio.PDB.Polypeptide.aa1=Bio.PDB.Polypeptide-module.html#aa1"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-25', 'aa1', 'link-25');">aa1</a></tt><tt class="py-op">=</tt><tt class="py-string">"ACDEFGHIKLMNPQRSTVWY"</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt id="link-26" class="py-name" targets="Variable Bio.PDB.Polypeptide.aa3=Bio.PDB.Polypeptide-module.html#aa3"><a title="Bio.PDB.Polypeptide.aa3" class="py-name" href="#" onclick="return doclink('link-26', 'aa3', 'link-26');">aa3</a></tt><tt class="py-op">=</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.standard_aa_names" class="py-name" href="#" onclick="return doclink('link-27', 'standard_aa_names', 'link-24');">standard_aa_names</a></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt id="link-28" class="py-name" targets="Variable Bio.PDB.Polypeptide.d1_to_index=Bio.PDB.Polypeptide-module.html#d1_to_index"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-28', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt id="link-29" class="py-name" targets="Variable Bio.PDB.Polypeptide.dindex_to_1=Bio.PDB.Polypeptide-module.html#dindex_to_1"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-29', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt id="link-30" class="py-name" targets="Variable Bio.PDB.Polypeptide.d3_to_index=Bio.PDB.Polypeptide-module.html#d3_to_index"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-30', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt id="link-31" class="py-name" targets="Variable Bio.PDB.Polypeptide.dindex_to_3=Bio.PDB.Polypeptide-module.html#dindex_to_3"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-31', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"># Create some lookup tables</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-32" 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-32', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-33" 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-33', 'range', 'link-33');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">20</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 id="link-34" class="py-name" targets="Variable Bio.PDB.Polypeptide.n1=Bio.PDB.Polypeptide-module.html#n1"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-34', 'n1', 'link-34');">n1</a></tt><tt class="py-op">=</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-35', 'aa1', 'link-25');">aa1</a></tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-36', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt id="link-37" class="py-name" targets="Variable Bio.PDB.Polypeptide.n3=Bio.PDB.Polypeptide-module.html#n3"><a title="Bio.PDB.Polypeptide.n3" class="py-name" href="#" onclick="return doclink('link-37', 'n3', 'link-37');">n3</a></tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.aa3" class="py-name" href="#" onclick="return doclink('link-38', 'aa3', 'link-26');">aa3</a></tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-40', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-41', 'n1', 'link-34');">n1</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-32');">i</a></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-43', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-44', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-45', 'n1', 'link-34');">n1</a></tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-46', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">[</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.n3" class="py-name" href="#" onclick="return doclink('link-47', 'n3', 'link-37');">n3</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-32');">i</a></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-49', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-51" class="py-name"><a title="Bio.PDB.Polypeptide.n3" class="py-name" href="#" onclick="return doclink('link-51', 'n3', 'link-37');">n3</a></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="index_to_one"></a><div id="index_to_one-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="index_to_one-toggle" onclick="return toggle('index_to_one');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#index_to_one">index_to_one</a><tt class="py-op">(</tt><tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="index_to_one-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="index_to_one-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-docstring">"""Index to corresponding one letter amino acid name.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> >>> index_to_one(0)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> 'A'</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> >>> index_to_one(19)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> 'Y'</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-52', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-53" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index,Function Bio.SeqIO.index()=Bio.SeqIO-module.html#index"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-53', 'index', 'link-53');">index</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="one_to_index"></a><div id="one_to_index-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="one_to_index-toggle" onclick="return toggle('one_to_index');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#one_to_index">one_to_index</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="one_to_index-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="one_to_index-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-docstring">"""One letter code to index.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> >>> one_to_index('A')</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> 0</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> >>> one_to_index('Y')</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> 19</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-54" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-54', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">]</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="index_to_three"></a><div id="index_to_three-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="index_to_three-toggle" onclick="return toggle('index_to_three');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#index_to_three">index_to_three</a><tt class="py-op">(</tt><tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="index_to_three-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="index_to_three-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""Index to corresponding three letter amino acid name.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> >>> index_to_three(0)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> 'ALA'</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> >>> index_to_three(19)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> 'TYR'</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-55" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-55', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">[</tt><tt id="link-56" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-56', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="three_to_index"></a><div id="three_to_index-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="three_to_index-toggle" onclick="return toggle('three_to_index');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#three_to_index">three_to_index</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="three_to_index-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="three_to_index-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-docstring">"""Three letter code to index.