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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.SCOP-module.html">Package&nbsp;SCOP</a> ::
        Module&nbsp;Raf
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<h1 class="epydoc">Source Code for <a href="Bio.SCOP.Raf-module.html">Module Bio.SCOP.Raf</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 2001 by Gavin E. Crooks.  All rights reserved.</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-comment"># Gavin E. Crooks 2001-10-10</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">"""ASTRAL RAF (Rapid Access Format) Sequence Maps.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">The ASTRAL RAF Sequence Maps record the relationship between the PDB SEQRES</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">records (representing the sequence of the molecule used in an experiment) to </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">the ATOM records (representing the atoms experimentally observed). </tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">This data is derived from the Protein Data Bank CIF files. Known errors in the</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">CIF files are corrected manually, with the original PDB file serving as the</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">final arbiter in case of discrepancies. </tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">Residues are referenced by residue ID. This consists of a the PDB residue</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">sequence number (upto 4 digits) and an optional PDB  insertion code (an</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">ascii alphabetic character, a-z, A-Z). e.g. "1", "10A", "1010b", "-1"</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">See "ASTRAL RAF Sequence Maps":http://astral.stanford.edu/raf.html</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">to_one_letter_code -- A mapping from the 3-letter amino acid codes found</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring">                        in PDB files to 1-letter codes.  The 3-letter codes</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">                        include chemically modified residues.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-1', 'copy', 'link-0');">copy</a></tt>  </tt>
<a name="L30"></a><tt class="py-lineno"> 30</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-op">*</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Class Bio.SCOP.Residues'.Residues=Bio.SCOP.Residues%27.Residues-class.html"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-2', 'Residues', 'link-2');">Residues</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-3', 'Residues', 'link-2');">Residues</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 class="py-comment"># This table is taken from the RAF release notes, and includes the</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># undocumented mapping "UNK" -&gt; "X"</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-4" 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-4', 'to_one_letter_code', 'link-4');">to_one_letter_code</a></tt><tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-string">'ALA'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'VAL'</tt><tt class="py-op">:</tt><tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'PHE'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'PRO'</tt><tt class="py-op">:</tt><tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'MET'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-string">'ILE'</tt><tt class="py-op">:</tt><tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'LEU'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASP'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GLU'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'LYS'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-string">'ARG'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'SER'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'THR'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'TYR'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'HIS'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-string">'CYS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASN'</tt><tt class="py-op">:</tt><tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'GLN'</tt><tt class="py-op">:</tt><tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'TRP'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'GLY'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-string">'2AS'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'3AH'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'5HP'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACL'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'AIB'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-string">'ALM'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'ALO'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ALY'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'ARM'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASA'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">    <tt class="py-string">'ASB'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASK'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASL'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASQ'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'AYA'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-string">'BCS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'BHD'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'BMT'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'BNN'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'BUC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">    <tt class="py-string">'BUG'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'C5C'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'C6C'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CEA'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">    <tt class="py-string">'CHG'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'CLE'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CME'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CSD'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'CSO'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt class="py-string">'CSP'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CSS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CSW'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CXM'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'CY1'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-string">'CY3'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CYG'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CYM'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'CYQ'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'DAH'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-string">'DAL'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'DAR'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'DAS'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'DCY'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'DGL'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-string">'DGN'</tt><tt class="py-op">:</tt><tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'DHA'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'DHI'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'DIL'</tt><tt class="py-op">:</tt><tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'DIV'</tt><tt class="py-op">:</tt><tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-string">'DLE'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'DLY'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'DNP'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'DPN'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'DPR'</tt><tt class="py-op">:</tt><tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">    <tt class="py-string">'DSN'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'DSP'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'DTH'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'DTR'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'DTY'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-string">'DVA'</tt><tt