<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.FSSP.FSSPTools</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.FSSP-module.html">Package FSSP</a> ::
Module FSSPTools
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.FSSP.FSSPTools-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.FSSP.FSSPTools-module.html">Module Bio.FSSP.FSSPTools</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Package Bio.FSSP=Bio.FSSP-module.html"><a title="Bio.FSSP" class="py-name" href="#" onclick="return doclink('link-1', 'FSSP', 'link-1');">FSSP</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-2', 'copy', 'link-2');">copy</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Package Bio.Align=Bio.Align-module.html"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-4', 'Align', 'link-4');">Align</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.Align.Generic=Bio.Align.Generic-module.html"><a title="Bio.Align.Generic" class="py-name" href="#" onclick="return doclink('link-5', 'Generic', 'link-5');">Generic</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'Alphabet', 'link-7');">Alphabet</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-8', 'time', 'link-8');">time</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="FSSPAlign"></a><div id="FSSPAlign-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="FSSPAlign-toggle" onclick="return toggle('FSSPAlign');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools.FSSPAlign-class.html">FSSPAlign</a><tt class="py-op">(</tt><tt class="py-base-class">Generic</tt><tt class="py-op">.</tt><tt class="py-base-class">Alignment</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FSSPAlign-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="FSSPAlign-expanded"><a name="FSSPAlign._add_numbering_table"></a><div id="FSSPAlign._add_numbering_table-def"><a name="L8"></a><tt class="py-lineno"> 8</tt> <a class="py-toggle" href="#" id="FSSPAlign._add_numbering_table-toggle" onclick="return toggle('FSSPAlign._add_numbering_table');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools.FSSPAlign-class.html#_add_numbering_table">_add_numbering_table</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">new_record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FSSPAlign._add_numbering_table-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FSSPAlign._add_numbering_table-expanded"><a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-9', 'annotations', 'link-9');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'abs2pdb'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-10', 'annotations', 'link-9');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'pdb2abs'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div></div><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="FSSPMultAlign"></a><div id="FSSPMultAlign-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="FSSPMultAlign-toggle" onclick="return toggle('FSSPMultAlign');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools.FSSPMultAlign-class.html">FSSPMultAlign</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FSSPMultAlign-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="FSSPMultAlign-expanded"><a name="FSSPMultAlign.__init__"></a><div id="FSSPMultAlign.__init__-def"><a name="L14"></a><tt class="py-lineno">14</tt> <a class="py-toggle" href="#" id="FSSPMultAlign.__init__-toggle" onclick="return toggle('FSSPMultAlign.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools.FSSPMultAlign-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FSSPMultAlign.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FSSPMultAlign.__init__-expanded"><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">abs_res</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_res</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <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>
</div></div><a name="mult_align"></a><div id="mult_align-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="mult_align-toggle" onclick="return toggle('mult_align');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools-module.html#mult_align">mult_align</a><tt class="py-op">(</tt><tt class="py-param">sum_dict</tt><tt class="py-op">,</tt><tt class="py-param">align_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="mult_align-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="mult_align-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a biopython multiple alignment instance (Bio.Align.Generic)"""</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">mult_align_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">align_dict</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-12', 'abs', 'link-12');">abs</a></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-name">pos_align_dict</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</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">mult_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-14" 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-14', 'i', 'link-14');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">align_dict</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="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-comment"># loop on positions</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">align_dict</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-15', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-16', 'i', 'link-14');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><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-17', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-comment"># loop within a position</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">mult_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">align_dict</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-18', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-19', 'i', 'link-14');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">aa</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">seq_order</tt> <tt class="py-op">=</tt> <tt class="py-name">mult_align_dict</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><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-20', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">seq_order</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-21', 'sort', 'link-21');">sort</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">fssp_align</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Align.Generic" class="py-name" href="#" onclick="return doclink('link-22', 'Generic', 'link-5');">Generic</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-23', 'Alignment', 'link-23');">Alignment</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-24', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Class Bio.Alphabet.Gapped=Bio.Alphabet.Gapped-class.html"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-25', 'Gapped', 'link-25');">Gapped</a></tt><tt class="py-op">(</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-26', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-27', 'IUPAC', 'link-27');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Variable Bio.Alphabet.IUPAC.extended_protein=Bio.Alphabet.IUPAC-module.html#extended_protein"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-28', 'extended_protein', 'link-28');">extended_protein</a></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-keyword">for</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-14');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_order</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">fssp_align</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Align.Generic.Alignment.add_sequence()=Bio.Align.Generic.Alignment-class.html#add_sequence,Method Bio.Nexus.Nexus.Nexus.add_sequence()=Bio.Nexus.Nexus.Nexus-class.html#add_sequence,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-30', 'add_sequence', 'link-30');">add_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">sum_dict</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-14');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">pdb2</tt><tt class="py-op">+</tt><tt class="py-name">sum_dict</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-14');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">chain2</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">mult_align_dict</tt><tt class="py-op">[</tt><tt id="link-33" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-33', 'i', 'link-14');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"># fssp_align._add_numbering_table()</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">fssp_align</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment"># Several routines used to extract information from FSSP sections</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># filter:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># filters a passed summary section and alignment section according to a numeric</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># attribute in the summary section. Returns new summary and alignment sections</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># For example, to filter in only those records which have a zscore greater than</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 4.0 and lesser than 7.5:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># new_sum, new_align = filter(sum, align, 'zscore', 4, 7.5)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Warning: this function really slows down when filtering large FSSP files.