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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"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-0', 'sum', 'link-0');">sum</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringType</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.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-2', 'Alphabet', 'link-2');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Alphabet.ProteinAlphabet=Bio.Alphabet.ProteinAlphabet-class.html"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-3', 'ProteinAlphabet', 'link-3');">ProteinAlphabet</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-5', 'Seq', 'link-5');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-6', 'Seq', 'link-5');">Seq</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Package Bio.SCOP=Bio.SCOP-module.html,Module Bio.WWW.SCOP=Bio.WWW.SCOP-module.html"><a title="Bio.SCOP
Bio.WWW.SCOP" class="py-name" href="#" onclick="return doclink('link-8', 'SCOP', 'link-8');">SCOP</a></tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'Raf', 'link-9');">Raf</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" 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.FragmentMapper'.to_one_letter_code=Bio.PDB.FragmentMapper%27-module.html#to_one_letter_code,Variable Bio.PDB.HSExposure.to_one_letter_code=Bio.PDB.HSExposure-module.html#to_one_letter_code,Variable Bio.PDB.PSEA.to_one_letter_code=Bio.PDB.PSEA-module.html#to_one_letter_code,Variable Bio.PDB.ResidueDepth'.to_one_letter_code=Bio.PDB.ResidueDepth%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.FragmentMapper'.to_one_letter_code
Bio.PDB.HSExposure.to_one_letter_code
Bio.PDB.PSEA.to_one_letter_code
Bio.PDB.ResidueDepth'.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-10', 'to_one_letter_code', 'link-10');">to_one_letter_code</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-11" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-11', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-12', 'PDB', 'link-12');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'PDBExceptions', 'link-13');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name" targets="Variable Bio.PDB.DSSP'.PDBException=Bio.PDB.DSSP%27-module.html#PDBException,Variable Bio.PDB.PDBExceptions.PDBException=Bio.PDB.PDBExceptions-module.html#PDBException,Variable Bio.PDB.Superimposer'.PDBException=Bio.PDB.Superimposer%27-module.html#PDBException"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-14', 'PDBException', 'link-14');">PDBException</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-15" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-15', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-16', 'PDB', 'link-12');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'Residue', 'link-17');">Residue</a></tt> <tt class="py-keyword">import</tt> <tt id="link-18" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-18', 'Residue', 'link-17');">Residue</a></tt><tt class="py-op">,</tt> <tt id="link-19" 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-19', 'DisorderedResidue', 'link-19');">DisorderedResidue</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-20" 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-20', 'Vector', 'link-20');">Vector</a></tt> <tt class="py-keyword">import</tt> <tt id="link-21" 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-21', 'calc_dihedral', 'link-21');">calc_dihedral</a></tt><tt class="py-op">,</tt> <tt id="link-22" 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-22', 'calc_angle', 'link-22');">calc_angle</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt id="link-23" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-23', '__doc__', 'link-23');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-string">Polypeptide related classes (construction and representation).</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-string">Example:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-string"> >>> ppb=PPBuilder()</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-string"> >>> for pp in ppb.build_peptides(structure):</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-string"> >>> print pp.get_sequence()</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable Bio.PDB.DSSP'.standard_aa_names=Bio.PDB.DSSP%27-module.html#standard_aa_names,Variable Bio.PDB.FragmentMapper'.standard_aa_names=Bio.PDB.FragmentMapper%27-module.html#standard_aa_names,Variable Bio.PDB.HSExposure.standard_aa_names=Bio.PDB.HSExposure-module.html#standard_aa_names,Variable Bio.PDB.PSEA.standard_aa_names=Bio.PDB.PSEA-module.html#standard_aa_names,Variable Bio.PDB.Polypeptide.standard_aa_names=Bio.PDB.Polypeptide-module.html#standard_aa_names,Variable Bio.PDB.ResidueDepth'.standard_aa_names=Bio.PDB.ResidueDepth%27-module.html#standard_aa_names,Variable Bio.PDB.StructureAlignment'.standard_aa_names=Bio.PDB.StructureAlignment%27-module.html#standard_aa_names"><a title="Bio.PDB.DSSP'.standard_aa_names
Bio.PDB.FragmentMapper'.standard_aa_names
Bio.PDB.HSExposure.standard_aa_names
Bio.PDB.PSEA.standard_aa_names
Bio.PDB.Polypeptide.standard_aa_names
Bio.PDB.ResidueDepth'.standard_aa_names
Bio.PDB.StructureAlignment'.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="L27"></a><tt class="py-lineno"> 27</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="L28"></a><tt class="py-lineno"> 28</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="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</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="L32"></a><tt class="py-lineno"> 32</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.DSSP'.standard_aa_names
Bio.PDB.FragmentMapper'.standard_aa_names
Bio.PDB.HSExposure.standard_aa_names
Bio.PDB.PSEA.standard_aa_names
Bio.PDB.Polypeptide.standard_aa_names
Bio.PDB.ResidueDepth'.standard_aa_names
Bio.PDB.StructureAlignment'.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="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</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="L35"></a><tt class="py-lineno"> 35</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="L36"></a><tt class="py-lineno"> 36</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="L37"></a><tt class="py-lineno"> 37</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="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"># Create some lookup tables</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt><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 class="py-name">range</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="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-33" 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-33', 'n1', 'link-33');">n1</a></tt><tt class="py-op">=</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-34', 'aa1', 'link-25');">aa1</a></tt><tt class="py-op">[</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-36" 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-36', 'n3', 'link-36');">n3</a></tt><tt class="py-op">=</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Polypeptide.aa3" class="py-name" href="#" onclick="return doclink('link-37', 'aa3', 'link-26');">aa3</a></tt><tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-39', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-40', 'n1', 'link-33');">n1</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-41', 'i', 'link-32');">i</a></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-42', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-44', 'n1', 'link-33');">n1</a></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-45', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.n3" class="py-name" href="#" onclick="return doclink('link-46', 'n3', 'link-36');">n3</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-32');">i</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-48', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.n3" class="py-name" href="#" onclick="return doclink('link-50', 'n3', 'link-36');">n3</a></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="index_to_one"></a><div id="index_to_one-def"><a name="L48"></a><tt class="py-lineno"> 48</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="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 class="py-docstring"> Index to corresponding one letter amino acid name.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> For example: 0 to A.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-51" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-51', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-52" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-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"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-52', 'index', 'link-52');">index</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="one_to_index"></a><div id="one_to_index-def"><a name="L55"></a><tt class="py-lineno"> 55</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="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> One letter code to index.