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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module MMCIF2Dict
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.MMCIF2Dict-module.html">Module Bio.PDB.MMCIF2Dict</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">import</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</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-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.PDB.mmCIF=Bio.PDB.mmCIF-module.html"><a title="Bio.PDB.mmCIF" class="py-name" href="#" onclick="return doclink('link-2', 'mmCIF', 'link-2');">mmCIF</a></tt><tt class="py-op">.</tt><tt class="py-name">MMCIFlex</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">UserDict</tt> <tt class="py-keyword">import</tt> <tt class="py-name">UserDict</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-3" 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-3', '__doc__', 'link-3');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"Turn an mmCIF file into a dictionary."</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="MMCIF2Dict"></a><div id="MMCIF2Dict-def"><a name="L13"></a><tt class="py-lineno"> 13</tt> <a class="py-toggle" href="#" id="MMCIF2Dict-toggle" onclick="return toggle('MMCIF2Dict');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html">MMCIF2Dict</a><tt class="py-op">(</tt><tt class="py-base-class">UserDict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MMCIF2Dict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MMCIF2Dict-expanded"><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-comment"># The token identifiers</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-4" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#NAME,Variable Bio.expressions.swissprot.speclist.NAME=Bio.expressions.swissprot.speclist-module.html#NAME"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME
Bio.expressions.swissprot.speclist.NAME" class="py-name" href="#" onclick="return doclink('link-4', 'NAME', 'link-4');">NAME</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.LOOP=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#LOOP"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.LOOP" class="py-name" href="#" onclick="return doclink('link-5', 'LOOP', 'link-5');">LOOP</a></tt><tt class="py-op">=</tt><tt class="py-number">2</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-6" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.DATA=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#DATA"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DATA" class="py-name" href="#" onclick="return doclink('link-6', 'DATA', 'link-6');">DATA</a></tt><tt class="py-op">=</tt><tt class="py-number">3</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt id="link-7" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.SEMICOLONS=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#SEMICOLONS"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SEMICOLONS" class="py-name" href="#" onclick="return doclink('link-7', 'SEMICOLONS', 'link-7');">SEMICOLONS</a></tt><tt class="py-op">=</tt><tt class="py-number">4</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt id="link-8" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.DOUBLEQUOTED=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#DOUBLEQUOTED"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DOUBLEQUOTED" class="py-name" href="#" onclick="return doclink('link-8', 'DOUBLEQUOTED', 'link-8');">DOUBLEQUOTED</a></tt><tt class="py-op">=</tt><tt class="py-number">5</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt id="link-9" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.QUOTED=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#QUOTED"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.QUOTED" class="py-name" href="#" onclick="return doclink('link-9', 'QUOTED', 'link-9');">QUOTED</a></tt><tt class="py-op">=</tt><tt class="py-number">6</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt id="link-10" class="py-name" targets="Variable Bio.PDB.MMCIF2Dict.MMCIF2Dict.SIMPLE=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#SIMPLE"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SIMPLE" class="py-name" href="#" onclick="return doclink('link-10', 'SIMPLE', 'link-10');">SIMPLE</a></tt><tt class="py-op">=</tt><tt class="py-number">7</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="MMCIF2Dict.__init__"></a><div id="MMCIF2Dict.__init__-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="MMCIF2Dict.__init__-toggle" onclick="return toggle('MMCIF2Dict.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIF2Dict.MMCIF2Dict-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">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MMCIF2Dict.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MMCIF2Dict.__init__-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-comment"># this dict will contain the name/data pairs </tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-11', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-comment"># entry for garbage</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-12', 'data', 'link-11');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-name">filename</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">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"File not found."</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-14', 'PDB', 'link-1');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.PDB.mmCIF" class="py-name" href="#" onclick="return doclink('link-15', 'mmCIF', 'link-2');">mmCIF</a></tt><tt class="py-op">.</tt><tt class="py-name">MMCIFlex</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Function Bio.Mindy.compression.open_file()=Bio.Mindy.compression-module.html#open_file"><a title="Bio.Mindy.compression.open_file" class="py-name" href="#" onclick="return doclink('link-16', 'open_file', 'link-16');">open_file</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</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">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.PDB.MMCIF2Dict.MMCIF2Dict._make_mmcif_dict()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#_make_mmcif_dict"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict._make_mmcif_dict" class="py-name" href="#" onclick="return doclink('link-17', '_make_mmcif_dict', 'link-17');">_make_mmcif_dict</a></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 id="link-18" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-18', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-19', 'PDB', 'link-1');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.PDB.mmCIF" class="py-name" href="#" onclick="return doclink('link-20', 'mmCIF', 'link-2');">mmCIF</a></tt><tt class="py-op">.</tt><tt class="py-name">MMCIFlex</tt><tt class="py-op">.</tt><tt class="py-name">close_file</tt><tt class="py-op">(</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="MMCIF2Dict._make_mmcif_dict"></a><div id="MMCIF2Dict._make_mmcif_dict-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="MMCIF2Dict._make_mmcif_dict-toggle" onclick="return toggle('MMCIF2Dict._make_mmcif_dict');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#_make_mmcif_dict">_make_mmcif_dict</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-comment"># local copies</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-21" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME
