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Module FragmentMapper'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.FragmentMapper%27-module.html">Module Bio.PDB.FragmentMapper'</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Affy.CelFile.Float0=Bio.Affy.CelFile-module.html#Float0,Variable Bio.LogisticRegression.Float0=Bio.LogisticRegression-module.html#Float0,Variable Bio.MarkovModel.Float0=Bio.MarkovModel-module.html#Float0,Variable Bio.MaxEntropy.Float0=Bio.MaxEntropy-module.html#Float0,Variable Bio.NaiveBayes.Float0=Bio.NaiveBayes-module.html#Float0,Variable Bio.PDB.FragmentMapper'.Float0=Bio.PDB.FragmentMapper%27-module.html#Float0,Variable Bio.PDB.PDBParser'.Float0=Bio.PDB.PDBParser%27-module.html#Float0,Variable Bio.PDB.Superimposer'.Float0=Bio.PDB.Superimposer%27-module.html#Float0,Variable Bio.Statistics.lowess.Float0=Bio.Statistics.lowess-module.html#Float0,Variable Bio.distance.Float0=Bio.distance-module.html#Float0,Variable Bio.kNN.Float0=Bio.kNN-module.html#Float0"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-0', 'Float0', 'link-0');">Float0</a></tt><tt class="py-op">,</tt> <tt class="py-name">zeros</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.SVDSuperimposer=Bio.SVDSuperimposer-module.html,Class Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-2', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-3', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-5', 'PDB', 'link-5');">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>
<a name="L12"></a><tt class="py-lineno"> 12</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="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-string">Classify protein backbone structure according to Kolodny et al's fragment</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-string">libraries. It can be regarded as a form of objective secondary structure</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-string">classification. Only fragments of length 5 or 7 are supported (ie. there is a</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-string">'central' residue).</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-string">Full reference:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-string">Kolodny R, Koehl P, Guibas L, Levitt M.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-string">Small libraries of protein fragments model native protein structures accurately.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-string">J Mol Biol. 2002 323(2):297-307.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-string">The definition files of the fragments can be obtained from:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-string">U{http://csb.stanford.edu/~rachel/fragments/}</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-string">You need these files to use this module.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-string">The following example uses the library with 10 fragments of length 5.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-string">The library files can be found in directory 'fragment_data'.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-string"> >>> model=structure[0]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-string"> >>> fm=FragmentMapper(lsize=10, flength=5, dir="fragment_data")</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-string"> >>> fm.map(model)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-string"> >>> fragment=fm[residue]</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"># fragment file (lib_SIZE_z_LENGTH.txt)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># SIZE=number of fragments</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># LENGTH=length of fragment (4,5,6,7)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-7" class="py-name" targets="Variable Bio.PDB.FragmentMapper'._FRAGMENT_FILE=Bio.PDB.FragmentMapper%27-module.html#_FRAGMENT_FILE"><a title="Bio.PDB.FragmentMapper'._FRAGMENT_FILE" class="py-name" href="#" onclick="return doclink('link-7', '_FRAGMENT_FILE', 'link-7');">_FRAGMENT_FILE</a></tt><tt class="py-op">=</tt><tt class="py-string">"lib_%s_z_%s.txt"</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="_read_fragments"></a><div id="_read_fragments-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="_read_fragments-toggle" onclick="return toggle('_read_fragments');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'-module.html#_read_fragments">_read_fragments</a><tt class="py-op">(</tt><tt class="py-param">size</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">,</tt> <tt class="py-param">dir</tt><tt class="py-op">=</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_read_fragments-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_read_fragments-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> Read a fragment spec file (available from </tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> U{http://csb.stanford.edu/rachel/fragments/} </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> and return a list of Fragment objects.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> @param size: number of fragments in the library</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> @type size: int</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> @param length: length of the fragments</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> @type length: int</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> @param dir: directory where the fragment spec files can be found</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> @type dir: string</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">dir</tt><tt class="py-op">+</tt><tt class="py-string">"/"</tt><tt class="py-op">+</tt><tt id="link-8" class="py-name"><a title="Bio.PDB.FragmentMapper'._FRAGMENT_FILE" class="py-name" href="#" onclick="return doclink('link-8', '_FRAGMENT_FILE', 'link-7');">_FRAGMENT_FILE</a></tt><tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-9', 'size', 'link-9');">size</a></tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-10', 'length', 'link-10');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt id="link-11" 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-11', 'open', 'link-11');">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="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">flist</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment"># ID