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> For example: A to 0.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-53', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt id="link-54" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-54', 's', 'link-54');">s</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="index_to_three"></a><div id="index_to_three-def"><a name="L62"></a><tt class="py-lineno"> 62</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="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> Index to corresponding three letter amino acid name.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> For example: 0 to ALA.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</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="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="three_to_index"></a><div id="three_to_index-def"><a name="L69"></a><tt class="py-lineno"> 69</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="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> Three letter code to index.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> For example: ALA to 0.</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</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 id="link-58" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-58', 's', 'link-54');">s</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="three_to_one"></a><div id="three_to_one-def"><a name="L76"></a><tt class="py-lineno"> 76</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="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> Three letter code to one letter code.</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> For example: ALA to A.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-32');">i</a></tt><tt class="py-op">=</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-60', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">[</tt><tt id="link-61" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-61', 's', 'link-54');">s</a></tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_1" class="py-name" href="#" onclick="return doclink('link-62', 'dindex_to_1', 'link-29');">dindex_to_1</a></tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-63', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> </tt>
<a name="one_to_three"></a><div id="one_to_three-def"><a name="L84"></a><tt class="py-lineno"> 84</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="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"> One letter code to three letter code.</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> For example: A to ALA.</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-64', 'i', 'link-32');">i</a></tt><tt class="py-op">=</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Polypeptide.d1_to_index" class="py-name" href="#" onclick="return doclink('link-65', 'd1_to_index', 'link-28');">d1_to_index</a></tt><tt class="py-op">[</tt><tt id="link-66" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-66', 's', 'link-54');">s</a></tt><tt class="py-op">]</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-67" class="py-name"><a title="Bio.PDB.Polypeptide.dindex_to_3" class="py-name" href="#" onclick="return doclink('link-67', 'dindex_to_3', 'link-31');">dindex_to_3</a></tt><tt class="py-op">[</tt><tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="is_aa"></a><div id="is_aa-def"><a name="L92"></a><tt class="py-lineno"> 92</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-number">0</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="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Return 1 if residue object/string is an amino acid.</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"> @param residue: a L{Residue} object OR a three letter amino acid code</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> @type residue: L{Residue} or string</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> @param standard: flag to check for the 20 AA (default false) </tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> @type standard: boolean</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-69" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-69', 'type', 'link-69');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-name">StringType</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-70" 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-70', 'get_resname', 'link-70');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</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 class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</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="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-71" class="py-name"><a title="Bio.PDB.Polypeptide.d3_to_index" class="py-name" href="#" onclick="return doclink('link-71', 'd3_to_index', 'link-30');">d3_to_index</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-72', 'has_key', 'link-72');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-73" class="py-name"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.FragmentMapper'.to_one_letter_code
Bio.PDB.HSExposure.to_one_letter_code
Bio.PDB.PSEA.to_one_letter_code
Bio.PDB.ResidueDepth'.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-73', 'to_one_letter_code', 'link-10');">to_one_letter_code</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-74', 'has_key', 'link-72');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="Polypeptide"></a><div id="Polypeptide-def"><a name="L111"></a><tt class="py-lineno">111</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="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> A polypeptide is simply a list of L{Residue} objects.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Polypeptide.get_ca_list"></a><div id="Polypeptide.get_ca_list-def"><a name="L115"></a><tt class="py-lineno">115</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="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> @return: the list of C-alpha atoms</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: [L{Atom}, L{Atom}, ...]</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</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="L121"></a><tt class="py-lineno">121</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="L122"></a><tt class="py-lineno">122</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="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">ca_list</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-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,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-75', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ca</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ca_list</tt> </tt>
</div><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_phi_psi_list"></a><div id="Polypeptide.get_phi_psi_list-def"><a name="L126"></a><tt class="py-lineno">126</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="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> Return the list of phi/psi dihedral angles</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</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="L131"></a><tt class="py-lineno">131</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="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-76" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-76', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">lng</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-77" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-77', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</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-78" 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-78', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">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-79" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-79', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</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-80" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-80', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment"># Some atoms are missing</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Phi/Psi cannot be calculated for this residue</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ppl</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-81', 'append', 'link-75');">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="L142"></a><tt class="py-lineno">142</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="L143"></a><tt class="py-lineno">143</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="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># Phi</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</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-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="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</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-84" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-84', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">phi</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-21');">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="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</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="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-comment"># No phi for residue 0!