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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module StructureAlignment'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.StructureAlignment%27-module.html">Module Bio.PDB.StructureAlignment'</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-comment"># make yield compatible with Python 2.2</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><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="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-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="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt id="link-2" 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-2', '__doc__', 'link-2');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-string">Map the residues of two structures to each other based on </tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-string">a FASTA alignment file.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="StructureAlignment"></a><div id="StructureAlignment-def"><a name="L17"></a><tt class="py-lineno"> 17</tt> <a class="py-toggle" href="#" id="StructureAlignment-toggle" onclick="return toggle('StructureAlignment');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.StructureAlignment'.StructureAlignment-class.html">StructureAlignment</a><tt class="py-op">:</tt> </tt>
</div><div id="StructureAlignment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StructureAlignment-expanded"><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> This class aligns two structures based on a FASTA alignment of their</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> sequences.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="StructureAlignment.__init__"></a><div id="StructureAlignment.__init__-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="StructureAlignment.__init__-toggle" onclick="return toggle('StructureAlignment.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureAlignment'.StructureAlignment-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">fasta_align</tt><tt class="py-op">,</tt> <tt class="py-param">m1</tt><tt class="py-op">,</tt> <tt class="py-param">m2</tt><tt class="py-op">,</tt> <tt class="py-param">si</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">sj</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureAlignment.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureAlignment.__init__-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> fasta_align --- A Bio.Fasta.FastaAlign object </tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> m1, m2 --- two models</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> si, sj --- the sequences in the Bio.Fasta.FastaAlign object that</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> correspond to the structures</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-name">fasta_align</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_alignment_length()=Bio.Align.Generic.Alignment-class.html#get_alignment_length"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-3', 'get_alignment_length', 'link-3');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-4', 's1', 'link-4');">s1</a></tt><tt class="py-op">=</tt><tt class="py-name">fasta_align</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_seq_by_num()=Bio.Align.Generic.Alignment-class.html#get_seq_by_num"><a title="Bio.Align.Generic.Alignment.get_seq_by_num" class="py-name" href="#" onclick="return doclink('link-5', 'get_seq_by_num', 'link-5');">get_seq_by_num</a></tt><tt class="py-op">(</tt><tt class="py-name">si</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt id="link-6" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-6', 's2', 'link-6');">s2</a></tt><tt class="py-op">=</tt><tt class="py-name">fasta_align</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Align.Generic.Alignment.get_seq_by_num" class="py-name" href="#" onclick="return doclink('link-7', 'get_seq_by_num', 'link-5');">get_seq_by_num</a></tt><tt class="py-op">(</tt><tt class="py-name">sj</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-comment"># Get the residues in the models</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rl1</tt><tt class="py-op">=</tt><tt id="link-8" 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-8', 'Selection', 'link-8');">Selection</a></tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'unfold_entities', 'link-9');">unfold_entities</a></tt><tt class="py-op">(</tt><tt class="py-name">m1</tt><tt class="py-op">,</tt> <tt class="py-string">'R'</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">rl2</tt><tt class="py-op">=</tt><tt id="link-10" class="py-name"><a title="Bio.GA.Selection
Bio.PDB.Selection" class="py-name" href="#" onclick="return doclink('link-10', 'Selection', 'link-8');">Selection</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.PDB.Selection.unfold_entities" class="py-name" href="#" onclick="return doclink('link-11', 'unfold_entities', 'link-9');">unfold_entities</a></tt><tt class="py-op">(</tt><tt class="py-name">m2</tt><tt class="py-op">,</tt> <tt class="py-string">'R'</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-comment"># Residue positions</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">p1</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">p2</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-comment"># Map equivalent residues to each other</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">map12</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 class="py-name">map21</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-comment"># List of residue pairs (None if -)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">duos</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-12" 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-12', 'i', 'link-12');">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">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">column</tt><tt class="py-op">=</tt><tt class="py-name">fasta_align</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Align.AlignInfo.SummaryInfo.get_column()=Bio.Align.AlignInfo.SummaryInfo-class.html#get_column,Method Bio.Align.Generic.Alignment.get_column()=Bio.Align.Generic.Alignment-class.html#get_column"><a title="Bio.Align.AlignInfo.SummaryInfo.get_column