of fragment=rank in spec file</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fid</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</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-12" 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-12', 'readlines', 'link-12');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># skip comment and blank lines</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"*"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">l</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">"\n"</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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-13" 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-13', 'split', 'link-13');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt 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">"------"</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment"># Start of fragment definition</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt id="link-14" class="py-name" targets="Class Bio.PDB.FragmentMapper'.Fragment=Bio.PDB.FragmentMapper%27.Fragment-class.html"><a title="Bio.PDB.FragmentMapper'.Fragment" class="py-name" href="#" onclick="return doclink('link-14', 'Fragment', 'link-14');">Fragment</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-15', 'length', 'link-10');">length</a></tt><tt class="py-op">,</tt> <tt class="py-name">fid</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">flist</tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-comment"># increase fragment id (rank)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fid</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># Add CA coord to Fragment</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">coord</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-17', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">sl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># XXX= dummy residue name</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.PDB.FragmentMapper'.Fragment.add_residue()=Bio.PDB.FragmentMapper%27.Fragment-class.html#add_residue"><a title="Bio.PDB.FragmentMapper'.Fragment.add_residue" class="py-name" href="#" onclick="return doclink('link-18', 'add_residue', 'link-18');">add_residue</a></tt><tt class="py-op">(</tt><tt class="py-string">"XXX"</tt><tt class="py-op">,</tt> <tt class="py-name">coord</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'close', 'link-19');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">flist</tt> </tt>
</div><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="Fragment"></a><div id="Fragment-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="Fragment-toggle" onclick="return toggle('Fragment');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html">Fragment</a><tt class="py-op">:</tt> </tt>
</div><div id="Fragment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Fragment-expanded"><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"> Represent a polypeptide C-alpha fragment.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Fragment.__init__"></a><div id="Fragment.__init__-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="Fragment.__init__-toggle" onclick="return toggle('Fragment.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-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">length</tt><tt class="py-op">,</tt> <tt class="py-param">fid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.__init__-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> @param length: length of the fragment</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> @type length: int</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> @param fid: id for the fragment</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> @type fid: int</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-comment"># nr of residues in fragment</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-20', 'length', 'link-10');">length</a></tt><tt class="py-op">=</tt><tt id="link-21" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-21', 'length', 'link-10');">length</a></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-comment"># nr of residues added</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counter</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">resname_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment"># CA coordinate matrix</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords_ca</tt><tt class="py-op">=</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-22', 'length', 'link-10');">length</a></tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"d"</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fid</tt><tt class="py-op">=</tt><tt class="py-name">fid</tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="Fragment.get_resname_list"></a><div id="Fragment.get_resname_list-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="Fragment.get_resname_list-toggle" onclick="return toggle('Fragment.get_resname_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#get_resname_list">get_resname_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.get_resname_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.get_resname_list-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> @return: the residue names</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: [string, string,...]</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">resname_list</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="Fragment.get_id"></a><div id="Fragment.get_id-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="Fragment.get_id-toggle" onclick="return toggle('Fragment.get_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#get_id">get_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.get_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.get_id-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> @return: id for the fragment</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fid</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="Fragment.get_coords"></a><div id="Fragment.get_coords-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="Fragment.get_coords-toggle" onclick="return toggle('Fragment.get_coords');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#get_coords">get_coords</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.get_coords-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.get_coords-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> @return: the CA coords in the fragment</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: Numeric (Nx3) array</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords_ca</tt> </tt>