</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">phi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment"># Psi</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-86" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-86', '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="L158"></a><tt class="py-lineno">158</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-87" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-87', '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="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</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-88" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-88', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">psi</tt><tt class="py-op">=</tt><tt id="link-89" class="py-name"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-89', 'calc_dihedral', 'link-21');">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="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</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="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment"># No psi for last residue!</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">psi</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-90', 'append', 'link-75');">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="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-comment"># Add Phi/Psi to xtra dict of residue</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt> <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="L170"></a><tt class="py-lineno">170</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="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ppl</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_tau_list"></a><div id="Polypeptide.get_tau_list-def"><a name="L173"></a><tt class="py-lineno">173</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="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> Return list of tau torsions angles for all 4 consecutive</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> Calpha atoms.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</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-91" 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-91', 'get_ca_list', 'link-91');">get_ca_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">tau_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">for</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-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">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="L181"></a><tt class="py-lineno">181</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-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-op">,</tt> <tt class="py-name">ca_list</tt><tt class="py-op">[</tt><tt id="link-94" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-94', '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-95" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-95', '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-96" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-96', '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="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">vector_list</tt><tt class="py-op">=</tt><tt id="link-97" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-97', 'map', 'link-97');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">a</tt><tt class="py-op">:</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-98', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">atom_list</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</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-name">vector_list</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">tau</tt><tt class="py-op">=</tt><tt id="link-99" class="py-name"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-99', 'calc_dihedral', 'link-21');">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="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">tau_list</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-100', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">tau</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># Put tau in xtra dict of residue</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', '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-102" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.get_parent()=Bio.EUtils.POM.ElementNode-class.html#get_parent,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.EUtils.POM.ElementNode.get_parent
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-102', 'get_parent', 'link-102');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt 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="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tau_list</tt> </tt>
</div><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_theta_list"></a><div id="Polypeptide.get_theta_list-def"><a name="L191"></a><tt class="py-lineno">191</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="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> Return list of theta angles for all 3 consecutive</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> Calpha atoms.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</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="L197"></a><tt class="py-lineno">197</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-103" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_ca_list" class="py-name" href="#" onclick="return doclink('link-103', 'get_ca_list', 'link-91');">get_ca_list</a></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-keyword">for</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-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">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="L199"></a><tt class="py-lineno">199</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-105" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-105', '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-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', '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-107" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-107', '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="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">vector_list</tt><tt class="py-op">=</tt><tt id="link-108" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-108', 'map', 'link-97');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">a</tt><tt class="py-op">:</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.PDB.Atom.Atom.get_vector" class="py-name" href="#" onclick="return doclink('link-109', 'get_vector', 'link-78');">get_vector</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">atom_list</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</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">vector_list</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">theta</tt><tt class="py-op">=</tt><tt id="link-110" class="py-name"><a title="Bio.PDB.Vector'.calc_angle" class="py-name" href="#" onclick="return doclink('link-110', 'calc_angle', 'link-22');">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="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">theta_list</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-111', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">theta</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-comment"># Put tau in xtra dict of residue</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-112" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-112', '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-113" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_parent
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-113', 'get_parent', 'link-102');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</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="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">theta_list</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.get_sequence"></a><div id="Polypeptide.get_sequence-def"><a name="L209"></a><tt class="py-lineno">209</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="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> Return the AA sequence.</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> @return: polypeptide sequence </tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: L{Seq}</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt id="link-114" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-114', 's', 'link-54');">s</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">res</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-115', 'get_resname', 'link-70');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-116" class="py-name"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.FragmentMapper'.to_one_letter_code
