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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module MMCIFParser
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.MMCIFParser-module.html">Module Bio.PDB.MMCIFParser</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">#Python stuff</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">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">atoi</tt><tt class="py-op">,</tt> <tt class="py-name">atof</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-0', 'letters', 'link-0');">letters</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</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-1" 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-1', 'Float0', 'link-1');">Float0</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"># My stuff</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.PDB.MMCIF2Dict=Bio.PDB.MMCIF2Dict-module.html,Class Bio.PDB.MMCIF2Dict.MMCIF2Dict=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html"><a title="Bio.PDB.MMCIF2Dict
Bio.PDB.MMCIF2Dict.MMCIF2Dict" class="py-name" href="#" onclick="return doclink('link-2', 'MMCIF2Dict', 'link-2');">MMCIF2Dict</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.PDB.MMCIF2Dict
Bio.PDB.MMCIF2Dict.MMCIF2Dict" class="py-name" href="#" onclick="return doclink('link-3', 'MMCIF2Dict', 'link-2');">MMCIF2Dict</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Module Bio.PDB.StructureBuilder=Bio.PDB.StructureBuilder-module.html,Class Bio.PDB.StructureBuilder.StructureBuilder=Bio.PDB.StructureBuilder.StructureBuilder-class.html"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-4', 'StructureBuilder', 'link-4');">StructureBuilder</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-5', 'StructureBuilder', 'link-4');">StructureBuilder</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt 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">"mmCIF parser (partly implemented in C)."</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="MMCIFParser"></a><div id="MMCIFParser-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="MMCIFParser-toggle" onclick="return toggle('MMCIFParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.MMCIFParser.MMCIFParser-class.html">MMCIFParser</a><tt class="py-op">:</tt> </tt>
</div><div id="MMCIFParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MMCIFParser-expanded"><a name="MMCIFParser.get_structure"></a><div id="MMCIFParser.get_structure-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="MMCIFParser.get_structure-toggle" onclick="return toggle('MMCIFParser.get_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure">get_structure</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">structure_id</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MMCIFParser.get_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MMCIFParser.get_structure-expanded"><a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mmcif_dict</tt><tt class="py-op">=</tt><tt id="link-7" class="py-name"><a title="Bio.PDB.MMCIF2Dict
Bio.PDB.MMCIF2Dict.MMCIF2Dict" class="py-name" href="#" onclick="return doclink('link-7', 'MMCIF2Dict', 'link-2');">MMCIF2Dict</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_structure_builder</tt><tt class="py-op">=</tt><tt id="link-8" class="py-name"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-8', 'StructureBuilder', 'link-4');">StructureBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser._build_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#_build_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser._build_structure" class="py-name" href="#" onclick="return doclink('link-9', '_build_structure', 'link-9');">_build_structure</a></tt><tt class="py-op">(</tt><tt class="py-name">structure_id</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</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">_structure_builder</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'get_structure', 'link-10');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="MMCIFParser._build_structure"></a><div id="MMCIFParser._build_structure-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="MMCIFParser._build_structure-toggle" onclick="return toggle('MMCIFParser._build_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIFParser.MMCIFParser-class.html#_build_structure">_build_structure</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">structure_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MMCIFParser._build_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MMCIFParser._build_structure-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-name">mmcif_dict</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mmcif_dict</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">atom_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_atom_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">residue_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_comp_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">seq_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_seq_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">chain_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_asym_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">x_list</tt><tt class="py-op">=</tt><tt id="link-11" 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-11', 'map', 'link-11');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">atof</tt><tt class="py-op">,</tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.Cartn_x"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">y_list</tt><tt class="py-op">=</tt><tt id="link-12" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-12', 'map', 'link-11');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">atof</tt><tt class="py-op">,</tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.Cartn_y"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">z_list</tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-13', 'map', 'link-11');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">atof</tt><tt class="py-op">,</tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.Cartn_z"</tt><tt class="py-op">]</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">alt_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_alt_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">b_factor_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.B_iso_or_equiv"</tt><tt class="py-op">]</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">occupancy_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.occupancy"</tt><tt class="py-op">]</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">fieldname_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.group_PDB"</tt><tt class="py-op">]</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">aniso_u11</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[1][1]"</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">aniso_u12</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[1][2]"</tt><tt class="py-op">]</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">aniso_u13</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[1][3]"</tt><tt class="py-op">]</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">aniso_u22</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[2][2]"</tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">aniso_u23</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[2][3]"</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">aniso_u33</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.aniso_U[3][3]"</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">aniso_flag</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-comment"># no anisotropic B factors</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">aniso_flag</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-comment"># if auth_seq_id is present, we use this.