Bio.Align.Generic.Alignment.get_column" class="py-name" href="#" onclick="return doclink('link-13', 'get_column', 'link-13');">get_column</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-14', 'i', 'link-12');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-15" class="py-name" targets="Variable Bio.PDB.Polypeptide.aa1=Bio.PDB.Polypeptide-module.html#aa1"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-15', 'aa1', 'link-15');">aa1</a></tt><tt class="py-op">=</tt><tt class="py-name">column</tt><tt class="py-op">[</tt><tt class="py-name">si</tt><tt class="py-op">]</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">aa2</tt><tt class="py-op">=</tt><tt class="py-name">column</tt><tt class="py-op">[</tt><tt class="py-name">sj</tt><tt class="py-op">]</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-16', 'aa1', 'link-15');">aa1</a></tt><tt class="py-op">!=</tt><tt class="py-string">"-"</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-comment"># Position in seq1 is not -</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-comment"># Loop until an aa is found</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">r1</tt><tt class="py-op">=</tt><tt class="py-name">rl1</tt><tt class="py-op">[</tt><tt class="py-name">p1</tt><tt class="py-op">]</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">p1</tt><tt class="py-op">=</tt><tt class="py-name">p1</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name" targets="Function Bio.PDB.Polypeptide.is_aa()=Bio.PDB.Polypeptide-module.html#is_aa"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-17', 'is_aa', 'link-17');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.PDB.StructureAlignment'.StructureAlignment._test_equivalence()=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html#_test_equivalence"><a title="Bio.PDB.StructureAlignment'.StructureAlignment._test_equivalence" class="py-name" href="#" onclick="return doclink('link-18', '_test_equivalence', 'link-18');">_test_equivalence</a></tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-19', 'aa1', 'link-15');">aa1</a></tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">r1</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">aa2</tt><tt class="py-op">!=</tt><tt class="py-string">"-"</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment"># Position in seq2 is not -</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment"># Loop until an aa is found</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">r2</tt><tt class="py-op">=</tt><tt class="py-name">rl2</tt><tt class="py-op">[</tt><tt class="py-name">p2</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">p2</tt><tt class="py-op">=</tt><tt class="py-name">p2</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-20', 'is_aa', 'link-17');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.StructureAlignment'.StructureAlignment._test_equivalence" class="py-name" href="#" onclick="return doclink('link-21', '_test_equivalence', 'link-18');">_test_equivalence</a></tt><tt class="py-op">(</tt><tt class="py-name">r2</tt><tt class="py-op">,</tt> <tt class="py-name">aa2</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">r2</tt><tt class="py-op">=</tt><tt class="py-name">None</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">r1</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># Map residue in seq1 to its equivalent in seq2</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">map12</tt><tt class="py-op">[</tt><tt class="py-name">r1</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">r2</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r2</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># Map residue in seq2 to its equivalent in seq1</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">map21</tt><tt class="py-op">[</tt><tt class="py-name">r2</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">r1</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-comment"># Append aligned pair (r is None if gap)</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">duos</tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'append', 'link-22');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt class="py-name">r2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map12</tt><tt class="py-op">=</tt><tt class="py-name">map12</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map21</tt><tt class="py-op">=</tt><tt class="py-name">map21</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">duos</tt><tt class="py-op">=</tt><tt class="py-name">duos</tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="StructureAlignment._test_equivalence"></a><div id="StructureAlignment._test_equivalence-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="StructureAlignment._test_equivalence-toggle" onclick="return toggle('StructureAlignment._test_equivalence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureAlignment'.StructureAlignment-class.html#_test_equivalence">_test_equivalence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r1</tt><tt class="py-op">,</tt> <tt class="py-param">aa1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureAlignment._test_equivalence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureAlignment._test_equivalence-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-docstring">"Test if aa in sequence fits aa in structure."</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-23" 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-23', 'get_resname', 'link-23');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt id="link-24" 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-24', 'to_one_letter_code', 'link-24');">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="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.aa1" class="py-name" href="#" onclick="return doclink('link-25', 'aa1', 'link-15');">aa1</a></tt><tt class="py-op">==</tt><tt class="py-name">resname</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="StructureAlignment.get_maps"></a><div id="StructureAlignment.get_maps-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="StructureAlignment.get_maps-toggle" onclick="return toggle('StructureAlignment.get_maps');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureAlignment'.StructureAlignment-class.html#get_maps">get_maps</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="StructureAlignment.get_maps-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureAlignment.get_maps-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> Return two dictionaries that map a residue in one structure to </tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> the equivealent residue in the other structure.</tt> </tt>