</div><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="Fragment.add_residue"></a><div id="Fragment.add_residue-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="Fragment.add_residue-toggle" onclick="return toggle('Fragment.add_residue');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#add_residue">add_residue</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">resname</tt><tt class="py-op">,</tt> <tt class="py-param">ca_coord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.add_residue-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.add_residue-expanded"><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> @param resname: residue name (eg. GLY).</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> @type resname: string</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> @param ca_coord: the c-alpha coorinates of the residues</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> @type ca_coord: Numeric array with length 3</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counter</tt><tt class="py-op">>=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-23', 'length', 'link-10');">length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-24" 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-24', 'PDBException', 'link-24');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Fragment boundary exceeded."</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">resname_list</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords_ca</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counter</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">ca_coord</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counter</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="Fragment.__len__"></a><div id="Fragment.__len__-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="Fragment.__len__-toggle" onclick="return toggle('Fragment.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.__len__-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> @return: length of fragment</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-26', 'length', 'link-10');">length</a></tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="Fragment.__sub__"></a><div id="Fragment.__sub__-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="Fragment.__sub__-toggle" onclick="return toggle('Fragment.__sub__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#__sub__">__sub__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.__sub__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.__sub__-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> Return rmsd between two fragments.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> >>> rmsd=fragment1-fragment2</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> @return: rmsd between fragments</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: float</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">=</tt><tt id="link-27" class="py-name"><a title="Bio.SVDSuperimposer
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer" class="py-name" href="#" onclick="return doclink('link-27', 'SVDSuperimposer', 'link-2');">SVDSuperimposer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set,Method Bio.config.DBRegistry.DBObject.set()=Bio.config.DBRegistry.DBObject-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-28', 'set', 'link-28');">set</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">coords_ca</tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">coords_ca</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.AlignAce.Applications.AlignAceCommandline.run()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#run,Method Bio.AlignAce.Applications.CompareAceCommandline.run()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#run,Method Bio.Entrez.Parser.DataHandler.run()=Bio.Entrez.Parser.DataHandler-class.html#run,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#run,Method Martel.setup.my_install.run()=Martel.setup.my_install-class.html#run,Method Martel.setup.run_install_tests.run()=Martel.setup.run_install_tests-class.html#run,Method Martel.setup.run_local_tests.run()=Martel.setup.run_local_tests-class.html#run"><a title="Bio.AlignAce.Applications.AlignAceCommandline.run
Bio.AlignAce.Applications.CompareAceCommandline.run
Bio.Entrez.Parser.DataHandler.run
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run
Martel.setup.my_install.run
Martel.setup.run_install_tests.run
Martel.setup.run_local_tests.run" class="py-name" href="#" onclick="return doclink('link-29', 'run', 'link-29');">run</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sup</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rms()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#get_rms"><a title="Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.get_rms" class="py-name" href="#" onclick="return doclink('link-30', 'get_rms', 'link-30');">get_rms</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="Fragment.__repr__"></a><div id="Fragment.__repr__-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="Fragment.__repr__-toggle" onclick="return toggle('Fragment.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.Fragment-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Fragment.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Fragment.__repr__-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Returns <Fragment length=L id=ID> where L=length of fragment</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> and ID the identifier (rank in the library).</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<Fragment length=%i id=%i>"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-31', 'length', 'link-10');">length</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fid</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="_make_fragment_list"></a><div id="_make_fragment_list-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="_make_fragment_list-toggle" onclick="return toggle('_make_fragment_list');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'-module.html#_make_fragment_list">_make_fragment_list</a><tt class="py-op">(</tt><tt class="py-param">pp</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_fragment_list-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_fragment_list-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> Dice up a peptide in fragments of length "length".