class="py-op">:</tt><tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'EFC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'FLA'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'FME'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGL'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt class="py-string">'GLZ'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GMA'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GSC'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'HAC'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'HAR'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-string">'HIC'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'HIP'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'HMR'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'HPQ'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'HTR'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-string">'HYP'</tt><tt class="py-op">:</tt><tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'IIL'</tt><tt class="py-op">:</tt><tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'IYR'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'KCX'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'LLP'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-string">'LLY'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'LTR'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'LYM'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'LYZ'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'MAA'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt class="py-string">'MEN'</tt><tt class="py-op">:</tt><tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'MHS'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'MIS'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'MLE'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'MPQ'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-string">'MSA'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'MSE'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'MVA'</tt><tt class="py-op">:</tt><tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'NEM'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'NEP'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-string">'NLE'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'NLN'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'NLP'</tt><tt class="py-op">:</tt><tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'NMC'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'OAS'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-string">'OCS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'OMT'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'PAQ'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'PCA'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'PEC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-string">'PHI'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'PHL'</tt><tt class="py-op">:</tt><tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'PR3'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'PRR'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'PTR'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-string">'SAC'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'SAR'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'SCH'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'SCS'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'SCY'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt class="py-string">'SEL'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'SEP'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'SET'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'SHC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'SHR'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-string">'SOC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'STY'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'SVA'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TIH'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'TPL'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-string">'TPO'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'TPQ'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'TRG'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'TRO'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TYB'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">    <tt class="py-string">'TYQ'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TYS'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TYY'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGM'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GL3'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-string">'SMC'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'ASX'</tt><tt class="py-op">:</tt><tt class="py-string">'B'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGU'</tt><tt class="py-op">:</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'CSX'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'GLX'</tt><tt class="py-op">:</tt><tt class="py-string">'Z'</tt><tt class="py-op">,</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-string">'UNK'</tt><tt class="py-op">:</tt><tt class="py-string">'X'</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-op">}</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="normalize_letters"></a><div id="normalize_letters-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="normalize_letters-toggle" onclick="return toggle('normalize_letters');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf-module.html#normalize_letters">normalize_letters</a><tt class="py-op">(</tt><tt class="py-param">one_letter_code</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="normalize_letters-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="normalize_letters-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt class="py-docstring">"""Convert RAF one-letter amino acid codes into IUPAC standard codes.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    Letters are uppercased, and "." ("Unknown") is converted to "X".</tt> </tt>
<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-keyword">if</tt> <tt class="py-name">one_letter_code</tt> <tt class="py-op">==</tt> <tt class="py-string">'.'</tt> <tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">'X'</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">one_letter_code</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="SeqMapIndex"></a><div id="SeqMapIndex-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="SeqMapIndex-toggle" onclick="return toggle('SeqMapIndex');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMapIndex-class.html">SeqMapIndex</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SeqMapIndex-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SeqMapIndex-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt class="py-docstring">"""An RAF file index.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-docstring">    The RAF file itself is about 50 MB. This index provides rapid, random</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-docstring">    access of RAF records without having to load the entire file into memory.</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 class="py-docstring">    The index key is a concatenation of the  PDB ID and chain ID. e.g</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring">    "2drcA", "155c_". RAF uses an underscore to indicate blank</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring">    chain IDs.    </tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"> </tt>
<a name="SeqMapIndex.__init__"></a><div id="SeqMapIndex.__init__-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="SeqMapIndex.__init__-toggle" onclick="return toggle('SeqMapIndex.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMapIndex-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">filename</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMapIndex.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMapIndex.__init__-expanded"><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">        Arguments:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">          filename  -- The file to index</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