</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The reason is the use of copy.deepcopy() to copy align_dict into</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"># new_align_dict. I have to figure out something better.</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Took me ~160 seconds for the largest FSSP file (1reqA.fssp)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="filter"></a><div id="filter-def"><a name="L54"></a><tt class="py-lineno">54</tt> <a class="py-toggle" href="#" id="filter-toggle" onclick="return toggle('filter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools-module.html#filter">filter</a><tt class="py-op">(</tt><tt class="py-param">sum_dict</tt><tt class="py-op">,</tt><tt class="py-param">align_dict</tt><tt class="py-op">,</tt><tt class="py-param">filter_attribute</tt><tt class="py-op">,</tt><tt class="py-param">low_bound</tt><tt class="py-op">,</tt> <tt class="py-param">high_bound</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="filter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="filter-expanded"><a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-docstring">"""filters a passed summary section and alignment section according to a numeric</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"><tt class="py-docstring"> attribute in the summary section. Returns new summary and alignment sections"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">new_sum_dict</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.FSSP" class="py-name" href="#" onclick="return doclink('link-34', 'FSSP', 'link-1');">FSSP</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Class Bio.FSSP.FSSPSumDict=Bio.FSSP.FSSPSumDict-class.html"><a title="Bio.FSSP.FSSPSumDict" class="py-name" href="#" onclick="return doclink('link-35', 'FSSPSumDict', 'link-35');">FSSPSumDict</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-36', 'copy', 'link-2');">copy</a></tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">align_dict</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"># for i in align_dict.keys():</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># new_align_dict[i] = copy.copy(align_dict[i])</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># new_align_dict = copy.copy(align_dict)</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">prot_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sum_dict</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><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-37', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">attr_value</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">filter_attribute</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">attr_value</tt> <tt class="py-op">>=</tt> <tt class="py-name">low_bound</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-name">attr_value</tt> <tt class="py-op"><=</tt> <tt class="py-name">high_bound</tt><tt class="py-op">)</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_sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</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">prot_numbers</tt> <tt class="py-op">=</tt> <tt class="py-name">new_sum_dict</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><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-38', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</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">prot_numbers</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-39', 'sort', 'link-21');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt class="py-name">abs_res_dict</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><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-40', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-41', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">prot_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prot_numbers</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-42', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</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">align_dict</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-43', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_sum_dict</tt><tt class="py-op">,</tt> <tt class="py-name">new_align_dict</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> </tt>
<a name="name_filter"></a><div id="name_filter-def"><a name="L76"></a><tt class="py-lineno">76</tt> <a class="py-toggle" href="#" id="name_filter-toggle" onclick="return toggle('name_filter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.FSSP.FSSPTools-module.html#name_filter">name_filter</a><tt class="py-op">(</tt><tt class="py-param">sum_dict</tt><tt class="py-op">,</tt> <tt class="py-param">align_dict</tt><tt class="py-op">,</tt> <tt class="py-param">name_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="name_filter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="name_filter-expanded"><a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-docstring">""" Accepts a list of names. Returns a new Summary block and Alignment block which</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"><tt class="py-docstring"> contain the info only for those names passed."""</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> <tt class="py-name">new_sum_dict</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.FSSP" class="py-name" href="#" onclick="return doclink('link-44', 'FSSP', 'link-1');">FSSP</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.FSSP.FSSPSumDict" class="py-name" href="#" onclick="return doclink('link-45', 'FSSPSumDict', 'link-35');">FSSPSumDict</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-46', 'copy', 'link-2');">copy</a></tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">align_dict</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">cur_pdb_name</tt> <tt class="py-keyword">in</tt> <tt class="py-name">name_list</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">prot_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sum_dict</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><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-47', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">pdb2</tt><tt class="py-op">+</tt><tt class="py-name">sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">chain2</tt> <tt class="py-op">==</tt> <tt class="py-name">cur_pdb_name</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">new_sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">sum_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">prot_numbers</tt> <tt class="py-op">=</tt> <tt class="py-name">new_sum_dict</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><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-48', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</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">prot_numbers</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-49', 'sort', 'link-21');">sort</a></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-keyword">for</tt> <tt class="py-name">pos_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt class="py-name">abs_res_dict</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><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-50', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-51', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">prot_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">prot_numbers</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> <tt class="py-name">new_align_dict</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-52', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</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">align_dict</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-53', 'abs', 'link-12');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">pos_num</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">pos_align_dict</tt><tt class="py-op">[</tt><tt class="py-name">prot_num</tt><tt class="py-op">]</tt> </tt>
<a name="L92"></a><tt class="py-lineno">92</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_sum_dict</tt><tt class="py-op">,</tt> <tt class="py-name">new_align_dict</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno">93</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:28:11 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