</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> @param pp: a list of residues (part of one peptide)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> @type pp: [L{Residue}, L{Residue}, ...]</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> @param length: fragment length</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> @type length: int</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">frag_list</tt><tt class="py-op">=</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-keyword">for</tt> <tt id="link-32" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-33" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-33', 'length', 'link-10');">length</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="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.FragmentMapper'.Fragment" class="py-name" href="#" onclick="return doclink('link-34', 'Fragment', 'link-14');">Fragment</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-35', 'length', 'link-10');">length</a></tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-36', 'length', 'link-10');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-37', 'i', 'link-32');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'get_resname', 'link-38');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.PDB.Chain.Chain.has_id()=Bio.PDB.Chain.Chain-class.html#has_id,Method Bio.PDB.Entity.Entity.has_id()=Bio.PDB.Entity.Entity-class.html#has_id"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-39', 'has_id', 'link-39');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"CA"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">ca</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt class="py-string">"CA"</tt><tt class="py-op">]</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"CHAINBREAK"</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ca</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.PDB.Atom.Atom.is_disordered()=Bio.PDB.Atom.Atom-class.html#is_disordered,Method Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#is_disordered,Method Bio.PDB.Residue.Residue.is_disordered()=Bio.PDB.Residue.Residue-class.html#is_disordered"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-40', 'is_disordered', 'link-40');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"CHAINBREAK"</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">ca_coord</tt><tt class="py-op">=</tt><tt class="py-name">ca</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_coord()=Bio.PDB.Atom.Atom-class.html#get_coord"><a title="Bio.PDB.Atom.Atom.get_coord" class="py-name" href="#" onclick="return doclink('link-41', 'get_coord', 'link-41');">get_coord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.FragmentMapper'.Fragment.add_residue" class="py-name" href="#" onclick="return doclink('link-42', 'add_residue', 'link-18');">add_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">ca_coord</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">frag_list</tt><tt class="py-op">.</tt><tt id="link-43" 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-43', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">frag_list</tt> </tt>
</div><a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="_map_fragment_list"></a><div id="_map_fragment_list-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="_map_fragment_list-toggle" onclick="return toggle('_map_fragment_list');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'-module.html#_map_fragment_list">_map_fragment_list</a><tt class="py-op">(</tt><tt class="py-param">flist</tt><tt class="py-op">,</tt> <tt class="py-param">reflist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_map_fragment_list-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_map_fragment_list-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> Map all frgaments in flist to the closest</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> (in RMSD) fragment in reflist.</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of reflist indices.</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> @param flist: list of protein fragments</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> @type flist: [L{Fragment}, L{Fragment}, ...]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> @param reflist: list of reference (ie. library) fragments</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> @type reflist: [L{Fragment}, L{Fragment}, ...]</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">mapped</tt><tt class="py-op">=</tt><tt class="py-op">[</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">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">flist</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">rank</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-44', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">reflist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">rf</tt><tt class="py-op">=</tt><tt class="py-name">reflist</tt><tt class="py-op">[</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-45', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">rms</tt><tt class="py-op">=</tt><tt class="py-name">f</tt><tt class="py-op">-</tt><tt class="py-name">rf</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">rank</tt><tt class="py-op">.</tt><tt id="link-46" 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-46', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">rms</tt><tt class="py-op">,</tt> <tt class="py-name">rf</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">rank</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-47', 'sort', 'link-47');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">fragment</tt><tt class="py-op">=</tt><tt class="py-name">rank</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-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">mapped</tt><tt class="py-op">.</tt><tt id="link-48" 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-48', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fragment</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mapped</tt> </tt>