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Bio.SCOP.Dom.Iterator.__init__
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Bio.SCOP.Domain.__init__
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Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
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Bio.SCOP.Raf.Iterator.__init__
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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__
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Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
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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__
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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__
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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__
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Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
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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__
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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-5', '__init__', 'link-5');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-6', 'open', 'link-6');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-name">position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt id="link-7" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-7', 'True', 'link-7');">True</a></tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-8', 'readline', 'link-8');">readline</a></tt><tt class="py-op">(</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                <tt id="link-9" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-9', 'key', 'link-9');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-10" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-10', 'key', 'link-9');">key</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-11" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-11', 'key', 'link-9');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">position</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">                <tt class="py-name">position</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-12', 'tell', 'link-12');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">        <tt class="py-keyword">finally</tt> <tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-13', 'close', 'link-13');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"> </tt>
<a name="SeqMapIndex.__getitem__"></a><div id="SeqMapIndex.__getitem__-def"><a name="L116"></a><tt class="py-lineno">116</tt> <a class="py-toggle" href="#" id="SeqMapIndex.__getitem__-toggle" onclick="return toggle('SeqMapIndex.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMapIndex-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMapIndex.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMapIndex.__getitem__-expanded"><a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-docstring">""" Return an item from the indexed file. """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-name">position</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Align.AlignInfo.PSSM.__getitem__()=Bio.Align.AlignInfo.PSSM-class.html#__getitem__,Method Bio.Crystal.Chain.__getitem__()=Bio.Crystal.Chain-class.html#__getitem__,Method Bio.Crystal.Crystal.__getitem__()=Bio.Crystal.Crystal-class.html#__getitem__,Method Bio.DBXRef.BioformatDBName.__getitem__()=Bio.DBXRef.BioformatDBName-class.html#__getitem__,Method Bio.DBXRef.UnknownDBName.__getitem__()=Bio.DBXRef.UnknownDBName-class.html#__getitem__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__getitem__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__getitem__,Method Bio.EUtils.Datatypes.DBIds.__getitem__()=Bio.EUtils.Datatypes.DBIds-class.html#__getitem__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__getitem__,Method Bio.EUtils.MultiDict._BaseMultiDict.__getitem__()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#__getitem__,Method Bio.EUtils.POM.ElementNode.__getitem__()=Bio.EUtils.POM.ElementNode-class.html#__getitem__,Method Bio.FSSP.fssp_rec.fff_rec.__getitem__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__getitem__,Method Bio.GFF.GenericTools.ForgivingDictionary.__getitem__()=Bio.GFF.GenericTools.ForgivingDictionary-class.html#__getitem__,Method Bio.GFF.easy.FeatureDict.__getitem__()=Bio.GFF.easy.FeatureDict-class.html#__getitem__,Method Bio.GenBank.NCBIDictionary.__getitem__()=Bio.GenBank.NCBIDictionary-class.html#__getitem__,Method Bio.Gobase.Dictionary.__getitem__()=Bio.Gobase.Dictionary-class.html#__getitem__,Method Bio.Mindy.BaseDB.DictLookup.__getitem__()=Bio.Mindy.BaseDB.DictLookup-class.html#__getitem__,Method Bio.Mindy.BaseDB.OpenDB.__getitem__()=Bio.Mindy.BaseDB.OpenDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.BisectFile.__getitem__()=Bio.Mindy.FlatDB.BisectFile-class.html#__getitem__,Method Bio.Mindy.FlatDB.DiskFlatDB.__getitem__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryTable.__getitem__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryTable.__getitem__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__getitem__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__getitem__,Method Bio.PDB.Chain.Chain.__getitem__()=Bio.PDB.Chain.Chain-class.html#__getitem__,Method Bio.PDB.Entity.Entity.__getitem__()=Bio.PDB.Entity.Entity-class.html#__getitem__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__getitem__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__getitem__,Method Bio.PDB.Vector'.Vector.__getitem__()=Bio.PDB.Vector%27.Vector-class.html#__getitem__,Method Bio.PropertyManager.CreateDict.__getitem__()=Bio.PropertyManager.CreateDict-class.html#__getitem__,Method Bio.Prosite.Dictionary.__getitem__()=Bio.Prosite.Dictionary-class.html#__getitem__,Method Bio.Prosite.ExPASyDictionary.__getitem__()=Bio.Prosite.ExPASyDictionary-class.html#__getitem__,Method Bio.Prosite.Pattern.Prosite.__getitem__()=Bio.Prosite.Pattern.Prosite-class.html#__getitem__,Method Bio.Prosite.Pattern.PrositeMatch.__getitem__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__getitem__,Method Bio.Prosite.Prodoc.Dictionary.__getitem__()=Bio.Prosite.Prodoc.Dictionary-class.html#__getitem__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__getitem__,Method Bio.PubMed.Dictionary.__getitem__()=Bio.PubMed.Dictionary-class.html#__getitem__,Method Bio.Rebase.Dictionary.__getitem__()=Bio.Rebase.Dictionary-class.html#__getitem__,Method Bio.Restriction.Restriction.FormattedSeq.__getitem__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__getitem__,Method Bio.SCOP.Cla.Index.__getitem__()=Bio.SCOP.Cla.Index-class.html#__getitem__,Method Bio.SCOP.FileIndex.FileIndex.__getitem__()=Bio.SCOP.FileIndex.FileIndex-class.html#__getitem__,Method Bio.SCOP.FileIndex.defaultdict.__getitem__()=Bio.SCOP.FileIndex.defaultdict-class.html#__getitem__,Method Bio.SCOP.Raf.SeqMapIndex.__getitem__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__getitem__,Method Bio.Seq.MutableSeq.__getitem__()=Bio.Seq.MutableSeq-class.html#__getitem__,Method Bio.Seq.Seq.__getitem__()=Bio.Seq.Seq-class.html#__getitem__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__getitem__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__getitem__,Method Bio.SwissProt.SProt.Dictionary.__getitem__()=Bio.SwissProt.SProt.Dictionary-class.html#__getitem__,Method Bio.SwissProt.SProt.ExPASyDictionary.__getitem__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__getitem__,Method Bio.config.DBRegistry.DBGroup.__getitem__()=Bio.config.DBRegistry.DBGroup-class.html#__getitem__,Method Bio.config.DBRegistry.DBObject.__getitem__()=Bio.config.DBRegistry.DBObject-class.html#__getitem__,Method Bio.config.Registry.Registry.__getitem__()=Bio.config.Registry.Registry-class.html#__getitem__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__getitem__,Method BioSQL.BioSeq.DBSeq.__getitem__()=BioSQL.BioSeq.DBSeq-class.html#__getitem__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__getitem__,Method BioSQL.BioSeqDatabase.DBServer.__getitem__()=BioSQL.BioSeqDatabase.DBServer-class.html#__getitem__,Method Martel.Iterator.Iterate.__getitem__()=Martel.Iterator.Iterate-class.html#__getitem__,Method Martel.Parser.MartelAttributeList.__getitem__()=Martel.Parser.MartelAttributeList-class.html#__getitem__,Method Martel.msre_parse.SubPattern.__getitem__()=Martel.msre_parse.SubPattern-class.html#__getitem__,Method Martel.test.support.Storage.__getitem__()=Martel.test.support.Storage-class.html#__getitem__"><a title="Bio.Align.AlignInfo.PSSM.__getitem__