</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-docstring"> >>> three_to_index('ALA')</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> 0</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> >>> three_to_index('TYR')</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> 19</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-57', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">]</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="three_to_one"></a><div id="three_to_one-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="three_to_one-toggle" onclick="return toggle('three_to_one');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#three_to_one">three_to_one</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="three_to_one-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="three_to_one-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-docstring">"""Three letter code to one letter code.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> >>> three_to_one('ALA')</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> 'A'</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> >>> three_to_one('TYR')</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> 'Y'</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> For non-standard amino acids, you get a KeyError:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> >>> three_to_one('MSE')</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> Traceback (most recent call last):</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> KeyError: 'MSE'</tt> </tt>
<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 id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-32');">i</a></tt><tt class="py-op">=</tt><tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-59', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">]</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-60', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-61', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="one_to_three"></a><div id="one_to_three-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="one_to_three-toggle" onclick="return toggle('one_to_three');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#one_to_three">one_to_three</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="one_to_three-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="one_to_three-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-docstring">"""One letter code to three letter code.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> >>> one_to_three('A')</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> 'ALA'</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> >>> one_to_three('Y')</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> 'TYR'</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 id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-62', 'i', 'link-32');">i</a></tt><tt class="py-op">=</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-63', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-64" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-64', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">[</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-65', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="is_aa"></a><div id="is_aa-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="is_aa-toggle" onclick="return toggle('is_aa');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide-module.html#is_aa">is_aa</a><tt class="py-op">(</tt><tt class="py-param">residue</tt><tt class="py-op">,</tt> <tt class="py-param">standard</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="is_aa-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="is_aa-expanded"><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-docstring">"""Return True if residue object/string is an amino acid.</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> @param residue: a L{Residue} object OR a three letter amino acid code</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> @type residue: L{Residue} or string</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> @param standard: flag to check for the 20 AA (default false) </tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> @type standard: boolean</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"> >>> is_aa('ALA')</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"> True</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> Known three letter codes for modified amino acids are supported,</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-docstring"> >>> is_aa('FME')</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> True</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> >>> is_aa('FME', standard=True)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> False</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-comment">#TODO - What about special cases like XXX, can they appear in PDB files?</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-66" 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-66', 'get_resname', 'link-66');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Method Bio.Seq.Seq.upper()=Bio.Seq.Seq-class.html#upper,Method Bio.Seq.UnknownSeq.upper()=Bio.Seq.UnknownSeq-class.html#upper,Method Bio.SeqRecord.SeqRecord.upper()=Bio.SeqRecord.SeqRecord-class.html#upper"><a title="Bio.Seq.Seq.upper
Bio.Seq.UnknownSeq.upper
Bio.SeqRecord.SeqRecord.upper" class="py-name" href="#" onclick="return doclink('link-67', 'upper', 'link-67');">upper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">standard</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">residue</tt> <tt class="py-keyword">in</tt> <tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-68', 'd3_to_index', 'link-30');">d3_to_index</a></tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">residue</tt> <tt class="py-keyword">in</tt> <tt id="link-69" class="py-name"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.StructureAlignment'.to_one_letter_code
Bio.SCOP.Raf.to_one_letter_code" class="py-name" href="#" onclick="return doclink('link-69', 'to_one_letter_code', 'link-9');">to_one_letter_code</a></tt> </tt>
</div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="Polypeptide"></a><div id="Polypeptide-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="Polypeptide-toggle" onclick="return toggle('Polypeptide');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html">Polypeptide</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Polypeptide-expanded"><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-docstring">"""A polypeptide is simply a list of L{Residue} objects."""</tt> </tt>
<a name="Polypeptide.get_ca_list"></a><div id="Polypeptide.get_ca_list-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="Polypeptide.get_ca_list-toggle" onclick="return toggle('Polypeptide.get_ca_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#get_ca_list">get_ca_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.get_ca_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.get_ca_list-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-docstring">"""Get list of C-alpha atoms in the polypeptide.</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> @return: the list of C-alpha atoms</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: [L{Atom}, L{Atom}, ...]</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">ca_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">res</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">ca</tt><tt class="py-op">=</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">ca_list</tt><tt class="py-op">.</tt><tt id="link-70" 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-70', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ca</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ca_list</tt> </tt>