Bio.PDB.HSExposure.to_one_letter_code
Bio.PDB.PSEA.to_one_letter_code
Bio.PDB.ResidueDepth'.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-116', 'to_one_letter_code', 'link-10');">to_one_letter_code</a></tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-117', 'has_key', 'link-72');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt id="link-118" class="py-name"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.FragmentMapper'.to_one_letter_code
Bio.PDB.HSExposure.to_one_letter_code
Bio.PDB.PSEA.to_one_letter_code
Bio.PDB.ResidueDepth'.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-118', 'to_one_letter_code', 'link-10');">to_one_letter_code</a></tt><tt class="py-op">[</tt><tt class="py-name">resname</tt><tt class="py-op">]</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-string">'X'</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-119', 's', 'link-54');">s</a></tt><tt class="py-op">=</tt><tt id="link-120" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-120', 's', 'link-54');">s</a></tt><tt class="py-op">+</tt><tt class="py-name">resname</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt id="link-121" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-121', 'seq', 'link-121');">seq</a></tt><tt class="py-op">=</tt><tt id="link-122" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-122', 'Seq', 'link-5');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-123', 's', 'link-54');">s</a></tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-124', 'ProteinAlphabet', 'link-3');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-125" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-125', 'seq', 'link-121');">seq</a></tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="Polypeptide.__repr__"></a><div id="Polypeptide.__repr__-def"><a name="L227"></a><tt class="py-lineno">227</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="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> Return <Polypeptide start=START end=END>, where START</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> and END are sequence identifiers of the outer residues.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt id="link-126" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-126', 'start', 'link-126');">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-127" 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-127', 'get_id', 'link-127');">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="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt id="link-128" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-128', 'end', 'link-128');">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-129" 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-129', 'get_id', 'link-127');">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="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt id="link-130" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-130', 's', 'link-54');">s</a></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-131" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-131', 'start', 'link-126');">start</a></tt><tt class="py-op">,</tt> <tt id="link-132" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-132', 'end', 'link-128');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-133" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-133', 's', 'link-54');">s</a></tt> </tt>
</div></div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder"></a><div id="_PPBuilder-def"><a name="L237"></a><tt class="py-lineno">237</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="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> Base class to extract polypeptides.</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> It checks if two consecutive residues in a chain </tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> are connected. The connectivity test is implemented by a </tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> subclass.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_PPBuilder.__init__"></a><div id="_PPBuilder.__init__-def"><a name="L244"></a><tt class="py-lineno">244</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="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> @param radius: distance</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> @type radius: float</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-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="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder._accept"></a><div id="_PPBuilder._accept-def"><a name="L251"></a><tt class="py-lineno">251</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-op">:</tt> </tt>
</div><div id="_PPBuilder._accept-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_PPBuilder._accept-expanded"><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-docstring">"Check if the residue is an amino acid."</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-134" 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-134', 'is_aa', 'link-134');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-comment"># not a standard AA so skip</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
<a name="_PPBuilder.build_peptides"></a><div id="_PPBuilder.build_peptides-def"><a name="L259"></a><tt class="py-lineno">259</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="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-docstring"> Build and return a list of Polypeptide objects.</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-docstring"> @param entity: polypeptides are searched for in this object</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"> @type entity: L{Structure}, L{Model} or L{Chain}</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</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="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> @type aa_only: int</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">is_connected</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" 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-135', '_is_connected', 'link-135');">_is_connected</a></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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-136" 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-136', '_accept', 'link-136');">_accept</a></tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</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-137" 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-137', 'get_level', 'link-137');">get_level</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-comment"># Decide wich entity we are dealing with</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-comment"></tt> <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="L274"></a><tt class="py-lineno">274</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="L275"></a><tt class="py-lineno">275</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-138" 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-138', 'get_list', 'link-138');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</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="L277"></a><tt class="py-lineno">277</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-139" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-139', 'get_list', 'link-138');">get_list</a></tt><tt class="py-op">(</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">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="L279"></a><tt class="py-lineno">279</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="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-140" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-140', 'PDBException', 'link-14');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Entity should be Structure, Model or Chain."</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</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="L283"></a><tt class="py-lineno">283</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="L284"></a><tt class="py-lineno">284</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="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt class="py-name">chain_it</tt><tt class="py-op">.</tt><tt id="link-141" 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.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-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.CDD.Iterator.next()=Bio.CDD.Iterator-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.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-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.