Bio.Crystal.Chain.__getitem__
Bio.Crystal.Crystal.__getitem__
Bio.DBXRef.BioformatDBName.__getitem__
Bio.DBXRef.UnknownDBName.__getitem__
Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__
Bio.EUtils.Datatypes.DBIds.__getitem__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__
Bio.EUtils.MultiDict._BaseMultiDict.__getitem__
Bio.EUtils.POM.ElementNode.__getitem__
Bio.FSSP.fssp_rec.fff_rec.__getitem__
Bio.GFF.GenericTools.ForgivingDictionary.__getitem__
Bio.GFF.easy.FeatureDict.__getitem__
Bio.GenBank.NCBIDictionary.__getitem__
Bio.Gobase.Dictionary.__getitem__
Bio.Mindy.BaseDB.DictLookup.__getitem__
Bio.Mindy.BaseDB.OpenDB.__getitem__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__
Bio.Mindy.FlatDB.BisectFile.__getitem__
Bio.Mindy.FlatDB.DiskFlatDB.__getitem__
Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__
Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__
Bio.Mindy.FlatDB.PrimaryTable.__getitem__
Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__
Bio.Mindy.FlatDB.SecondaryTable.__getitem__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__
Bio.PDB.Chain.Chain.__getitem__
Bio.PDB.Entity.Entity.__getitem__
Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__
Bio.PDB.Vector'.Vector.__getitem__
Bio.PropertyManager.CreateDict.__getitem__
Bio.Prosite.Dictionary.__getitem__
Bio.Prosite.ExPASyDictionary.__getitem__
Bio.Prosite.Pattern.Prosite.__getitem__
Bio.Prosite.Pattern.PrositeMatch.__getitem__
Bio.Prosite.Prodoc.Dictionary.__getitem__
Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__
Bio.PubMed.Dictionary.__getitem__
Bio.Rebase.Dictionary.__getitem__
Bio.Restriction.Restriction.FormattedSeq.__getitem__
Bio.SCOP.Cla.Index.__getitem__
Bio.SCOP.FileIndex.FileIndex.__getitem__
Bio.SCOP.FileIndex.defaultdict.__getitem__
Bio.SCOP.Raf.SeqMapIndex.__getitem__
Bio.Seq.MutableSeq.__getitem__
Bio.Seq.Seq.__getitem__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__
Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__
Bio.SwissProt.SProt.Dictionary.__getitem__
Bio.SwissProt.SProt.ExPASyDictionary.__getitem__
Bio.config.DBRegistry.DBGroup.__getitem__
Bio.config.DBRegistry.DBObject.__getitem__
Bio.config.Registry.Registry.__getitem__
Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__
BioSQL.BioSeq.DBSeq.__getitem__
BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__
BioSQL.BioSeqDatabase.DBServer.__getitem__
Martel.Iterator.Iterate.__getitem__
Martel.Parser.MartelAttributeList.__getitem__
Martel.msre_parse.SubPattern.__getitem__
Martel.test.support.Storage.__getitem__" class="py-name" href="#" onclick="return doclink('link-14', '__getitem__', 'link-14');">__getitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt id="link-15" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-15', 'key', 'link-9');">key</a></tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-16', 'open', 'link-6');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</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">try</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">f</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-17', 'seek', 'link-17');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">position</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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-18', 'readline', 'link-8');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">            <tt id="link-19" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-19', 'record', 'link-19');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name" targets="Class Bio.SCOP.Raf.SeqMap=Bio.SCOP.Raf.SeqMap-class.html"><a title="Bio.SCOP.Raf.SeqMap" class="py-name" href="#" onclick="return doclink('link-20', 'SeqMap', 'link-20');">SeqMap</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">            <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-21', 'close', 'link-13');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-22" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-22', 'record', 'link-19');">record</a></tt> </tt>
</div><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"> </tt>
<a name="SeqMapIndex.getSeqMap"></a><div id="SeqMapIndex.getSeqMap-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="SeqMapIndex.getSeqMap-toggle" onclick="return toggle('SeqMapIndex.getSeqMap');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMapIndex-class.html#getSeqMap">getSeqMap</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">residues</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMapIndex.getSeqMap-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMapIndex.getSeqMap-expanded"><a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt class="py-docstring">"""Get the sequence map for a collection of residues.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring">        residues -- A Residues instance, or a string that can be converted into</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">                    a Residues instance.</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-23" 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-23', 'type', 'link-23');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">residues</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="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">            <tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-24', 'Residues', 'link-2');">Residues</a></tt><tt class="py-op">(</tt><tt class="py-name">residues</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-name">pdbid</tt>  <tt class="py-op">=</tt> <tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-name">frags</tt> <tt class="py-op">=</tt> <tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">fragments</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">frags</tt><tt class="py-op">:</tt> <tt class="py-name">frags</tt> <tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">'_'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-comment"># All residues of unnamed chain</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-name">seqMap</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">for</tt> <tt class="py-name">frag</tt> <tt class="py-keyword">in</tt> <tt class="py-name">frags</tt> <tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">            <tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-name">frag</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">chainid</tt><tt class="py-op">==</tt><tt class="py-string">''</tt> <tt class="py-keyword">or</tt> <tt class="py-name">chainid</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">chainid</tt><tt class="py-op">==</tt><tt class="py-string">' '</tt> <tt class="py-keyword">or</tt> <tt class="py-name">chainid</tt><tt class="py-op">==</tt><tt class="py-string">'_'</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">chainid</tt> <tt class="py-op">=</tt> <tt class="py-string">'_'</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">            <tt id="link-25" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-25', 'id', 'link-25');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">pdbid</tt> <tt class="py-op">+</tt> <tt class="py-name">chainid</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">             </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">             </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">            <tt class="py-name">sm</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-26', 'id', 'link-25');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">             </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">            <tt class="py-comment">#Cut out fragment of interest</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-27" 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-27', 'start', 