Bio.expressions.swissprot.speclist.NAME" class="py-name" href="#" onclick="return doclink('link-21', 'NAME', 'link-4');">NAME</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME
Bio.expressions.swissprot.speclist.NAME" class="py-name" href="#" onclick="return doclink('link-22', 'NAME', 'link-4');">NAME</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.LOOP" class="py-name" href="#" onclick="return doclink('link-23', 'LOOP', 'link-5');">LOOP</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.LOOP" class="py-name" href="#" onclick="return doclink('link-24', 'LOOP', 'link-5');">LOOP</a></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DATA" class="py-name" href="#" onclick="return doclink('link-25', 'DATA', 'link-6');">DATA</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DATA" class="py-name" href="#" onclick="return doclink('link-26', 'DATA', 'link-6');">DATA</a></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SEMICOLONS" class="py-name" href="#" onclick="return doclink('link-27', 'SEMICOLONS', 'link-7');">SEMICOLONS</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SEMICOLONS" class="py-name" href="#" onclick="return doclink('link-28', 'SEMICOLONS', 'link-7');">SEMICOLONS</a></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DOUBLEQUOTED" class="py-name" href="#" onclick="return doclink('link-29', 'DOUBLEQUOTED', 'link-8');">DOUBLEQUOTED</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DOUBLEQUOTED" class="py-name" href="#" onclick="return doclink('link-30', 'DOUBLEQUOTED', 'link-8');">DOUBLEQUOTED</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.QUOTED" class="py-name" href="#" onclick="return doclink('link-31', 'QUOTED', 'link-9');">QUOTED</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.QUOTED" class="py-name" href="#" onclick="return doclink('link-32', 'QUOTED', 'link-9');">QUOTED</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SIMPLE" class="py-name" href="#" onclick="return doclink('link-33', 'SIMPLE', 'link-10');">SIMPLE</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.SIMPLE" class="py-name" href="#" onclick="return doclink('link-34', 'SIMPLE', 'link-10');">SIMPLE</a></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">get_token</tt><tt class="py-op">=</tt><tt id="link-35" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-35', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-36', 'PDB', 'link-1');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.mmCIF" class="py-name" href="#" onclick="return doclink('link-37', 'mmCIF', 'link-2');">mmCIF</a></tt><tt class="py-op">.</tt><tt class="py-name">MMCIFlex</tt><tt class="py-op">.</tt><tt class="py-name">get_token</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-comment"># are we looping?</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">loop_flag</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment"># list of names in loop</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">temp_list</tt><tt class="py-op">=</tt><tt class="py-op">[</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"># last encountered name</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">current_name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-comment"># get first token/value pair</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">token</tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-38', 'value', 'link-38');">value</a></tt><tt class="py-op">=</tt><tt class="py-name">get_token</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-comment"># print token, value</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-39', 'data', 'link-11');">data</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-comment"># loop until EOF (token==0)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">token</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">if</tt> <tt class="py-name">token</tt><tt class="py-op">==</tt><tt id="link-40" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME
Bio.expressions.swissprot.speclist.NAME" class="py-name" href="#" onclick="return doclink('link-40', 'NAME', 'link-4');">NAME</a></tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">loop_flag</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment"># Make lists for all the names in the loop</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">token</tt><tt class="py-op">==</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.NAME
Bio.expressions.swissprot.speclist.NAME" class="py-name" href="#" onclick="return doclink('link-41', 'NAME', 'link-4');">NAME</a></tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-comment"># create a list for each name encountered in loop</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_list</tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-42', 'value', 'link-38');">value</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</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">temp_list</tt><tt class="py-op">.</tt><tt id="link-43" 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-43', 'append', 'link-43');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new_list</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">token</tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-44', 'value', 'link-38');">value</a></tt><tt class="py-op">=</tt><tt class="py-name">get_token</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment"># print token, value</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">loop_flag</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-comment"># nr of data items parsed</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">data_counter</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-comment"># corresponding data name</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pos</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">nr_fields</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">temp_list</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-comment"># Now fill all lists with the data</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">token</tt><tt class="py-op">></tt><tt class="py-number">3</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">pos</tt><tt class="py-op">=</tt><tt class="py-name">data_counter</tt><tt class="py-op">%</tt><tt class="py-name">nr_fields</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">data_counter</tt><tt class="py-op">=</tt><tt class="py-name">data_counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">temp_list</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-45" 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-45', 'append', 'link-43');">append</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-46', 'value', 'link-38');">value</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">token</tt><tt class="py-op">,</tt> <tt id="link-47" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-47', 'value', 'link-38');">value</a></tt><tt class="py-op">=</tt><tt class="py-name">get_token</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-comment"># print token, value</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt><tt class="py-op">!=</tt><tt class="py-name">nr_fields</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"ERROR: broken name-data pair (data missing)!"