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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.PDB-module.html">Package&nbsp;PDB</a> ::
        Module&nbsp;DSSP'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.DSSP%27-module.html">Module Bio.PDB.DSSP'</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license.  Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">__future__</tt> <tt class="py-keyword">import</tt> <tt class="py-name">generators</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">tempfile</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-1', 'PDB', 'link-1');">PDB</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.PDB.PDBExceptions=Bio.PDB.PDBExceptions-module.html"><a title="Bio.PDB.PDBExceptions" class="py-name" href="#" onclick="return doclink('link-2', 'PDBExceptions', 'link-2');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Variable Bio.PDB.DSSP'.PDBException=Bio.PDB.DSSP%27-module.html#PDBException,Variable Bio.PDB.PDBExceptions.PDBException=Bio.PDB.PDBExceptions-module.html#PDBException,Variable Bio.PDB.Superimposer'.PDBException=Bio.PDB.Superimposer%27-module.html#PDBException"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-3', 'PDBException', 'link-3');">PDBException</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Module Bio.PDB.AbstractPropertyMap=Bio.PDB.AbstractPropertyMap-module.html,Class Bio.PDB.AbstractPropertyMap.AbstractPropertyMap=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html"><a title="Bio.PDB.AbstractPropertyMap
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap" class="py-name" href="#" onclick="return doclink('link-4', 'AbstractPropertyMap', 'link-4');">AbstractPropertyMap</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap=Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html"><a title="Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap" class="py-name" href="#" onclick="return doclink('link-5', 'AbstractResiduePropertyMap', 'link-5');">AbstractResiduePropertyMap</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-6', '__doc__', 'link-6');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-string">Use the DSSP program to calculate secondary structure and accessibility.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-string">You need to have a working version of DSSP (and a license, free for </tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-string">academic use) in order to use this. For DSSP, see U{http://www.cmbi.kun.nl/gv/dssp/}.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-string">The DSSP codes for secondary structure used here are:</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-string">    - H        Alpha helix (4-12)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-string">    - B        Isolated beta-bridge residue</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-string">    - E        Strand</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-string">    - G        3-10 helix</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-string">    - I        pi helix</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-string">    - T        Turn</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-string">    - S        Bend</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-string">    - -        None</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-comment"># Match C in DSSP</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-7" class="py-name" targets="Variable Bio.PDB.DSSP'._dssp_cys=Bio.PDB.DSSP%27-module.html#_dssp_cys"><a title="Bio.PDB.DSSP'._dssp_cys" class="py-name" href="#" onclick="return doclink('link-7', '_dssp_cys', 'link-7');">_dssp_cys</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-8', 'compile', 'link-8');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">'[a-z]'</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-comment"># Maximal ASA of amino acids</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Values from Sander &amp; Rost, (1994), Proteins, 20:216-226</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Used for relative accessibility</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-9" class="py-name" targets="Variable Bio.PDB.DSSP'.MAX_ACC=Bio.PDB.DSSP%27-module.html#MAX_ACC"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-9', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt id="link-10" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-10', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"ALA"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">106.0</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt id="link-11" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-11', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"CYS"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">135.0</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt id="link-12" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-12', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"ASP"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">163.0</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt id="link-13" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-13', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"GLU"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">194.0</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt id="link-14" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-14', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"PHE"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">197.0</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt id="link-15" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-15', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"GLY"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">84.0</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt id="link-16" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-16', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"HIS"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">184.0</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt id="link-17" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-17', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"ILE"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">169.0</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt id="link-18" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-18', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"LYS"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">205.0</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt id="link-19" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-19', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"LEU"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">164.0</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt id="link-20" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-20', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"MET"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">188.0</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt id="link-21" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-21', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"ASN"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">157.0</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt id="link-22" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-22', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"PRO"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">136.0</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt id="link-23" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-23', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"GLN"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">198.0</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt id="link-24" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-24', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"ARG"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">248.0</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt id="link-25" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-25', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"SER"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">130.0</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt id="link-26" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-26', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"THR"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">142.0</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt id="link-27" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-27', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"VAL"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">142.0</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt id="link-28" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-28', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"TRP"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">227.0</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt id="link-29" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-29', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-string">"TYR"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">222.0</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="ss_to_index"></a><div id="ss_to_index-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="ss_to_index-toggle" onclick="return toggle('ss_to_index');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.DSSP'-module.html#ss_to_index">ss_to_index</a><tt class="py-op">(</tt><tt class="py-param">ss</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ss_to_index-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ss_to_index-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">    Secondary structure symbol to index.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">    H=0</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">    E=1</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    C=2</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">'H'</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">'E'</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">'C'</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">2</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"> </tt>
<a name="dssp_dict_from_pdb_file"></a><div id="dssp_dict_from_pdb_file-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="dssp_dict_from_pdb_file-toggle" onclick="return toggle('dssp_dict_from_pdb_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.DSSP'-module.html#dssp_dict_from_pdb_file">dssp_dict_from_pdb_file</a><tt class="py-op">(</tt><tt class="py-param">in_file</tt><tt class="py-op">,</tt> <tt class="py-param">DSSP</tt><tt class="py-op">=</tt><tt class="py-string">"dssp"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="dssp_dict_from_pdb_file-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="dssp_dict_from_pdb_file-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">    Create a DSSP dictionary from a PDB file.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">    Example:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; dssp_dict=dssp_dict_from_pdb_file("1fat.pdb")</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; aa, ss, acc=dssp_dict[('A', 1)]</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-docstring">    @param in_file: pdb file</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-docstring">    @type in_file: string</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-docstring">    @param DSSP: DSSP executable (argument to os.system)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-docstring">    @type DSSP: string</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring">    @return: a dictionary that maps (chainid, resid) to </tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">        amino acid type, secondary structure code and </tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">        accessibility.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: {}</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-name">out_file</tt><tt class="py-op">=</tt><tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">mktemp</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">    <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name" targets="Class Bio.PDB.DSSP'.DSSP=Bio.PDB.DSSP%27.DSSP-class.html"><a title="Bio.PDB.DSSP'.DSSP" class="py-name" href="#" onclick="return doclink('link-30', 'DSSP', 'link-30');">DSSP</a></tt><tt class="py-op">+</tt><tt class="py-string">" %s &gt; %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">in_file</tt><tt class="py-op">,</tt> <tt class="py-name">out_file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-name">dict</tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-31', 'keys', 'link-31');">keys</a></tt><tt class="py-op">=</tt><tt id="link-32" class="py-name" targets="Function Bio.PDB.DSSP'.make_dssp_dict()=Bio.PDB.DSSP%27-module.html#make_dssp_dict"><a title="Bio.PDB.DSSP'.make_dssp_dict" class="py-name" href="#" onclick="return doclink('link-32', 'make_dssp_dict', 'link-32');">make_dssp_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">out_file</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">    <tt class="py-comment"># This can be dangerous...