'link-27');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">            <tt id="link-28" 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-28', 'end', 'link-28');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sm</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">frag</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-29" 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-29', 'start', 'link-27');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">sm</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'index', 'link-30');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">frag</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">chainid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">frag</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-31" 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-31', 'end', 'link-28');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">sm</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><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-32', 'index', 'link-30');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">frag</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">chainid</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="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">             </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt class="py-name">sm</tt> <tt class="py-op">=</tt> <tt class="py-name">sm</tt><tt class="py-op">[</tt><tt id="link-33" 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-33', 'start', 'link-27');">start</a></tt><tt class="py-op">:</tt><tt id="link-34" 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-34', 'end', 'link-28');">end</a></tt><tt class="py-op">]</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">seqMap</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">                <tt class="py-name">seqMap</tt> <tt class="py-op">=</tt> <tt class="py-name">sm</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">                <tt class="py-name">seqMap</tt> <tt class="py-op">+=</tt> <tt class="py-name">sm</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">                             </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">seqMap</tt> </tt>
</div></div><a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"> </tt>
<a name="SeqMap"></a><div id="SeqMap-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="SeqMap-toggle" onclick="return toggle('SeqMap');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html">SeqMap</a> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SeqMap-expanded"><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt class="py-docstring">"""An ASTRAL RAF (Rapid Access Format) Sequence Map.</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-docstring">    This is a list like object; You can find the location of particular residues</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">    with index(), slice this SeqMap into fragments, and glue fragments back</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring">    together with extend().</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">    pdbid -- The PDB 4 character ID</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring">    pdb_datestamp -- From the PDB file</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-docstring">    version -- The RAF format version. e.g. 0.01</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-docstring">    flags -- RAF flags. (See release notes for more information.)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">    res -- A list of Res objects, one for each residue in this sequence map</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.__init__"></a><div id="SeqMap.__init__-def"><a name="L188"></a><tt class="py-lineno">188</tt> <a class="py-toggle" href="#" id="SeqMap.__init__-toggle" onclick="return toggle('SeqMap.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-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">line</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.__init__-expanded"><a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_datestamp</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-35', 'version', 'link-35');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.SCOP.Cla.Record._process()=Bio.SCOP.Cla.Record-class.html#_process,Method Bio.SCOP.Des.Record._process()=Bio.SCOP.Des.Record-class.html#_process,Method Bio.SCOP.Dom.Record._process()=Bio.SCOP.Dom.Record-class.html#_process,Method Bio.SCOP.Hie.Record._process()=Bio.SCOP.Hie.Record-class.html#_process,Method Bio.SCOP.Raf.SeqMap._process()=Bio.SCOP.Raf.SeqMap-class.html#_process"><a title="Bio.SCOP.Cla.Record._process
Bio.SCOP.Des.Record._process
Bio.SCOP.Dom.Record._process
Bio.SCOP.Hie.Record._process
Bio.SCOP.Raf.SeqMap._process" class="py-name" href="#" onclick="return doclink('link-36', '_process', 'link-36');">_process</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">         </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"> </tt>
<a name="SeqMap._process"></a><div id="SeqMap._process-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="SeqMap._process-toggle" onclick="return toggle('SeqMap._process');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#_process">_process</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SeqMap._process-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap._process-expanded"><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-docstring">"""Parses a RAF record into a SeqMap object.</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-name">header_len</tt> <tt class="py-op">=</tt> <tt class="py-number">38</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">  </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>  <tt class="py-comment"># no trailing whitespace        </tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">&lt;</tt><tt class="py-name">header_len</tt><tt class="py-op">:</tt>  </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Incomplete header: "</tt><tt class="py-op">+</tt><tt class="py-name">line</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line"> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">         </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-37', 'version', 'link-35');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-number">10</tt><tt class="py-op">]</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">        <tt class="py-comment">#Raf format versions 0.01 and 0.02 are identical for practical purposes</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-38', 'version', 'link-35');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"0.01"</tt> <tt class="py-keyword">and</tt>  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-39', 'version', 'link-35');">version</a></tt> <tt class="py-op">!=</tt><tt class="py-string">"0.02"</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Incompatible RAF version: "</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-40', 'version', 'link-35');">version</a></tt>  </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_datestamp</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">14</tt><tt class="py-op">:</tt><tt class="py-number">20</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">self</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">21</tt><tt class="py-op">:</tt><tt class="py-number">27</tt><tt class="py-op">]</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-41" 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-41', 'i', 'link-41');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">header_len</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">7</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">            <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-41');">i</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-41');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Corrupt Field: ("</tt><tt class="py-op">+</tt><tt class="py-name">f</tt><tt class="py-op">+</tt><tt class="py-string">")"</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">            <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name" targets="Class Bio.SCOP.Raf.Res=Bio.SCOP.Raf.Res-class.html"><a