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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module Selection
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.Selection-module.html">Module Bio.PDB.Selection</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ListType</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Bio.PDB.PDBExceptions=Bio.PDB.PDBExceptions-module.html"><a title="Bio.PDB.PDBExceptions" class="py-name" href="#" onclick="return doclink('link-0', 'PDBExceptions', 'link-0');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Variable Bio.PDB.DSSP'.PDBException=Bio.PDB.DSSP%27-module.html#PDBException,Variable Bio.PDB.PDBExceptions.PDBException=Bio.PDB.PDBExceptions-module.html#PDBException,Variable Bio.PDB.Superimposer'.PDBException=Bio.PDB.Superimposer%27-module.html#PDBException"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-1', 'PDBException', 'link-1');">PDBException</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 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">"Selection of atoms, residues, etc."</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.PDB.Selection.entity_levels=Bio.PDB.Selection-module.html#entity_levels"><a title="Bio.PDB.Selection.entity_levels" class="py-name" href="#" onclick="return doclink('link-3', 'entity_levels', 'link-3');">entity_levels</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt> <tt class="py-string">"R"</tt><tt class="py-op">,</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> <tt class="py-string">"M"</tt><tt class="py-op">,</tt> <tt class="py-string">"S"</tt><tt class="py-op">]</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="uniqueify"></a><div id="uniqueify-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="uniqueify-toggle" onclick="return toggle('uniqueify');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Selection-module.html#uniqueify">uniqueify</a><tt class="py-op">(</tt><tt class="py-param">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="uniqueify-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="uniqueify-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"Return unique items in list l."</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-4', 'd', 'link-4');">d</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-5" 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-5', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-6" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-6', 'd', 'link-4');">d</a></tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'has_key', 'link-7');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-8', 'i', 'link-5');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-9', 'd', 'link-4');">d</a></tt><tt class="py-op">[</tt><tt id="link-10" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-10', 'i', 'link-5');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-11" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-11', 'd', 'link-4');">d</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-12', 'keys', 'link-12');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt>
<a name="get_unique_parents"></a><div id="get_unique_parents-def"><a name="L23"></a><tt class="py-lineno">23</tt> <a class="py-toggle" href="#" id="get_unique_parents-toggle" onclick="return toggle('get_unique_parents');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Selection-module.html#get_unique_parents">get_unique_parents</a><tt class="py-op">(</tt><tt class="py-param">entity_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_unique_parents-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="get_unique_parents-expanded"><a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> Translate a list of entities to a list of their</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> (unique) parents.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entity</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entity_list</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">parent</tt><tt class="py-op">=</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.get_parent()=Bio.EUtils.POM.ElementNode-class.html#get_parent,Method Bio.PDB.Atom.Atom.get_parent()=Bio.PDB.Atom.Atom-class.html#get_parent,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_parent()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_parent,Method Bio.PDB.Entity.Entity.get_parent()=Bio.PDB.Entity.Entity-class.html#get_parent"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-13', 'get_parent', 'link-13');">get_parent</a></tt><tt class="py-op">(</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">l</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'append', 'link-14');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name" targets="Function Bio.PDB.Selection.uniqueify()=Bio.PDB.Selection-module.html#uniqueify"><a title="Bio.PDB.Selection.uniqueify" class="py-name" href="#" onclick="return doclink('link-15', 'uniqueify', 'link-15');">uniqueify</a></tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> </tt>
<a name="unfold_entities"></a><div id="unfold_entities-def"><a name="L34"></a><tt class="py-lineno">34</tt> <a class="py-toggle" href="#" id="unfold_entities-toggle" onclick="return toggle('unfold_entities');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Selection-module.html#unfold_entities">unfold_entities</a><tt class="py-op">(</tt><tt class="py-param">entity_list</tt><tt class="py-op">,</tt> <tt class="py-param">target_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="unfold_entities-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="unfold_entities-expanded"><a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> Unfold a list of entities to a list of entities of another </tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"> level. E.g.:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> list of atoms -> list of residues</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> list of modules -> list of atoms</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-docstring"> list of residues -> list of chains</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-docstring"> o entity_list - list of entities or a single entity</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-docstring"> o target_level - char (A, R, C, M, S)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">target_level</tt> <tt class="py-keyword">in</tt> <tt id="link-16" class="py-name"><a title="Bio.PDB.Selection.entity_levels" class="py-name" href="#" onclick="return doclink('link-16', 'entity_levels', 'link-3');">entity_levels</a></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">raise</tt> <tt id="link-17" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-17', 'PDBException', 'link-1');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"%s: Not an entity level."