<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-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map12</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map21</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="StructureAlignment.get_iterator"></a><div id="StructureAlignment.get_iterator-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="StructureAlignment.get_iterator-toggle" onclick="return toggle('StructureAlignment.get_iterator');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureAlignment'.StructureAlignment-class.html#get_iterator">get_iterator</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="StructureAlignment.get_iterator-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureAlignment.get_iterator-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> Iterator over all residue pairs.</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-keyword">for</tt> <tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-12');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">duos</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">duos</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-12');">i</a></tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</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="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-28" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-28', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Package Bio.Fasta=Bio.Fasta-module.html"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-29', 'Fasta', 'link-29');">Fasta</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Module Bio.Fasta.FastaAlign=Bio.Fasta.FastaAlign-module.html"><a title="Bio.Fasta.FastaAlign" class="py-name" href="#" onclick="return doclink('link-30', 'FastaAlign', 'link-30');">FastaAlign</a></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-31" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-31', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-32', 'PDB', 'link-1');">PDB</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-comment"># The alignment</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fa</tt><tt class="py-op">=</tt><tt id="link-33" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-33', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-34', 'Fasta', 'link-29');">Fasta</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Fasta.FastaAlign" class="py-name" href="#" onclick="return doclink('link-35', 'FastaAlign', 'link-30');">FastaAlign</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Function Bio.Clustalw.parse_file()=Bio.Clustalw-module.html#parse_file,Function Bio.Fasta.FastaAlign.parse_file()=Bio.Fasta.FastaAlign-module.html#parse_file,Method Bio.ParserSupport.AbstractParser.parse_file()=Bio.ParserSupport.AbstractParser-class.html#parse_file"><a title="Bio.Clustalw.parse_file
Bio.Fasta.FastaAlign.parse_file
Bio.ParserSupport.AbstractParser.parse_file" class="py-name" href="#" onclick="return doclink('link-36', 'parse_file', 'link-36');">parse_file</a></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 class="py-string">'PROTEIN'</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">pdb_file1</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">2</tt><tt class="py-op">]</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">pdb_file2</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">3</tt><tt class="py-op">]</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-comment"># The structures</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-37" 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-37', 'PDBParser', 'link-37');">PDBParser</a></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 id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-38', 's1', 'link-4');">s1</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-39" 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-39', 'get_structure', 'link-39');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">,</tt> <tt class="py-name">pdb_file1</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">p</tt><tt class="py-op">=</tt><tt id="link-40" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-40', 'PDBParser', 'link-37');">PDBParser</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 id="link-41" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-41', 's2', 'link-6');">s2</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><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-42', 'get_structure', 'link-39');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">'2'</tt><tt class="py-op">,</tt> <tt class="py-name">pdb_file2</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment"># Get the models</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">m1</tt><tt class="py-op">=</tt><tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-43', 's1', 'link-4');">s1</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">m2</tt><tt class="py-op">=</tt><tt id="link-44" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-44', 's2', 'link-6');">s2</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">al</tt><tt class="py-op">=</tt><tt id="link-45" class="py-name" targets="Class Bio.PDB.StructureAlignment'.StructureAlignment=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html"><a title="Bio.PDB.StructureAlignment'.StructureAlignment" class="py-name" href="#" onclick="return doclink('link-45', 'StructureAlignment', 'link-45');">StructureAlignment</a></tt><tt class="py-op">(</tt><tt class="py-name">fa</tt><tt class="py-op">,</tt> <tt class="py-name">m1</tt><tt class="py-op">,</tt> <tt class="py-name">m2</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># Print aligned pairs (r is None if gap)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">r1</tt><tt class="py-op">,</tt><tt class="py-name">r2</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">al</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.PDB.Entity.Entity.get_iterator()=Bio.PDB.Entity.Entity-class.html#get_iterator,Method Bio.PDB.StructureAlignment'.StructureAlignment.get_iterator()=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html#get_iterator"><a title="Bio.PDB.Entity.Entity.get_iterator
Bio.PDB.StructureAlignment'.StructureAlignment.get_iterator" class="py-name" href="#" onclick="return doclink('link-46', 'get_iterator', 'link-46');">get_iterator</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt class="py-name">r2</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt><script type="text/javascript">
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