</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#os.system("rm "+out_file)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt class="py-name">dict</tt><tt class="py-op">,</tt> <tt id="link-33" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-33', 'keys', 'link-31');">keys</a></tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="make_dssp_dict"></a><div id="make_dssp_dict-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="make_dssp_dict-toggle" onclick="return toggle('make_dssp_dict');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.DSSP'-module.html#make_dssp_dict">make_dssp_dict</a><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="make_dssp_dict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_dssp_dict-expanded"><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">    Return a DSSP dictionary that maps (chainid, resid) to</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">    aa, ss and accessibility, from a DSSP file.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">    @param filename: the DSSP output file</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    @type filename: string</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-name">dssp</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt id="link-34" 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-34', 'open', 'link-34');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt id="link-35" 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-35', 'start', 'link-35');">start</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt id="link-36" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-36', 'keys', 'link-31');">keys</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-37', 'readlines', 'link-37');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-name">sl</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-38', 'split', 'link-38');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">sl</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-string">"RESIDUE"</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt class="py-comment"># start</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-39" 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-39', 'start', 'link-35');">start</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">            <tt class="py-keyword">continue</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-40" 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-40', 'start', 'link-35');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">            <tt class="py-keyword">continue</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">            <tt class="py-comment"># skip -- missing residue</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">continue</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt class="py-name">resseq</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-number">10</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-name">icode</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">        <tt class="py-name">chainid</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">11</tt><tt class="py-op">]</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt class="py-name">aa</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">13</tt><tt class="py-op">]</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt class="py-name">ss</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">16</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">            <tt class="py-name">ss</tt><tt class="py-op">=</tt><tt class="py-string">"-"</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt id="link-41" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.acc=Bio.FSSP.fssp_rec.align-class.html#acc"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-41', 'acc', 'link-41');">acc</a></tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">34</tt><tt class="py-op">:</tt><tt class="py-number">38</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-name">res_id</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-name">dssp</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">res_id</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">aa</tt><tt class="py-op">,</tt> <tt class="py-name">ss</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-42', 'acc', 'link-41');">acc</a></tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt id="link-43" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-43', 'keys', 'link-31');">keys</a></tt><tt class="py-op">.</tt><tt id="link-44" 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-44', 'append', 'link-44');">append</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">res_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-45" 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-45', 'close', 'link-45');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">dssp</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-46', 'keys', 'link-31');">keys</a></tt> </tt>
</div><a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"> </tt>
<a name="DSSP"></a><div id="DSSP-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="DSSP-toggle" onclick="return toggle('DSSP');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.DSSP'.DSSP-class.html">DSSP</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractResiduePropertyMap</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DSSP-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DSSP-expanded"><a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring">    Run DSSP on a pdb file, and provide a handle to the </tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    DSSP secondary structure and accessibility.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-docstring">    Note that DSSP can only handle one model.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"><tt class="py-docstring">    Example:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; p=PDBParser()</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; structure=parser.get_structure("1fat.pdb")</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; model=structure[0]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; dssp=DSSP(model, "1fat.pdb")</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; # print dssp data for a residue</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-docstring">        &gt;&gt;&gt; secondary_structure, accessibility=dssp[(chain_id, res_id)]</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="DSSP.__init__"></a><div id="DSSP.__init__-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="DSSP.__init__-toggle" onclick="return toggle('DSSP.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.DSSP'.DSSP-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">,</tt> <tt class="py-param">pdb_file</tt><tt class="py-op">,</tt> <tt class="py-param">dssp</tt><tt class="py-op">=</tt><tt class="py-string">"dssp"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DSSP.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DSSP.