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="FragmentMapper"></a><div id="FragmentMapper-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="FragmentMapper-toggle" onclick="return toggle('FragmentMapper');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.FragmentMapper-class.html">FragmentMapper</a><tt class="py-op">:</tt> </tt>
</div><div id="FragmentMapper-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FragmentMapper-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> Map polypeptides in a model to lists of representative fragments.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="FragmentMapper.__init__"></a><div id="FragmentMapper.__init__-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="FragmentMapper.__init__-toggle" onclick="return toggle('FragmentMapper.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.FragmentMapper-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">lsize</tt><tt class="py-op">=</tt><tt class="py-number">20</tt><tt class="py-op">,</tt> <tt class="py-param">flength</tt><tt class="py-op">=</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-param">fdir</tt><tt class="py-op">=</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FragmentMapper.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FragmentMapper.__init__-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> @param model: the model that will be mapped</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> @param lsize: number of fragments in the library</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> @type lsize: int</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> @param flength: length of fragments in the library</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> @type flength: int</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> @param fdir: directory where the definition files are</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> found (default=".")</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> @type fdir: string</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">flength</tt><tt class="py-op">==</tt><tt class="py-number">5</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">edge</tt><tt class="py-op">=</tt><tt class="py-number">2</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">flength</tt><tt class="py-op">==</tt><tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">edge</tt><tt class="py-op">=</tt><tt class="py-number">3</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-49" 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-49', 'PDBException', 'link-24');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Fragment length should be 5 or 7."</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flength</tt><tt class="py-op">=</tt><tt class="py-name">flength</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lsize</tt><tt class="py-op">=</tt><tt class="py-name">lsize</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reflist</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name" targets="Function Bio.PDB.FragmentMapper'._read_fragments()=Bio.PDB.FragmentMapper%27-module.html#_read_fragments"><a title="Bio.PDB.FragmentMapper'._read_fragments" class="py-name" href="#" onclick="return doclink('link-50', '_read_fragments', 'link-50');">_read_fragments</a></tt><tt class="py-op">(</tt><tt class="py-name">lsize</tt><tt class="py-op">,</tt> <tt class="py-name">flength</tt><tt class="py-op">,</tt> <tt class="py-name">fdir</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">=</tt><tt class="py-name">model</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fd</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.PDB.FragmentMapper'.FragmentMapper._map()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#_map"><a title="Bio.PDB.FragmentMapper'.FragmentMapper._map" class="py-name" href="#" onclick="return doclink('link-51', '_map', 'link-51');">_map</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt>
</div><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="FragmentMapper._map"></a><div id="FragmentMapper._map-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="FragmentMapper._map-toggle" onclick="return toggle('FragmentMapper._map');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.FragmentMapper-class.html#_map">_map</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-op">:</tt> </tt>
</div><div id="FragmentMapper._map-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FragmentMapper._map-expanded"><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> @param model: the model that will be mapped</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring"> @type model: L{Model}</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">ppb</tt><tt class="py-op">=</tt><tt id="link-52" class="py-name" targets="Class Bio.PDB.Polypeptide.PPBuilder=Bio.PDB.Polypeptide.PPBuilder-class.html"><a title="Bio.PDB.Polypeptide.PPBuilder" class="py-name" href="#" onclick="return doclink('link-52', 'PPBuilder', 'link-52');">PPBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">ppl</tt><tt class="py-op">=</tt><tt class="py-name">ppb</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.PDB.Polypeptide._PPBuilder.build_peptides()=Bio.PDB.Polypeptide._PPBuilder-class.html#build_peptides"><a title="Bio.PDB.Polypeptide._PPBuilder.build_peptides" class="py-name" href="#" onclick="return doclink('link-53', 'build_peptides', 'link-53');">build_peptides</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">fd</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ppl</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-comment"># make fragments</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">flist</tt><tt class="py-op">=</tt><tt id="link-54" class="py-name" targets="Function Bio.PDB.FragmentMapper'._make_fragment_list()=Bio.PDB.FragmentMapper%27-module.html#_make_fragment_list"><a title="Bio.PDB.FragmentMapper'._make_fragment_list" class="py-name" href="#" onclick="return doclink('link-54', '_make_fragment_list', 'link-54');">_make_fragment_list</a></tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flength</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-comment"># classify fragments</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">mflist</tt><tt class="py-op">=</tt><tt id="link-55" class="py-name" targets="Function