</div><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_phi_psi_list"></a><div id="Polypeptide.get_phi_psi_list-def"><a name="L195"></a><tt class="py-lineno">195</tt> <a class="py-toggle" href="#" id="Polypeptide.get_phi_psi_list-toggle" onclick="return toggle('Polypeptide.get_phi_psi_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#get_phi_psi_list">get_phi_psi_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.get_phi_psi_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.get_phi_psi_list-expanded"><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the list of phi/psi dihedral angles."""</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">lng</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-71" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-71', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-72" 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-72', 'range', 'link-33');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">lng</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-73" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-73', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">res</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-74" 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-74', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">ca</tt><tt class="py-op">=</tt><tt class="py-name">res</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-75" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-75', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">res</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-76" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-76', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-comment"># Some atoms are missing</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># Phi/Psi cannot be calculated for this residue</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">.</tt><tt id="link-77" 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-77', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</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">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"PHI"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"PSI"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-comment"># Phi</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-78" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-78', 'i', 'link-32');">i</a></tt><tt class="py-op">></tt><tt class="py-number">0</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">rp</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-79" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-79', 'i', 'link-32');">i</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">try</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">cp</tt><tt class="py-op">=</tt><tt class="py-name">rp</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-80" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-80', 'get_vector', 'link-74');">get_vector</a></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-name">phi</tt><tt class="py-op">=</tt><tt id="link-81" class="py-name"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-81', 'calc_dihedral', 'link-22');">calc_dihedral</a></tt><tt class="py-op">(</tt><tt class="py-name">cp</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">ca</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">except</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">phi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment"># No phi for residue 0!</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">phi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-comment"># Psi</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-82" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-82', 'i', 'link-32');">i</a></tt><tt class="py-op"><</tt><tt class="py-op">(</tt><tt class="py-name">lng</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="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">rn</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-83" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-83', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">nn</tt><tt class="py-op">=</tt><tt class="py-name">rn</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-84" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-84', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">psi</tt><tt class="py-op">=</tt><tt id="link-85" class="py-name"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-85', 'calc_dihedral', 'link-22');">calc_dihedral</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">ca</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt class="py-name">nn</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">psi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment"># No psi for last residue!</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">psi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">psi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-comment"># Add Phi/Psi to xtra dict of residue</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"PHI"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">phi</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"PSI"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">psi</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ppl</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_tau_list"></a><div id="Polypeptide.get_tau_list-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="Polypeptide.get_tau_list-toggle" onclick="return toggle('Polypeptide.get_tau_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#get_tau_list">get_tau_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.get_tau_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.get_tau_list-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-docstring">"""List of tau torsions angles for all 4 consecutive Calpha atoms."""</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">ca_list</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Method Bio.PDB.Polypeptide.Polypeptide.get_ca_list()=Bio.PDB.Polypeptide.Polypeptide-class.html#get_ca_list"><a title="Bio.PDB.Polypeptide.Polypeptide.get_ca_list" class="py-name" href="#" onclick="return doclink('link-87', 'get_ca_list', 'link-87');">get_ca_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">tau_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-88" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-88', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-89" 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-89', 'range', 'link-33');">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">ca_list</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">atom_list</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-90" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-90', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-91" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-91', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-92" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-92', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-93" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-93', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">,</tt> <tt class="py-name">v4</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-94', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">atom_list</tt><tt class="py-op">]</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">tau</tt><tt class="py-op">=</tt><tt id="link-95" class="py-name"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-95', 'calc_dihedral', 'link-22');">calc_dihedral</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">,</tt> <tt class="py-name">v4</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">tau_list</tt><tt class="py-op">.