__init__-expanded"><a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"><tt class="py-docstring">        @param model: the first model of the structure</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line"><tt class="py-docstring">        @type model: L{Model}</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"><tt class="py-docstring">        @param pdb_file: a PDB file</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-docstring">        @type pdb_file: string</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring">        @param dssp: the dssp executable (ie. the argument to os.system)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-docstring">        @type dssp: string</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">        <tt class="py-comment"># create DSSP dictionary</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">dssp_dict</tt><tt class="py-op">,</tt> <tt class="py-name">dssp_keys</tt><tt class="py-op">=</tt><tt id="link-47" class="py-name" targets="Function Bio.PDB.DSSP'.dssp_dict_from_pdb_file()=Bio.PDB.DSSP%27-module.html#dssp_dict_from_pdb_file"><a title="Bio.PDB.DSSP'.dssp_dict_from_pdb_file" class="py-name" href="#" onclick="return doclink('link-47', 'dssp_dict_from_pdb_file', 'link-47');">dssp_dict_from_pdb_file</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_file</tt><tt class="py-op">,</tt> <tt class="py-name">dssp</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-name">dssp_map</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">        <tt class="py-name">dssp_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">        <tt class="py-comment"># Now create a dictionary that maps Residue objects to </tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># secondary structure and accessibility, and a list of </tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># (residue, (secondary structure, accessibility)) tuples</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt id="link-48" 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-48', 'key', 'link-48');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dssp_keys</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">            <tt id="link-49" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.chain_id=Bio.FSSP.fssp_rec.align-class.html#chain_id"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-49', 'chain_id', 'link-49');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">res_id</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-50', 'key', 'link-48');">key</a></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">            <tt class="py-name">chain</tt><tt class="py-op">=</tt><tt class="py-name">model</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-51', 'chain_id', 'link-49');">chain_id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">            <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">res_id</tt><tt class="py-op">]</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">            <tt class="py-name">aa</tt><tt class="py-op">,</tt> <tt class="py-name">ss</tt><tt class="py-op">,</tt> <tt id="link-52" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-52', 'acc', 'link-41');">acc</a></tt><tt class="py-op">=</tt><tt class="py-name">dssp_dict</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-53', 'key', 'link-48');">key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">            <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"SS_DSSP"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">ss</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">            <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"EXP_DSSP_ASA"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-54" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-54', 'acc', 'link-41');">acc</a></tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">            <tt class="py-comment"># relative accessibility</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.PDB.Residue.Residue.get_resname()=Bio.PDB.Residue.Residue-class.html#get_resname"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-55', 'get_resname', 'link-55');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">            <tt class="py-name">rel_acc</tt><tt class="py-op">=</tt><tt id="link-56" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-56', 'acc', 'link-41');">acc</a></tt><tt class="py-op">/</tt><tt id="link-57" class="py-name"><a title="Bio.PDB.DSSP'.MAX_ACC" class="py-name" href="#" onclick="return doclink('link-57', 'MAX_ACC', 'link-9');">MAX_ACC</a></tt><tt class="py-op">[</tt><tt class="py-name">resname</tt><tt class="py-op">]</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">rel_acc</tt><tt class="py-op">&gt;</tt><tt class="py-number">1.0</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">                <tt class="py-name">rel_acc</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">            <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"EXP_DSSP_RASA"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">rel_acc</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-comment"># Verify if AA in DSSP == AA in Structure</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># Something went wrong if this is not true!</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt id="link-58" 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-58', 'to_one_letter_code', 'link-58');">to_one_letter_code</a></tt><tt class="py-op">[</tt><tt class="py-name">resname</tt><tt class="py-op">]</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">resname</tt><tt class="py-op">==</tt><tt class="py-string">"C"</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">                <tt class="py-comment"># DSSP renames C in C-bridges to a,b,c,d,...</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment"># - we rename it back to 'C'</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.DSSP'._dssp_cys" class="py-name" href="#" onclick="return doclink('link-59', '_dssp_cys', 'link-7');">_dssp_cys</a></tt><tt class="py-op">.</tt><tt id="link-60" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-60', 'match', 'link-60');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">aa</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-name">aa</tt><tt class="py-op">=</tt><tt class="py-string">'C'</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">==</tt><tt class="py-name">aa</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt id="link-61" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-61', 'PDBException', 'link-3');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Structure/DSSP mismatch at "</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">)</tt>  </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">            <tt class="py-name">dssp_map</tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-62', 'key', 'link-48');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt> <tt class="py-name">ss</tt><tt class="py-op">,</tt> <tt id="link-63" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-63', 'acc', 'link-41');">acc</a></tt><tt class="py-op">,</tt> <tt class="py-name">rel_acc</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">            <tt class="py-name">dssp_list</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'append', 'link-44');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt> <tt class="py-name">ss</tt><tt class="py-op">,</tt> <tt id="link-65" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-65', 'acc', 'link-41');">acc</a></tt><tt class="py-op">,</tt> <tt class="py-name">rel_acc</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt id="link-66" class="py-name"><a title="Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap" class="py-name" href="#" onclick="return doclink('link-66', 'AbstractResiduePropertyMap', 'link-5');">AbstractResiduePropertyMap</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__init__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__init__,Method Bio.EUtils.Datatypes.IdCheck.