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Otherwise label_seq_id is used.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'has_key', 'link-14');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"_atom_site.auth_seq_id"</tt><tt class="py-op">)</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">seq_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.auth_seq_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">seq_id_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_atom_site.label_seq_id"</tt><tt class="py-op">]</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-comment"># Now loop over atoms and build the structure</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</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-name">current_model_id</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_structure_builder</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_structure"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_structure" class="py-name" href="#" onclick="return doclink('link-15', 'init_structure', 'link-15');">init_structure</a></tt><tt class="py-op">(</tt><tt class="py-name">structure_id</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_model()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_model"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_model" class="py-name" href="#" onclick="return doclink('link-16', 'init_model', 'link-16');">init_model</a></tt><tt class="py-op">(</tt><tt class="py-name">current_model_id</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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_seg()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_seg"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_seg" class="py-name" href="#" onclick="return doclink('link-17', 'init_seg', 'link-17');">init_seg</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-18" 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-18', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-19" class="py-name" targets="Method Bio.GFF.Feature.xrange()=Bio.GFF.Feature-class.html#xrange"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-19', 'xrange', 'link-19');">xrange</a></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">atom_id_list</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 id="link-20" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-20', 'x', 'link-20');">x</a></tt><tt class="py-op">=</tt><tt class="py-name">x_list</tt><tt class="py-op">[</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">=</tt><tt class="py-name">y_list</tt><tt class="py-op">[</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">z</tt><tt class="py-op">=</tt><tt class="py-name">z_list</tt><tt class="py-op">[</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">residue_id_list</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-18');">i</a></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">chainid</tt><tt class="py-op">=</tt><tt class="py-name">chain_id_list</tt><tt class="py-op">[</tt><tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">altloc</tt><tt class="py-op">=</tt><tt class="py-name">alt_list</tt><tt class="py-op">[</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-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">altloc</tt><tt class="py-op">==</tt><tt class="py-string">"."</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">altloc</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">resseq</tt><tt class="py-op">=</tt><tt class="py-name">seq_id_list</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-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt id="link-28" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-28', 'name', 'link-28');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">atom_id_list</tt><tt class="py-op">[</tt><tt id="link-29" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-18');">i</a></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">tempfactor</tt><tt class="py-op">=</tt><tt class="py-name">b_factor_list</tt><tt class="py-op">[</tt><tt id="link-30" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-30', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">occupancy</tt><tt class="py-op">=</tt><tt class="py-name">occupancy_list</tt><tt class="py-op">[</tt><tt id="link-31" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">fieldname</tt><tt class="py-op">=</tt><tt class="py-name">fieldname_list</tt><tt class="py-op">[</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fieldname</tt><tt class="py-op">==</tt><tt class="py-string">"HETATM"</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">hetatm_flag</tt><tt class="py-op">=</tt><tt class="py-string">"H"</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">hetatm_flag</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_chain_id</tt><tt class="py-op">!=</tt><tt class="py-name">chainid</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">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">chainid</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_chain()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_chain"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_chain" class="py-name" href="#" onclick="return doclink('link-33', 'init_chain', 'link-33');">init_chain</a></tt><tt class="py-op">(</tt><tt class="py-name">current_chain_id</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">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">resseq</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt class="py-name">int_resseq</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser._get_icode()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#_get_icode"><a title="Bio.PDB.MMCIFParser.MMCIFParser._get_icode" class="py-name" href="#" onclick="return doclink('link-34', '_get_icode', 'link-34');">_get_icode</a></tt><tt class="py-op">(</tt><tt class="py-name">resseq</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_residue()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_residue"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_residue" class="py-name" href="#" onclick="return doclink('link-35', 'init_residue', 'link-35');">init_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">hetatm_flag</tt><tt class="py-op">,</tt> <tt class="py-name">int_resseq</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">current_residue_id</tt><tt class="py-op">!=</tt><tt class="py-name">resseq</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">resseq</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt class="py-name">int_resseq</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.MMCIFParser.MMCIFParser._get_icode" class="py-name" href="#" onclick="return doclink('link-36', '_get_icode', 'link-34');">_get_icode</a></tt><tt class="py-op">(</tt><tt class="py-name">resseq</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_residue" class="py-name" href="#" onclick="return doclink('link-37', 'init_residue', 'link-35');">init_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">hetatm_flag</tt><tt class="py-op">,</tt> <tt class="py-name">int_resseq</tt><tt class="py-op">,</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">coord</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-38', 'x', 'link-20');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">z</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><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-39', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_atom()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_atom"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_atom" class="py-name" href="#" onclick="return doclink('link-40', 'init_atom', 'link-40');">init_atom</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-41', 'name', 