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-141', 'next', 'link-141');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-142" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-142', 'next', 'link-141');">next</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">chain_it</tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">aa_only</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">accept</tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt id="link-143" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-143', 'next', 'link-141');">next</a></tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">is_connected</tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">,</tt> <tt id="link-144" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-144', 'next', 'link-141');">next</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-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="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">=</tt><tt id="link-145" 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-145', 'Polypeptide', 'link-145');">Polypeptide</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-146', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">pp_list</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-147', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">pp</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-148', 'append', 'link-75');">append</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-149', 'next', 'link-141');">next</a></tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</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="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt id="link-150" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-150', 'next', 'link-141');">next</a></tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">pp_list</tt> </tt>
</div></div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> </tt>
<a name="CaPPBuilder"></a><div id="CaPPBuilder-def"><a name="L303"></a><tt class="py-lineno">303</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="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> Use CA--CA distance to find polypeptides.</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="CaPPBuilder.__init__"></a><div id="CaPPBuilder.__init__-def"><a name="L307"></a><tt class="py-lineno">307</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>
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Martel.Generate.print_debug.__init__
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Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
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Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
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Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
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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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
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Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
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Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
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Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-155', 'next', 'link-141');">next</a></tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">prev</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment"># Unpack disordered</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-156" 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-156', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</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-157" 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-157', 'disordered_get_list', 'link-157');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">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="L321"></a><tt class="py-lineno">321</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-158" 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-158', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</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-159" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-159', 'disordered_get_list', 'link-157');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">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="L325"></a><tt class="py-lineno">325</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="L326"></a><tt class="py-lineno">326</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="L327"></a><tt class="py-lineno">327</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="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
<a name="PPBuilder"></a><div id="PPBuilder-def"><a name="L332"></a><tt class="py-lineno">332</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="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"> Use C--N distance to find polypeptides.</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PPBuilder.__init__"></a><div id="PPBuilder.__init__-def"><a name="L336"></a><tt class="py-lineno">336</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="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder" class="py-name" href="#" onclick="return doclink('link-160', '_PPBuilder', 'link-151');">_PPBuilder</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__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.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__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.NCBIWWW.BlastParser.__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.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__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.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__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.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__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.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__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.NCBIDictionary.__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.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__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.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.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__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.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.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__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.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__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.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__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.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.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__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.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__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.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__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__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-161', '__init__', 'link-152');">__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="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="PPBuilder._is_connected"></a><div id="PPBuilder._is_connected-def"><a name="L339"></a><tt class="py-lineno">339</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</tt><tt class="py-op">,</tt> <tt class="py-param">next</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="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">prev</tt><tt class="py-op">.</tt><tt id="link-162" 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-162', 'has_id', 'link-154');">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="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-163" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-163', 'next', 'link-141');">next</a></tt><tt class="py-op">.</tt><tt id="link-164" 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-164', 'has_id', 'link-154');">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="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</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-165" 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-165', '_test_dist', 'link-165');">_test_dist</a></tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">prev</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt id="link-166" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-166', 'next', 'link-141');">next</a></tt><tt class="py-op">[</tt><tt class="py-string">"N"</tt><tt class="py-op">]</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-comment"># Test all disordered atom positions!