title="Bio.SCOP.Raf.Res" class="py-name" href="#" onclick="return doclink('link-44', 'Res', 'link-44');">Res</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">            <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-name">chainid</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">            <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">resid</tt> <tt class="py-op">=</tt>  <tt class="py-name">f</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-45', 'strip', 'link-45');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">            <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name" targets="Function Bio.SCOP.Raf.normalize_letters()=Bio.SCOP.Raf-module.html#normalize_letters"><a title="Bio.SCOP.Raf.normalize_letters" class="py-name" href="#" onclick="return doclink('link-46', 'normalize_letters', 'link-46');">normalize_letters</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">            <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">seqres</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Bio.SCOP.Raf.normalize_letters" class="py-name" href="#" onclick="return doclink('link-47', 'normalize_letters', 'link-46');">normalize_letters</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-48" 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-48', 'append', 'link-48');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">)</tt> </tt>
</div><a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.index"></a><div id="SeqMap.index-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="SeqMap.index-toggle" onclick="return toggle('SeqMap.index');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#index">index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">resid</tt><tt class="py-op">,</tt> <tt class="py-param">chainid</tt><tt class="py-op">=</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.index-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.index-expanded"><a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-keyword">for</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-41');">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">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-41');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">resid</tt> <tt class="py-op">==</tt> <tt class="py-name">resid</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-51', 'i', 'link-41');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">chainid</tt> <tt class="py-op">==</tt> <tt class="py-name">chainid</tt> <tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-41');">i</a></tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-string">"No such residue "</tt><tt class="py-op">+</tt><tt class="py-name">chainid</tt><tt class="py-op">+</tt><tt class="py-name">resid</tt> </tt>
</div><a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.__getslice__"></a><div id="SeqMap.__getslice__-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="SeqMap.__getslice__-toggle" onclick="return toggle('SeqMap.__getslice__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#__getslice__">__getslice__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">j</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.__getslice__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.__getslice__-expanded"><a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">        <tt id="link-53" 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-53', 's', 'link-53');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-54', 'copy', 'link-0');">copy</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">        <tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-53');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-56', 's', 'link-53');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">[</tt><tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-57', 'i', 'link-41');">i</a></tt><tt class="py-op">:</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">        <tt class="py-keyword">return</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-53');">s</a></tt> </tt>
</div><a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.append"></a><div id="SeqMap.append-def"><a name="L244"></a><tt class="py-lineno">244</tt> <a class="py-toggle" href="#" id="SeqMap.append-toggle" onclick="return toggle('SeqMap.append');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">res</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.append-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.append-expanded"><a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">        <tt class="py-docstring">"""Append another Res object onto the list of residue mappings."""</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'append', 'link-48');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">)</tt> </tt>
</div><a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.extend"></a><div id="SeqMap.extend-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="SeqMap.extend-toggle" onclick="return toggle('SeqMap.extend');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#extend">extend</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.extend-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.extend-expanded"><a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-docstring">"""Append another SeqMap onto the end of self.</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"><tt class="py-docstring">        Both SeqMaps must have the same PDB ID, PDB datestamp and</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-docstring">        RAF version.  The RAF flags are erased if they are inconsistent. This</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-docstring">        may happen when fragments are taken from different chains.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="Bio.SCOP.Raf.SeqMap" class="py-name" href="#" onclick="return doclink('link-60', 'SeqMap', 'link-20');">SeqMap</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Can only extend a SeqMap with a SeqMap."</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">!=</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Cannot add fragments from different proteins"</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-61', 'version', 'link-35');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-62', 'version', 'link-35');">version</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Incompatible rafs"</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_datestamp</tt> <tt class="py-op">!=</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">pdb_datestamp</tt> <tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Different pdb dates!"</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">!=</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">+=</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.__iadd__"></a><div id="SeqMap.__iadd__-def"><a name="L267"></a><tt class="py-lineno">267</tt> <a class="py-toggle" href="#" id="SeqMap.__iadd__-toggle" onclick="return toggle('SeqMap.__iadd__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#__iadd__">__iadd__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.__iadd__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.__iadd__-expanded"><a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-63', 'extend', 'link-63');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.__add__"></a><div id="SeqMap.__add__-def"><a name="L271"></a><tt class="py-lineno">271</tt> <a class="py-toggle" href="#" id="SeqMap.__add__-toggle" onclick="return toggle('SeqMap.__add__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#__add__">__add__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.__add__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.__add__-expanded"><a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt id="link-64" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-64', 's', 'link-53');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-65', 'copy', 'link-0');">copy</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">        <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-53');">s</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-67', 'extend', 'link-63');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-53');">s</a></tt> </tt>