'link-28');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">coord</tt><tt class="py-op">,</tt> <tt class="py-name">tempfactor</tt><tt class="py-op">,</tt> <tt class="py-name">occupancy</tt><tt class="py-op">,</tt> <tt class="py-name">altloc</tt><tt class="py-op">,</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-42', 'name', 'link-28');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">aniso_flag</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">u</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">aniso_u11</tt><tt class="py-op">[</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">aniso_u12</tt><tt class="py-op">[</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-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">aniso_u13</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-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">aniso_u22</tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">aniso_u23</tt><tt class="py-op">[</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">aniso_u33</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-18');">i</a></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-name">mapped_anisou</tt><tt class="py-op">=</tt><tt id="link-49" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-49', 'map', 'link-11');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">atof</tt><tt class="py-op">,</tt> <tt class="py-name">u</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">anisou_array</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">mapped_anisou</tt><tt class="py-op">,</tt> <tt id="link-50" class="py-name"><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-50', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.PDB.Atom.Atom.set_anisou()=Bio.PDB.Atom.Atom-class.html#set_anisou,Method Bio.PDB.StructureBuilder.StructureBuilder.set_anisou()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_anisou"><a title="Bio.PDB.Atom.Atom.set_anisou
Bio.PDB.StructureBuilder.StructureBuilder.set_anisou" class="py-name" href="#" onclick="return doclink('link-51', 'set_anisou', 'link-51');">set_anisou</a></tt><tt class="py-op">(</tt><tt class="py-name">anisou_array</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># Now try to set the cell</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.length_a"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">b</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.length_b"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.length_c"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.angle_alpha"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.angle_beta"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">gamma</tt><tt class="py-op">=</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_cell.angle_gamma"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">cell</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">b</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt class="py-name">alpha</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-52" class="py-name"><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-52', 'Float0', 'link-1');">Float0</a></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">spacegroup</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-string">"_symmetry.space_group_name_H-M"</tt><tt class="py-op">]</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">spacegroup</tt><tt class="py-op">=</tt><tt class="py-name">spacegroup</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-number">1</tt><tt class="py-op">]</tt> <tt class="py-comment"># get rid of quotes!!</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">spacegroup</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.set_symmetry()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_symmetry"><a title="Bio.PDB.StructureBuilder.StructureBuilder.set_symmetry" class="py-name" href="#" onclick="return doclink('link-53', 'set_symmetry', 'link-53');">set_symmetry</a></tt><tt class="py-op">(</tt><tt class="py-name">spacegroup</tt><tt class="py-op">,</tt> <tt class="py-name">cell</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> <tt class="py-comment"># no cell found, so just ignore</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="MMCIFParser._get_icode"></a><div id="MMCIFParser._get_icode-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="MMCIFParser._get_icode-toggle" onclick="return toggle('MMCIFParser._get_icode');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIFParser.MMCIFParser-class.html#_get_icode">_get_icode</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">resseq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-docstring">"""Tries to return the icode. In MMCIF files this is just part of</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> resseq! In PDB files, it's a separate field."""</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">last_resseq_char</tt><tt class="py-op">=</tt><tt class="py-name">resseq</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="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">last_resseq_char</tt> <tt class="py-keyword">in</tt> <tt id="link-54" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-54', 'letters', 'link-0');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">=</tt><tt class="py-name">last_resseq_char</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">int_resseq</tt><tt class="py-op">=</tt><tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt class="py-name">resseq</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 class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">int_resseq</tt><tt class="py-op">=</tt><tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt class="py-name">resseq</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt class="py-name">int_resseq</tt> </tt>
</div></div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</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="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">filename</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>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-55" class="py-name" targets="Module Bio.PDB.MMCIFParser=Bio.PDB.MMCIFParser-module.html,Class Bio.PDB.MMCIFParser.MMCIFParser=Bio.PDB.MMCIFParser.MMCIFParser-class.html"><a title="Bio.PDB.MMCIFParser
Bio.PDB.MMCIFParser.MMCIFParser" class="py-name" href="#" onclick="return doclink('link-55', 'MMCIFParser', 'link-55');">MMCIFParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-56" class="py-name" targets="Variable Bio.SubsMat.MatrixInfo.structure=Bio.SubsMat.MatrixInfo-module.html#structure"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-56', 'structure', 'link-56');">structure</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'get_structure', 'link-10');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"test"</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">model</tt> <tt class="py-keyword">in</tt> <tt id="link-58" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-58', 'structure', 'link-56');">structure</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.PDB.Entity.Entity.get_list()=Bio.PDB.Entity.Entity-class.html#get_list"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-59', 'get_list', 'link-59');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">model</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">chain</tt> <tt class="py-keyword">in</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-60', 'get_list', 'link-59');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">chain</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Found %d residues."</tt> <tt class="py-op">%</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-61', 'get_list', 'link-59');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt><script type="text/javascript">
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