</tt><tt id="link-96" 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-96', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">tau</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-comment"># Put tau in xtra dict of residue</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-97" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-97', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-98" 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-98', 'get_parent', 'link-98');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"TAU"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">tau</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tau_list</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_theta_list"></a><div id="Polypeptide.get_theta_list-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="Polypeptide.get_theta_list-toggle" onclick="return toggle('Polypeptide.get_theta_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#get_theta_list">get_theta_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.get_theta_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.get_theta_list-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-docstring">"""List of theta angles for all 3 consecutive Calpha atoms."""</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">theta_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">ca_list</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_ca_list" class="py-name" href="#" onclick="return doclink('link-99', 'get_ca_list', 'link-87');">get_ca_list</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">for</tt> <tt id="link-100" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-100', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-101" 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-101', 'range', 'link-33');">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">ca_list</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">atom_list</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-102" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-102', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-103" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-103', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-104" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-104', 'i', 'link-32');">i</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="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-105', 'get_vector', 'link-74');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">atom_list</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">theta</tt><tt class="py-op">=</tt><tt id="link-106" class="py-name"><a title="Bio.PDB.Vector'.calc_angle" class="py-name" href="#" onclick="return doclink('link-106', 'calc_angle', 'link-23');">calc_angle</a></tt><tt class="py-op">(</tt><tt class="py-name">v1</tt><tt class="py-op">,</tt> <tt class="py-name">v2</tt><tt class="py-op">,</tt> <tt class="py-name">v3</tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">theta_list</tt><tt class="py-op">.</tt><tt id="link-107" 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-107', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-comment"># Put tau in xtra dict of residue</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">ca_list</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-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-109" 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-109', 'get_parent', 'link-98');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"THETA"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">theta</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">theta_list</tt> </tt>
</div><a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_sequence"></a><div id="Polypeptide.get_sequence-def"><a name="L268"></a><tt class="py-lineno">268</tt> <a class="py-toggle" href="#" id="Polypeptide.get_sequence-toggle" onclick="return toggle('Polypeptide.get_sequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#get_sequence">get_sequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.get_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.get_sequence-expanded"><a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the AA sequence as a Seq object.</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> @return: polypeptide sequence </tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: L{Seq}</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">res</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">+=</tt> <tt id="link-110" class="py-name"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.StructureAlignment'.to_one_letter_code
Bio.SCOP.Raf.to_one_letter_code" class="py-name" href="#" onclick="return doclink('link-110', 'to_one_letter_code', 'link-9');">to_one_letter_code</a></tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-111', 'get', 'link-111');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-112', 'get_resname', 'link-66');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'X'</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt id="link-113" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-113', 'seq', 'link-113');">seq</a></tt><tt class="py-op">=</tt><tt id="link-114" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-114', 'Seq', 'link-4');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-115', 'generic_protein', 'link-2');">generic_protein</a></tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-116" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-116', 'seq', 'link-113');">seq</a></tt> </tt>
</div><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.__repr__"></a><div id="Polypeptide.__repr__-def"><a name="L280"></a><tt class="py-lineno">280</tt> <a class="py-toggle" href="#" id="Polypeptide.__repr__-toggle" onclick="return toggle('Polypeptide.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.Polypeptide-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Polypeptide.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Polypeptide.__repr__-expanded"><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-docstring">"""Return string representation of the polypeptide.</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> Return <Polypeptide start=START end=END>, where START</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> and END are sequence identifiers of the outer residues.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt id="link-117" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-117', 'start', 'link-117');">start</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-118" 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-118', 'get_id', 'link-118');">get_id</a></tt><tt class="py-op">(</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="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt id="link-119" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-119', 'end', 'link-119');">end</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-120" 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-120', 'get_id', 'link-118');">get_id</a></tt><tt class="py-op">(</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="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-string">"<Polypeptide start=%s end=%s>"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-121', 'start', 'link-117');">start</a></tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-122', 'end', 'link-119');">end</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">return</tt> <tt class="py-name">s</tt> </tt>