</tt> <tt class="py-op">%</tt> <tt class="py-name">target_level</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-18" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-18', 'type', 'link-18');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">entity_list</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-name">ListType</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-comment"># single entity</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">entity_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">entity_list</tt><tt class="py-op">]</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-comment"># level of entity list</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">level</tt><tt class="py-op">=</tt><tt class="py-name">entity_list</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_level()=Bio.PDB.Atom.Atom-class.html#get_level,Method Bio.PDB.Entity.Entity.get_level()=Bio.PDB.Entity.Entity-class.html#get_level"><a title="Bio.PDB.Atom.Atom.get_level
Bio.PDB.Entity.Entity.get_level" class="py-name" href="#" onclick="return doclink('link-19', 'get_level', 'link-19');">get_level</a></tt><tt class="py-op">(</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">for</tt> <tt class="py-name">entity</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entity_list</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.PDB.Atom.Atom.get_level
Bio.PDB.Entity.Entity.get_level" class="py-name" href="#" onclick="return doclink('link-20', 'get_level', 'link-19');">get_level</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-name">level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-21" class="py-name"><a title="Bio.PDB.DSSP'.PDBException
Bio.PDB.PDBExceptions.PDBException
Bio.PDB.Superimposer'.PDBException" class="py-name" href="#" onclick="return doclink('link-21', 'PDBException', 'link-1');">PDBException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Entity list is not homogeneous."</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-name">target_index</tt><tt class="py-op">=</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Selection.entity_levels" class="py-name" href="#" onclick="return doclink('link-22', 'entity_levels', 'link-3');">entity_levels</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-23', 'index', 'link-23');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">target_level</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">level_index</tt><tt class="py-op">=</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.Selection.entity_levels" class="py-name" href="#" onclick="return doclink('link-24', 'entity_levels', 'link-3');">entity_levels</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-25', 'index', 'link-23');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">)</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">level_index</tt><tt class="py-op">==</tt><tt class="py-name">target_index</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"># already right level</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">return</tt> <tt class="py-name">entity_list</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">level_index</tt><tt class="py-op">></tt><tt class="py-name">target_index</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-comment"># we're going down, e.g. S->A</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">target_index</tt><tt class="py-op">,</tt> <tt class="py-name">level_index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">new_entity_list</tt><tt class="py-op">=</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">for</tt> <tt class="py-name">entity</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entity_list</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">new_entity_list</tt><tt class="py-op">=</tt><tt class="py-name">new_entity_list</tt><tt class="py-op">+</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'get_list', 'link-27');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-name">entity_list</tt><tt class="py-op">=</tt><tt class="py-name">new_entity_list</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-comment"># we're going up, e.g. A->S</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">level_index</tt><tt class="py-op">,</tt> <tt class="py-name">target_index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-name">new_entity_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entity</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entity_list</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">parent</tt><tt class="py-op">=</tt><tt class="py-name">entity</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-29', 'get_parent', 'link-13');">get_parent</a></tt><tt class="py-op">(</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">new_entity_list</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-30', 'append', 'link-14');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-comment"># find unique parents</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">entity_list</tt><tt class="py-op">=</tt><tt id="link-31" class="py-name"><a title="Bio.PDB.Selection.uniqueify" class="py-name" href="#" onclick="return doclink('link-31', 'uniqueify', 'link-15');">uniqueify</a></tt><tt class="py-op">(</tt><tt class="py-name">new_entity_list</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">return</tt> <tt class="py-name">entity_list</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> </tt><script type="text/javascript">
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