</div><a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"> </tt>
<a name="SeqMap.getAtoms"></a><div id="SeqMap.getAtoms-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="SeqMap.getAtoms-toggle" onclick="return toggle('SeqMap.getAtoms');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.SeqMap-class.html#getAtoms">getAtoms</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">pdb_handle</tt><tt class="py-op">,</tt> <tt class="py-param">out_handle</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="SeqMap.getAtoms-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqMap.getAtoms-expanded"><a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">        <tt class="py-docstring">"""Extract all relevant ATOM and HETATOM records from a PDB file.</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-docstring">        The PDB file is scanned for ATOM and HETATOM records. If the</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-docstring">        chain ID, residue ID (seqNum and iCode), and residue type match</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-docstring">        a residue in this sequence map, then the record is echoed to the</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"><tt class="py-docstring">        output handle.</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-docstring">        This is typically used to find the coordinates of a domain, or other</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-docstring">        residue subset.</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"><tt class="py-docstring">        pdb_handle -- A handle to the relevant PDB file.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-docstring">        out_handle -- All output is written to this file like object.</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">        <tt class="py-comment">#This code should be refactored when (if?) biopython gets a PDB parser </tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">        <tt class="py-comment">#The set of residues that I have to find records for. </tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">resSet</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt><tt class="py-op">==</tt><tt class="py-string">'X'</tt> <tt class="py-op">:</tt> <tt class="py-comment">#Unknown residue type</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">            <tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">chainid</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">chainid</tt> <tt class="py-op">==</tt> <tt class="py-string">'_'</tt><tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">                <tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">            <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">resid</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">            <tt class="py-name">resSet</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">chainid</tt><tt class="py-op">,</tt><tt class="py-name">resid</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">        <tt class="py-name">resFound</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pdb_handle</tt><tt class="py-op">.</tt><tt class="py-name">xreadlines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"ATOM  "</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"HETATM"</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">                <tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">21</tt><tt class="py-op">:</tt><tt class="py-number">22</tt><tt class="py-op">]</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">                <tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">22</tt><tt class="py-op">:</tt><tt class="py-number">27</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-69', 'strip', 'link-45');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">                <tt id="link-70" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-70', 'key', 'link-9');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">chainid</tt><tt class="py-op">,</tt> <tt class="py-name">resid</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">resSet</tt><tt class="py-op">.</tt><tt id="link-71" 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-71', 'has_key', 'link-71');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-72', 'key', 'link-9');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">                    <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">resSet</tt><tt class="py-op">[</tt><tt id="link-73" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-73', 'key', 'link-9');">key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">                    <tt class="py-name">atom_aa</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">                    <tt class="py-name">resName</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">17</tt><tt class="py-op">:</tt><tt class="py-number">20</tt><tt class="py-op">]</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt id="link-74" 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-74', 'to_one_letter_code', 'link-4');">to_one_letter_code</a></tt><tt class="py-op">.</tt><tt id="link-75" 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-75', 'has_key', 'link-71');">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="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt id="link-76" 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-76', 'to_one_letter_code', 'link-4');">to_one_letter_code</a></tt><tt class="py-op">[</tt><tt class="py-name">resName</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">atom_aa</tt> <tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">                            <tt class="py-name">out_handle</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-77', 'write', 'link-77');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">                            <tt class="py-name">resFound</tt><tt class="py-op">[</tt><tt id="link-78" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-78', 'key', 'link-9');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">resSet</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">resFound</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">            <tt class="py-comment">#for k in resFound.keys():</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#    del resSet[k]</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#print resSet</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-comment"></tt>                                      </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">'I could not find at least one ATOM or '</tt> \ </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">               <tt class="py-op">+</tt><tt class="py-string">'HETATM record for each and every residue in this sequence map.'</tt> </tt>
</div></div><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">         </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">         </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">         </tt>
<a name="Res"></a><div id="Res-def"><a name="L329"></a><tt class="py-lineno">329</tt> <a class="py-toggle" href="#" id="Res-toggle" onclick="return toggle('Res');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Res-class.html">Res</a> <tt class="py-op">:</tt> </tt>
</div><div id="Res-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Res-expanded"><a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">    <tt class="py-docstring">""" A single residue mapping from a RAF record.</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"><tt class="py-docstring">    chainid -- A single character chain ID.</tt> </tt>