</div></div><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder"></a><div id="_PPBuilder-def"><a name="L291"></a><tt class="py-lineno">291</tt> <a class="py-toggle" href="#" id="_PPBuilder-toggle" onclick="return toggle('_PPBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide._PPBuilder-class.html">_PPBuilder</a><tt class="py-op">:</tt> </tt>
</div><div id="_PPBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_PPBuilder-expanded"><a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class to extract polypeptides.</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> It checks if two consecutive residues in a chain are connected.</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> The connectivity test is implemented by a subclass.</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> This assumes you want both standard and non-standard amino acids.</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_PPBuilder.__init__"></a><div id="_PPBuilder.__init__-def"><a name="L299"></a><tt class="py-lineno">299</tt> <a class="py-toggle" href="#" id="_PPBuilder.__init__-toggle" onclick="return toggle('_PPBuilder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide._PPBuilder-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">radius</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PPBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PPBuilder.__init__-expanded"><a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> @param radius: distance</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">radius</tt><tt class="py-op">=</tt><tt class="py-name">radius</tt> </tt>
</div><a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder._accept"></a><div id="_PPBuilder._accept-def"><a name="L306"></a><tt class="py-lineno">306</tt> <a class="py-toggle" href="#" id="_PPBuilder._accept-toggle" onclick="return toggle('_PPBuilder._accept');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide._PPBuilder-class.html#_accept">_accept</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-param">standard_aa_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PPBuilder._accept-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PPBuilder._accept-expanded"><a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-docstring">"""Check if the residue is an amino acid (PRIVATE)."""</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-123" 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-123', 'is_aa', 'link-123');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">,</tt> <tt class="py-name">standard</tt><tt class="py-op">=</tt><tt class="py-name">standard_aa_only</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-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">standard_aa_only</tt> <tt class="py-keyword">and</tt> <tt class="py-string">"CA"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt class="py-name">child_dict</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment">#It has an alpha carbon...</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-comment">#We probably need to update the hard coded list of</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-comment">#non-standard residues, see function is_aa for details.</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</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">"Assuming residue %s is an unknown modified "</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-string">"amino acid"</tt> <tt class="py-op">%</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-124', 'get_resname', 'link-66');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-comment"># not a standard AA so skip</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder.build_peptides"></a><div id="_PPBuilder.build_peptides-def"><a name="L321"></a><tt class="py-lineno">321</tt> <a class="py-toggle" href="#" id="_PPBuilder.build_peptides-toggle" onclick="return toggle('_PPBuilder.build_peptides');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide._PPBuilder-class.html#build_peptides">build_peptides</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">entity</tt><tt class="py-op">,</tt> <tt class="py-param">aa_only</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_PPBuilder.build_peptides-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PPBuilder.build_peptides-expanded"><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-docstring">"""Build and return a list of Polypeptide objects.</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"> @param entity: polypeptides are searched for in this object</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> @type entity: L{Structure}, L{Model} or L{Chain}</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> @param aa_only: if 1, the residue needs to be a standard AA</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-docstring"> @type aa_only: int</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">is_connected</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name" targets="Method Bio.PDB.Polypeptide.CaPPBuilder._is_connected()=Bio.PDB.Polypeptide.CaPPBuilder-class.html#_is_connected,Method Bio.PDB.Polypeptide.PPBuilder._is_connected()=Bio.PDB.Polypeptide.PPBuilder-class.html#_is_connected"><a title="Bio.PDB.Polypeptide.CaPPBuilder._is_connected
Bio.PDB.Polypeptide.PPBuilder._is_connected" class="py-name" href="#" onclick="return doclink('link-125', '_is_connected', 'link-125');">_is_connected</a></tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">accept</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name" targets="Method Bio.PDB.Polypeptide._PPBuilder._accept()=Bio.PDB.Polypeptide._PPBuilder-class.html#_accept"><a title="Bio.PDB.Polypeptide._PPBuilder._accept" class="py-name" href="#" onclick="return doclink('link-126', '_accept', 'link-126');">_accept</a></tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">level</tt><tt class="py-op">=</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_level()=Bio.PDB.Atom.Atom-class.html#get_level,Method Bio.PDB.Entity.Entity.get_level()=Bio.PDB.Entity.Entity-class.html#get_level"><a title="Bio.PDB.Atom.Atom.get_level