</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># The last token was not used, so</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># don't set token to None! (this means the </tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># last parsed token goes through the loop again)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># simple name-data pair (no loop)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># so next token should be the data</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">next_token</tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-48', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt class="py-name">get_token</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># print token, value</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-49', 'value', 'link-38');">value</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-50', 'data', 'link-11');">data</a></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">next_token</tt><tt class="py-op"><</tt><tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"ERROR: broken name-data pair (name-non data pair)!"</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment"># print token, value</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># get next token</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">token</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">token</tt><tt class="py-op">==</tt><tt id="link-51" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.LOOP" class="py-name" href="#" onclick="return doclink('link-51', 'LOOP', 'link-5');">LOOP</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-name">loop_flag</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">temp_list</tt><tt class="py-op">=</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-comment"># get next token</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">token</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">token</tt><tt class="py-op">==</tt><tt id="link-52" class="py-name"><a title="Bio.PDB.MMCIF2Dict.MMCIF2Dict.DATA" class="py-name" href="#" onclick="return doclink('link-52', 'DATA', 'link-6');">DATA</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">mmcif_dict</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-53', 'value', 'link-38');">value</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-54" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-54', 'value', 'link-38');">value</a></tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">token</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># we found some complete garbage</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">"ERROR: broken name-data pair (missing name)!"</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">token</tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-55', 'value', 'link-38');">value</a></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-56" 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-56', 'append', 'link-43');">append</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-57', 'value', 'link-38');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># get next token</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">token</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">token</tt><tt class="py-op">==</tt><tt class="py-name">None</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">token</tt><tt class="py-op">,</tt> <tt id="link-58" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-58', 'value', 'link-38');">value</a></tt><tt class="py-op">=</tt><tt class="py-name">get_token</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-comment"># print token, value</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="MMCIF2Dict.__getitem__"></a><div id="MMCIF2Dict.__getitem__-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="MMCIF2Dict.__getitem__-toggle" onclick="return toggle('MMCIF2Dict.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MMCIF2Dict.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MMCIF2Dict.__getitem__-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-59', 'data', 'link-11');">data</a></tt><tt class="py-op">[</tt><tt id="link-60" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-60', 'key', 'link-60');">key</a></tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</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="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</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-op">!=</tt><tt class="py-number">2</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">print</tt> <tt class="py-string">"Usage: python MMCIF2Dict filename."</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-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="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">mmcif_dict</tt><tt class="py-op">=</tt><tt id="link-61" 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-61', 'MMCIF2Dict', 'link-61');">MMCIF2Dict</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">input</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Now type a key ('q' to end, 'k' for a list of all keys):"</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">while</tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">!=</tt><tt class="py-string">"q"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">input</tt><tt class="py-op">=</tt><tt class="py-name">raw_input</tt><tt class="py-op">(</tt><tt class="py-string">"MMCIF dictionary key ==> "</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">if</tt> <tt class="py-name">input</tt><tt class="py-op">==</tt><tt class="py-string">"q"</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">input</tt><tt class="py-op">==</tt><tt class="py-string">"k"</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-62" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-62', 'key', 'link-60');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">mmcif_dict</tt><tt class="py-op">.</tt><tt id="link-63" 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-63', 'keys', 'link-63');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-64" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-64', 'key', 'link-60');">key</a></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-65', 'value', 'link-38');">value</a></tt><tt class="py-op">=</tt><tt class="py-name">mmcif_dict</tt><tt class="py-op">[</tt><tt class="py-name">input</tt><tt class="py-op">]</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-66" 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-66', 'type', 'link-66');">type</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-67', 'value', 'link-38');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt id="link-68" class="py-name"><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-68', 'type', 'link-66');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-69" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-69', 'item', 'link-69');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-70" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-70', 'value', 'link-38');">value</a></tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-71" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-71', 'item', 'link-69');">item</a></tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-72" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-72', 'value', 'link-38');">value</a></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</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="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"No such key found."</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt><script type="text/javascript">
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