</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-167" 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-167', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</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">clist</tt><tt class="py-op">=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-168', 'disordered_get_list', 'link-157');">disordered_get_list</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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</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="L352"></a><tt class="py-lineno">352</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-169" 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-169', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</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-170" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_get_list" class="py-name" href="#" onclick="return doclink('link-170', 'disordered_get_list', 'link-157');">disordered_get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</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="L356"></a><tt class="py-lineno">356</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="L357"></a><tt class="py-lineno">357</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="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-comment"># To form a peptide bond, N and C must be </tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># within radius and have the same altloc</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># identifier or one altloc blanc</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-171" 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-171', 'get_altloc', 'link-171');">get_altloc</a></tt><tt class="py-op">(</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">c_altloc</tt><tt class="py-op">=</tt><tt class="py-name">cc</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.PDB.Atom.Atom.get_altloc" class="py-name" href="#" onclick="return doclink('link-172', 'get_altloc', 'link-171');">get_altloc</a></tt><tt class="py-op">(</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">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="L364"></a><tt class="py-lineno">364</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="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment"># Select the disordered atoms that</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># are indeed bonded</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-173" 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-173', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-174" 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-174', 'disordered_select', 'link-174');">disordered_select</a></tt><tt class="py-op">(</tt><tt class="py-name">c_altloc</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</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-175" 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-175', 'is_disordered', 'link-156');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select" class="py-name" href="#" onclick="return doclink('link-176', 'disordered_select', 'link-174');">disordered_select</a></tt><tt class="py-op">(</tt><tt class="py-name">n_altloc</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="PPBuilder._test_dist"></a><div id="PPBuilder._test_dist-def"><a name="L374"></a><tt class="py-lineno">374</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="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-docstring">"Return 1 if distance between atoms<radius"</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</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="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">else</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-number">0</tt> </tt>
</div></div><a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-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="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-177" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-177', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-178', 'PDB', 'link-12');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-179" 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-179', 'PDBParser', 'link-179');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-180" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-180', 'PDBParser', 'link-179');">PDBParser</a></tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-181" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-181', 'PDBParser', 'link-179');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-name">PERMISSIVE</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt id="link-182" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-182', 's', 'link-54');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-183" 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-183', 'get_structure', 'link-183');">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="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-184" 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-184', 'PPBuilder', 'link-184');">PPBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"C-N"</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</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-185" 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-185', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-186" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-186', 's', 'link-54');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</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-187" 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-187', 'get_sequence', 'link-187');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</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-188" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-188', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-189" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-189', 's', 'link-54');">s</a></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="L398"></a><tt class="py-lineno">398</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-190" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-190', 'get_sequence', 'link-187');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</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-191" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-191', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-192', 's', 'link-54');">s</a></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="L400"></a><tt class="py-lineno">400</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-193" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-193', 'get_sequence', 'link-187');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</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-194" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-194', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-195', 's', 'link-54');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</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-196" 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-196', 'get_phi_psi_list', 'link-196');">get_phi_psi_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</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="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-197" 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-197', 'CaPPBuilder', 'link-197');">CaPPBuilder</a></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>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"CA-CA"</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</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-198" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-198', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-199" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-199', 's', 'link-54');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</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-200" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-200', 'get_sequence', 'link-187');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</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-201" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-201', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-202" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-202', 's', 'link-54');">s</a></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="L412"></a><tt class="py-lineno">412</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-203" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-203', 'get_sequence', 'link-187');">get_sequence</a></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-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-204" class="py-name"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-204', 'build_peptides', 'link-185');">build_peptides</a></tt><tt class="py-op">(</tt><tt id="link-205" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-205', 's', 'link-54');">s</a></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="L414"></a><tt class="py-lineno">414</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-206" class="py-name"><a title="Bio.PDB.Polypeptide.Polypeptide.get_sequence" class="py-name" href="#" onclick="return doclink('link-206', 'get_sequence', 'link-187');">get_sequence</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> </tt><script type="text/javascript">
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