Bio.PDB.Entity.Entity.get_level" class="py-name" href="#" onclick="return doclink('link-127', 'get_level', 'link-127');">get_level</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment"># Decide wich entity we are dealing with</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">level</tt><tt class="py-op">==</tt><tt class="py-string">"S"</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">model</tt><tt class="py-op">=</tt><tt class="py-name">entity</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">chain_list</tt><tt class="py-op">=</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name" targets="Method Bio.PDB.Entity.Entity.get_list()=Bio.PDB.Entity.Entity-class.html#get_list"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-128', 'get_list', 'link-128');">get_list</a></tt><tt class="py-op">(</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">elif</tt> <tt class="py-name">level</tt><tt class="py-op">==</tt><tt class="py-string">"M"</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">chain_list</tt><tt class="py-op">=</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-129', 'get_list', 'link-128');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">level</tt><tt class="py-op">==</tt><tt class="py-string">"C"</tt><tt class="py-op">:</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">chain_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">entity</tt><tt class="py-op">]</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">else</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">raise</tt> <tt id="link-130" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBException" class="py-name" href="#" onclick="return doclink('link-130', 'PDBException', 'link-13');">PDBException</a></tt><tt class="py-op">(</tt><tt class="py-string">"Entity should be Structure, Model or Chain."</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">pp_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">chain</tt> <tt class="py-keyword">in</tt> <tt class="py-name">chain_list</tt><tt class="py-op">:</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">chain_it</tt><tt class="py-op">=</tt><tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">chain</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">prev_res</tt> <tt class="py-op">=</tt> <tt class="py-name">chain_it</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-131', 'next', 'link-131');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">accept</tt><tt class="py-op">(</tt><tt class="py-name">prev_res</tt><tt class="py-op">,</tt> <tt class="py-name">aa_only</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">prev_res</tt> <tt class="py-op">=</tt> <tt class="py-name">chain_it</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-132', 'next', 'link-131');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-comment">#No interesting residues at all in this chain</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">next_res</tt> <tt class="py-keyword">in</tt> <tt class="py-name">chain_it</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">accept</tt><tt class="py-op">(</tt><tt class="py-name">prev_res</tt><tt class="py-op">,</tt> <tt class="py-name">aa_only</tt><tt class="py-op">)</tt> \ </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-name">accept</tt><tt class="py-op">(</tt><tt class="py-name">next_res</tt><tt class="py-op">,</tt> <tt class="py-name">aa_only</tt><tt class="py-op">)</tt> \ </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-name">is_connected</tt><tt class="py-op">(</tt><tt class="py-name">prev_res</tt><tt class="py-op">,</tt> <tt class="py-name">next_res</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">=</tt><tt id="link-133" 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-133', 'Polypeptide', 'link-133');">Polypeptide</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-134" 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-134', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">prev_res</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">pp_list</tt><tt class="py-op">.</tt><tt id="link-135" 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-135', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-136" 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-136', 'append', 'link-70');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">next_res</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-comment">#Either too far apart, or one of the residues is unwanted.</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment">#End the current peptide</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">prev_res</tt><tt class="py-op">=</tt><tt class="py-name">next_res</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">pp_list</tt> </tt>
</div></div><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="CaPPBuilder"></a><div id="CaPPBuilder-def"><a name="L371"></a><tt class="py-lineno">371</tt> <a class="py-toggle" href="#" id="CaPPBuilder-toggle" onclick="return toggle('CaPPBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.CaPPBuilder-class.html">CaPPBuilder</a><tt class="py-op">(</tt><tt class="py-base-class">_PPBuilder</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CaPPBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CaPPBuilder-expanded"><a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-docstring">"""Use CA--CA distance to find polypeptides."""</tt> </tt>
<a name="CaPPBuilder.__init__"></a><div id="CaPPBuilder.__init__-def"><a name="L373"></a><tt class="py-lineno">373</tt> <a class="py-toggle" href="#" id="CaPPBuilder.__init__-toggle" onclick="return toggle('CaPPBuilder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.CaPPBuilder-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">radius</tt><tt class="py-op">=</tt><tt class="py-number">4.3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CaPPBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CaPPBuilder.__init__-expanded"><a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt id="link-137" class="py-name" targets="Class Bio.PDB.Polypeptide._PPBuilder=Bio.PDB.Polypeptide._PPBuilder-class.html"><a title="Bio.PDB.Polypeptide._PPBuilder" class="py-name" href="#" onclick="return doclink('link-137', '_PPBuilder', 'link-137');">_PPBuilder</a></tt><tt class="py-op">.</tt><tt id="link-138" 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 Bio.Application.ApplicationError.__init__()=Bio.Application.ApplicationError-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Application._Argument.__init__()=Bio.Application._Argument-class.html#__init__,Method Bio.Application._Option.__init__()=Bio.Application._Option-class.html#__init__,Method Bio.Application._Switch.__init__()=Bio.Application._Switch-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.BlastpgpCommandline.__init__()=Bio.Blast.Applications.BlastpgpCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastformatterCommandline.__init__()=Bio.Blast.Applications.NcbiblastformatterCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastnCommandline.__init__()=Bio.Blast.Applications.NcbiblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastpCommandline.__init__()=Bio.Blast.Applications.NcbiblastpCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastxCommandline.__init__()=Bio.Blast.Applications.NcbiblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbipsiblastCommandline.__init__()=Bio.Blast.Applications.NcbipsiblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpsblastCommandline.__init__()=Bio.Blast.Applications.NcbirpsblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpstblastnCommandline.__init__()=Bio.Blast.Applications.NcbirpstblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastnCommandline.__init__()=Bio.Blast.Applications.NcbitblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastxCommandline.__init__()=Bio.Blast.Applications.NcbitblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.RpsBlastCommandline.__init__()=Bio.Blast.Applications.RpsBlastCommandline-class.html#__init__,Method Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__()=Bio.Blast.Applications._BlastAllOrPgpCommandLine-class.html#__init__,Method Bio.Blast.Applications._BlastCommandLine.__init__()=Bio.Blast.Applications._BlastCommandLine-class.html#__init__,Method Bio.Blast.Applications._NcbibaseblastCommandline.__init__()=Bio.Blast.Applications._NcbibaseblastCommandline-class.html#__init__,Method Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__()=Bio.Blast.Applications._Ncbiblast2SeqCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastCommandline.__init__()=Bio.Blast.Applications._NcbiblastCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__()=Bio.Blast.Applications._NcbiblastMain2SeqCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method 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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-138', '__init__', 'link-138');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">)</tt> </tt>