<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">    resid   -- The residue ID. </tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line"><tt class="py-docstring">    atom    -- amino acid one-letter code from ATOM records. </tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line"><tt class="py-docstring">    seqres  -- amino acid one-letter code from SEQRES records.</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Res.__init__"></a><div id="Res.__init__-def"><a name="L340"></a><tt class="py-lineno">340</tt> <a class="py-toggle" href="#" id="Res.__init__-toggle" onclick="return toggle('Res.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Res-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Res.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Res.__init__-expanded"><a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chainid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">resid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqres</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div></div><a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line"> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L347"></a><tt class="py-lineno">347</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">    <tt class="py-docstring">"""Iterates over a RAF file, returning a SeqMap object for each line</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"><tt class="py-docstring">    in the file.</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-docstring">    Arguments:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line"><tt class="py-docstring">        handle -- file-like object.</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt>  </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-79" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-79', 'handle', 'link-79');">handle</a></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">yield</tt> <tt id="link-80" class="py-name"><a title="Bio.SCOP.Raf.SeqMap" class="py-name" href="#" onclick="return doclink('link-80', 'SeqMap', 'link-20');">SeqMap</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line"> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">     </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">    <tt class="py-docstring">"""Iterates over a RAF file.</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L362"></a><tt class="py-lineno">362</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Iterator-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">handle</tt><tt class="py-op">,</tt> <tt class="py-param">parser</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">        <tt class="py-docstring">"""Create an object that iterates over a RAF file.</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line"><tt class="py-docstring">        handle -- file-like object.</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line"><tt class="py-docstring">        parser -- an optional Parser object to change the results into</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line"><tt class="py-docstring">                  another form.  If set to None, then the raw contents</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line"><tt class="py-docstring">                  of the file will be returned.</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line"><tt class="py-docstring">                  </tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">        <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.SCOP.Raf.Iterator is deprecated. Please use Bio.SCOP.Raf.parse() instead."</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line"> </tt>
<a name="L375"></a><tt class="py-lineno">375</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">FileType</tt><tt class="py-op">,</tt> <tt class="py-name">InstanceType</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-81" class="py-name"><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-81', 'type', 'link-23');">type</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-82', 'handle', 'link-79');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">FileType</tt> <tt class="py-keyword">and</tt> <tt id="link-83" class="py-name"><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-83', 'type', 'link-23');">type</a></tt><tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-84', 'handle', 'link-79');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">InstanceType</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">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"I expected a file handle or file-like object"</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-85', 'handle', 'link-79');">handle</a></tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L381"></a><tt class="py-lineno">381</tt> <a class="py-toggle" href="#" id="Iterator.next-toggle" onclick="return toggle('Iterator.next');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Iterator-class.html#next">next</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="Iterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.next-expanded"><a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">        <tt class="py-docstring">"""Retrieve the next record."""</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-86', 'readline', 'link-8');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">line</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">'#'</tt><tt class="py-op">:</tt>  <tt class="py-keyword">break</tt>  <tt class="py-comment"># Not a comment line</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt>     </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-87', 'parse', 'link-87');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">     </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L391"></a><tt class="py-lineno">391</tt> <a class="py-toggle" href="#" id="Iterator.__iter__-toggle" onclick="return toggle('Iterator.__iter__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Iterator-class.html#__iter__">__iter__</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="Iterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__iter__-expanded"><a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" 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
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Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-88', 'next', 'link-88');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><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>
<a name="Parser"></a><div id="Parser-def"><a name="L395"></a><tt class="py-lineno">395</tt> <a class="py-toggle" href="#" id="Parser-toggle" onclick="return toggle('Parser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Parser-class.html">Parser</a><tt class="py-op">:</tt> </tt>
</div><div id="Parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Parser-expanded"><a name="Parser.__init__"></a><div id="Parser.__init__-def"><a name="L396"></a><tt class="py-lineno">396</tt> <a class="py-toggle" href="#" id="Parser.__init__-toggle" onclick="return toggle('Parser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Parser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.__init__-expanded"><a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">        <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"""Bio.SCOP.Raf.Parser is deprecated.</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line"><tt class="py-string">        Instead of</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"><tt class="py-string">        parser = Raf.Parser()</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"><tt class="py-string">        record = parser.parse(entry)</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-string">        please use</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line"><tt class="py-string">        record = Raf.SeqMap(entry)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"><tt class="py-string">        """</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
</div><a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line"> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line"> </tt>
<a name="Parser.parse"></a><div id="Parser.parse-def"><a name="L410"></a><tt class="py-lineno">410</tt> <a class="py-toggle" href="#" id="Parser.parse-toggle" onclick="return toggle('Parser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Raf.Parser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.parse-expanded"><a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a SeqMap """</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-89" class="py-name"><a title="Bio.SCOP.Raf.SeqMap" class="py-name" href="#" onclick="return doclink('link-89', 'SeqMap', 'link-20');">SeqMap</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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