__init__()=Bio.EUtils.Datatypes.IdCheck-class.html#__init__,Method Bio.EUtils.Datatypes.IdUrlSet.__init__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__init__,Method Bio.EUtils.Datatypes.Link.__init__()=Bio.EUtils.Datatypes.Link-class.html#__init__,Method Bio.EUtils.Datatypes.LinkSetDb.__init__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__init__,Method Bio.EUtils.Datatypes.LinksLinkSet.__init__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__init__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.ObjUrl.__init__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__init__,Method Bio.EUtils.Datatypes.PostResult.__init__()=Bio.EUtils.Datatypes.PostResult-class.html#__init__,Method Bio.EUtils.Datatypes.Problem.__init__()=Bio.EUtils.Datatypes.Problem-class.html#__init__,Method Bio.EUtils.Datatypes.Provider.__init__()=Bio.EUtils.Datatypes.Provider-class.html#__init__,Method Bio.EUtils.Datatypes.Range.__init__()=Bio.EUtils.Datatypes.Range-class.html#__init__,Method Bio.EUtils.Datatypes.SearchResult.__init__()=Bio.EUtils.Datatypes.SearchResult-class.html#__init__,Method Bio.EUtils.Datatypes.Summary.__init__()=Bio.EUtils.Datatypes.Summary-class.html#__init__,Method Bio.EUtils.Datatypes.Term.__init__()=Bio.EUtils.Datatypes.Term-class.html#__init__,Method Bio.EUtils.Datatypes.WithinNDays.__init__()=Bio.EUtils.Datatypes.WithinNDays-class.html#__init__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryClient.__init__()=Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryCookie.__init__()=Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryLookup.__init__()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryRecord.__init__()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__init__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__init__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__init__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__init__,Method Bio.EUtils.POM.Comment.__init__()=Bio.EUtils.POM.Comment-class.html#__init__,Method Bio.EUtils.POM.ContentModel.__init__()=Bio.EUtils.POM.ContentModel-class.html#__init__,Method Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__()=Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html#__init__,Method Bio.EUtils.POM.ElementNode.__init__()=Bio.EUtils.POM.ElementNode-class.html#__init__,Method Bio.EUtils.POM.IndentedText.__init__()=Bio.EUtils.POM.IndentedText-class.html#__init__,Method Bio.EUtils.POM.ObjectParserHandler.__init__()=Bio.EUtils.POM.ObjectParserHandler-class.html#__init__,Method Bio.EUtils.POM.POMDocument.__init__()=Bio.EUtils.POM.POMDocument-class.html#__init__,Method Bio.EUtils.POM.XMLAttribute.__init__()=Bio.EUtils.POM.XMLAttribute-class.html#__init__,Method Bio.EUtils.POM._ContentModelGenerator.__init__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__init__,Method 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Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-67', '__init__', 'link-67');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">dssp_map</tt><tt class="py-op">,</tt> <tt class="py-name">dssp_keys</tt><tt class="py-op">,</tt> <tt class="py-name">dssp_list</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-68" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-68', 'PDBParser', 'link-68');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    <tt id="link-69" 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-69', 's', 'link-69');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser.get_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure,Method Bio.PDB.PDBParser'.PDBParser.get_structure()=Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure,Method Bio.PDB.StructureBuilder.StructureBuilder.get_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-70', 'get_structure', 'link-70');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">'X'</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-name">model</tt><tt class="py-op">=</tt><tt id="link-71" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-71', 's', 'link-69');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">0</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 id="link-72" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-72', 'd', 'link-72');">d</a></tt><tt class="py-op">=</tt><tt id="link-73" class="py-name"><a title="Bio.PDB.DSSP'.DSSP" class="py-name" href="#" onclick="return doclink('link-73', 'DSSP', 'link-30');">DSSP</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="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-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt id="link-74" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-74', 'd', 'link-72');">d</a></tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-name">r</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt id="link-75" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-75', 'd', 'link-72');">d</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-76', 'keys', 'link-31');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-77', 'd', 'link-72');">d</a></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">print</tt> <tt id="link-78" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-78', 'd', 'link-72');">d</a></tt><tt class="py-op">.</tt><tt id="link-79" 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-79', 'has_key', 'link-79');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-number">1</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>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt id="link-80" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-80', 'd', 'link-72');">d</a></tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt id="link-81" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-81', 's', 'link-69');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'A'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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