</div><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> </tt>
<a name="CaPPBuilder._is_connected"></a><div id="CaPPBuilder._is_connected-def"><a name="L376"></a><tt class="py-lineno">376</tt> <a class="py-toggle" href="#" id="CaPPBuilder._is_connected-toggle" onclick="return toggle('CaPPBuilder._is_connected');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.CaPPBuilder-class.html#_is_connected">_is_connected</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prev_res</tt><tt class="py-op">,</tt> <tt class="py-param">next_res</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CaPPBuilder._is_connected-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CaPPBuilder._is_connected-expanded"><a name="L377"></a><tt class="py-lineno">377</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-op">[</tt><tt class="py-name">prev_res</tt><tt class="py-op">,</tt> <tt class="py-name">next_res</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-139" 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-139', 'has_id', 'link-139');">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="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">next_res</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">prev_res</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-comment"># Unpack disordered</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Method Bio.PDB.Atom.Atom.is_disordered()=Bio.PDB.Atom.Atom-class.html#is_disordered,Method Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#is_disordered,Method Bio.PDB.Residue.Residue.is_disordered()=Bio.PDB.Residue.Residue-class.html#is_disordered"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-140', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">nlist</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Method Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_get_list"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-141', 'disordered_get_list', 'link-141');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">nlist</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-142', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">plist</tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-143', 'disordered_get_list', 'link-141');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">plist</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">nn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nlist</tt><tt class="py-op">:</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">plist</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">nn</tt><tt class="py-op">-</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">radius</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div></div><a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> </tt>
<a name="PPBuilder"></a><div id="PPBuilder-def"><a name="L398"></a><tt class="py-lineno">398</tt> <a class="py-toggle" href="#" id="PPBuilder-toggle" onclick="return toggle('PPBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.PPBuilder-class.html">PPBuilder</a><tt class="py-op">(</tt><tt class="py-base-class">_PPBuilder</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PPBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PPBuilder-expanded"><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-docstring">"""Use C--N distance to find polypeptides."""</tt> </tt>
<a name="PPBuilder.__init__"></a><div id="PPBuilder.__init__-def"><a name="L400"></a><tt class="py-lineno">400</tt> <a class="py-toggle" href="#" id="PPBuilder.__init__-toggle" onclick="return toggle('PPBuilder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.PPBuilder-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">radius</tt><tt class="py-op">=</tt><tt class="py-number">1.8</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PPBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PPBuilder.__init__-expanded"><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt id="link-144" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder" class="py-name" href="#" onclick="return doclink('link-144', '_PPBuilder', 'link-137');">_PPBuilder</a></tt><tt class="py-op">.</tt><tt id="link-145" 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-145', '__init__', 'link-138');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">radius</tt><tt class="py-op">)</tt> </tt>
</div><a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="PPBuilder._is_connected"></a><div id="PPBuilder._is_connected-def"><a name="L403"></a><tt class="py-lineno">403</tt> <a class="py-toggle" href="#" id="PPBuilder._is_connected-toggle" onclick="return toggle('PPBuilder._is_connected');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.PPBuilder-class.html#_is_connected">_is_connected</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prev_res</tt><tt class="py-op">,</tt> <tt class="py-param">next_res</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PPBuilder._is_connected-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PPBuilder._is_connected-expanded"><a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">prev_res</tt><tt class="py-op">.</tt><tt id="link-146" 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-146', 'has_id', 'link-139');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"C"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">next_res</tt><tt class="py-op">.</tt><tt id="link-147" 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-147', 'has_id', 'link-139');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"N"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">test_dist</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name" targets="Method Bio.PDB.Polypeptide.PPBuilder._test_dist()=Bio.PDB.Polypeptide.PPBuilder-class.html#_test_dist"><a title="Bio.PDB.Polypeptide.PPBuilder._test_dist" class="py-name" href="#" onclick="return doclink('link-148', '_test_dist', 'link-148');">_test_dist</a></tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">prev_res</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">next_res</tt><tt class="py-op">[</tt><tt class="py-string">"N"</tt><tt class="py-op">]</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-comment"># Test all disordered atom positions!