<?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.dbdefs.prodoc</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.dbdefs-module.html">Package dbdefs</a> :: Module prodoc </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.dbdefs.prodoc-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.dbdefs.prodoc-module.html">Module Bio.dbdefs.prodoc</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 2002 by Jeffrey Chang. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt 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.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.DBRegistry=Bio.config.DBRegistry-module.html,Class Bio.config.DBRegistry.DBRegistry=Bio.config.DBRegistry.DBRegistry-class.html"><a title="Bio.config.DBRegistry Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'DBRegistry', 'link-2');">DBRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.DBRegistry.CGIDB=Bio.config.DBRegistry.CGIDB-class.html"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-3', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.DBRegistry.DBGroup=Bio.config.DBRegistry.DBGroup-class.html"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-4', 'DBGroup', 'link-4');">DBGroup</a></tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.dbdefs.prodoc.prodoc_expasy_cgi=Bio.dbdefs.prodoc-module.html#prodoc_expasy_cgi"><a title="Bio.dbdefs.prodoc.prodoc_expasy_cgi" class="py-name" href="#" onclick="return doclink('link-5', 'prodoc_expasy_cgi', 'link-5');">prodoc_expasy_cgi</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-6', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">(</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt id="link-7" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"prodoc-expasy-cgi"</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">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Retrieve a prodoc entry by ID"</tt><tt class="py-op">,</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-name">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://us.expasy.org/cgi-bin/get-prosite-raw.pl'</tt><tt class="py-op">,</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt id="link-8" 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-8', 'key', 'link-8');">key</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt id="link-9" class="py-name" targets="Module Bio.dbdefs.prodoc=Bio.dbdefs.prodoc-module.html,Variable Bio.dbdefs.prodoc.prodoc=Bio.dbdefs.prodoc-module.html#prodoc"><a title="Bio.dbdefs.prodoc Bio.dbdefs.prodoc.prodoc" class="py-name" href="#" onclick="return doclink('link-9', 'prodoc', 'link-9');">prodoc</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-10', 'DBGroup', 'link-4');">DBGroup</a></tt><tt class="py-op">(</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"prodoc"</tt><tt class="py-op">,</tt> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">behavior</tt> <tt class="py-op">=</tt> <tt class="py-string">"serial"</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt id="link-12" class="py-name"><a title="Bio.dbdefs.prodoc Bio.dbdefs.prodoc.prodoc" class="py-name" href="#" onclick="return doclink('link-12', 'prodoc', 'link-9');">prodoc</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add Bio.EUtils.POM.ElementNode.add Bio.GFF.easy.Location.add Bio.Graphics.BasicChromosome._ChromosomeComponent.add Bio.LogisticRegression.add Bio.MarkovModel.add Bio.MaxEntropy.add Bio.NaiveBayes.add Bio.Nexus.Nexus.StepMatrix.add Bio.Nexus.Nodes.Chain.add Bio.PDB.Entity.Entity.add Bio.PDB.Residue.DisorderedResidue.add Bio.PDB.Residue.Residue.add Bio.Pathway.Rep.HashSet.HashSet.add Bio.Restriction.Restriction.RestrictionBatch.add Bio.Statistics.lowess.add Bio.config.FormatRegistry.FormatGroup.add Bio.config.Registry.RegisterableGroup.add Bio.distance.add Bio.kNN.add Martel.Dispatch.MulticallEnd.add Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-13', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.dbdefs.prodoc.prodoc_expasy_cgi" class="py-name" href="#" onclick="return doclink('link-14', 'prodoc_expasy_cgi', 'link-5');">prodoc_expasy_cgi</a></tt><tt class="py-op">)</tt> </tt> <a name="L22"></a><tt class="py-lineno">22</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 09:26:54 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. 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