Bio.PDB.FragmentMapper'._map_fragment_list()=Bio.PDB.FragmentMapper%27-module.html#_map_fragment_list"><a title="Bio.PDB.FragmentMapper'._map_fragment_list" class="py-name" href="#" onclick="return doclink('link-55', '_map_fragment_list', 'link-55');">_map_fragment_list</a></tt><tt class="py-op">(</tt><tt class="py-name">flist</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reflist</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-56" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-56', 'i', 'link-32');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-name">pp</tt><tt class="py-op">[</tt><tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-57', 'i', 'link-32');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-32');">i</a></tt><tt class="py-op"><</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">edge</tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-comment"># start residues</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-32');">i</a></tt><tt class="py-op">>=</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pp</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">edge</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-comment"># end residues</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-comment"># fragment</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-60" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-60', 'index', 'link-60');">index</a></tt><tt class="py-op">=</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-61', 'i', 'link-32');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">edge</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-62', 'index', 'link-60');">index</a></tt><tt class="py-op">>=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">fd</tt><tt class="py-op">[</tt><tt class="py-name">res</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">mflist</tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-63', 'index', 'link-60');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-string">"CHAINBREAK"</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-comment"># Funny polypeptide - skip</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fd</tt> </tt>
</div><a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> </tt>
<a name="FragmentMapper.has_key"></a><div id="FragmentMapper.has_key-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="FragmentMapper.has_key-toggle" onclick="return toggle('FragmentMapper.has_key');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.FragmentMapper-class.html#has_key">has_key</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">res</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FragmentMapper.has_key-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FragmentMapper.has_key-expanded"><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> @type res: L{Residue}</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fd</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'has_key', 'link-64');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">)</tt> </tt>
</div><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> </tt>
<a name="FragmentMapper.__getitem__"></a><div id="FragmentMapper.__getitem__-def"><a name="L295"></a><tt class="py-lineno">295</tt> <a class="py-toggle" href="#" id="FragmentMapper.__getitem__-toggle" onclick="return toggle('FragmentMapper.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.FragmentMapper'.FragmentMapper-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">res</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FragmentMapper.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FragmentMapper.__getitem__-expanded"><a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> @type res: L{Residue}</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> @return: fragment classification</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: L{Fragment}</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fd</tt><tt class="py-op">[</tt><tt class="py-name">res</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</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="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-65" 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-65', 'PDBParser', 'link-65');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt id="link-66" 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-66', 's', 'link-66');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-67" 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-67', 'get_structure', 'link-67');">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="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">m</tt><tt class="py-op">=</tt><tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-66');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">fm</tt><tt class="py-op">=</tt><tt id="link-69" class="py-name" targets="Class Bio.PDB.FragmentMapper'.FragmentMapper=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html"><a title="Bio.PDB.FragmentMapper'.FragmentMapper" class="py-name" href="#" onclick="return doclink('link-69', 'FragmentMapper', 'link-69');">FragmentMapper</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-string">"levitt_data"</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt id="link-70" class="py-name" targets="Package Bio.GA.Selection=Bio.GA.Selection-module.html,Module Bio.PDB.Selection=Bio.PDB.Selection-module.html"><a title="Bio.GA.Selection
Bio.PDB.Selection" class="py-name" href="#" onclick="return doclink('link-70', 'Selection', 'link-70');">Selection</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Function Bio.PDB.Selection.unfold_entities()=Bio.PDB.Selection-module.html#unfold_entities"><a title="Bio.PDB.Selection.unfold_entities" class="py-name" href="#" onclick="return doclink('link-71', 'unfold_entities', 'link-71');">unfold_entities</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-string">"R"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">r</tt><tt class="py-op">,</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fm</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-72', 'has_key', 'link-64');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">fm</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">]</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt><script type="text/javascript">
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