</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-149', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">clist</tt><tt class="py-op">=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-150', 'disordered_get_list', 'link-141');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">clist</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-151', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">nlist</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-152', 'disordered_get_list', 'link-141');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">nlist</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">nn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nlist</tt><tt class="py-op">:</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">cc</tt> <tt class="py-keyword">in</tt> <tt class="py-name">clist</tt><tt class="py-op">:</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-comment"># To form a peptide bond, N and C must be </tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-comment"># within radius and have the same altloc</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-comment"># identifier or one altloc blank</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">n_altloc</tt><tt class="py-op">=</tt><tt class="py-name">nn</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_altloc()=Bio.PDB.Atom.Atom-class.html#get_altloc"><a title="Bio.PDB.Atom.Atom.get_altloc" class="py-name" href="#" onclick="return doclink('link-153', 'get_altloc', 'link-153');">get_altloc</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">c_altloc</tt><tt class="py-op">=</tt><tt class="py-name">cc</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.PDB.Atom.Atom.get_altloc" class="py-name" href="#" onclick="return doclink('link-154', 'get_altloc', 'link-153');">get_altloc</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n_altloc</tt><tt class="py-op">==</tt><tt class="py-name">c_altloc</tt> <tt class="py-keyword">or</tt> <tt class="py-name">n_altloc</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c_altloc</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">test_dist</tt><tt class="py-op">(</tt><tt class="py-name">nn</tt><tt class="py-op">,</tt> <tt class="py-name">cc</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-comment"># Select the disordered atoms that</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-comment"># are indeed bonded</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-155', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name" targets="Method Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_select"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select" class="py-name" href="#" onclick="return doclink('link-156', 'disordered_select', 'link-156');">disordered_select</a></tt><tt class="py-op">(</tt><tt class="py-name">c_altloc</tt><tt class="py-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-157', 'is_disordered', 'link-140');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select" class="py-name" href="#" onclick="return doclink('link-158', 'disordered_select', 'link-156');">disordered_select</a></tt><tt class="py-op">(</tt><tt class="py-name">n_altloc</tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> </tt>
<a name="PPBuilder._test_dist"></a><div id="PPBuilder._test_dist-def"><a name="L438"></a><tt class="py-lineno">438</tt> <a class="py-toggle" href="#" id="PPBuilder._test_dist-toggle" onclick="return toggle('PPBuilder._test_dist');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Polypeptide.PPBuilder-class.html#_test_dist">_test_dist</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PPBuilder._test_dist-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PPBuilder._test_dist-expanded"><a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-docstring">"""Return 1 if distance between atoms<radius (PRIVATE)."""</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">-</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">radius</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> </tt>
<a name="L446"></a><tt class="py-lineno">446</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="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-159" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-159', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-160', 'PDB', 'link-11');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-161" 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-161', 'PDBParser', 'link-161');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-162" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-162', 'PDBParser', 'link-161');">PDBParser</a></tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-163" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-163', 'PDBParser', 'link-161');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-name">PERMISSIVE</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> </tt>
<a name="L452"></a><tt class="py-lineno">452</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-164" 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-164', 'get_structure', 'link-164');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"scr"</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="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-165" class="py-name" targets="Class Bio.PDB.Polypeptide.PPBuilder=Bio.PDB.Polypeptide.PPBuilder-class.html"><a title="Bio.PDB.Polypeptide.PPBuilder" class="py-name" href="#" onclick="return doclink('link-165', 'PPBuilder', 'link-165');">PPBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"C-N"</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-166" 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-166', 'build_peptides', 'link-166');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name" targets="Method Bio.PDB.Polypeptide.Polypeptide.get_sequence()=Bio.PDB.Polypeptide.Polypeptide-class.html#get_sequence"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-167', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-168', 'build_peptides', 'link-166');">build_peptides</a></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 class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-169', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-170', 'build_peptides', 'link-166');">build_peptides</a></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 class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-171', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-172', 'build_peptides', 'link-166');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">psi</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name" targets="Method Bio.PDB.Polypeptide.Polypeptide.get_phi_psi_list()=Bio.PDB.Polypeptide.Polypeptide-class.html#get_phi_psi_list"><a title="Bio.PDB.Polypeptide.Polypeptide.get_phi_psi_list" class="py-name" href="#" onclick="return doclink('link-173', 'get_phi_psi_list', 'link-173');">get_phi_psi_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">psi</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-174" 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-174', 'CaPPBuilder', 'link-174');">CaPPBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"CA-CA"</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-175', 'build_peptides', 'link-166');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-176', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-177', 'build_peptides', 'link-166');">build_peptides</a></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 class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-178', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-179', 'build_peptides', 'link-166');">build_peptides</a></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 class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-180', 'get_sequence', 'link-167');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> </tt><script type="text/javascript">
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