<?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.SCOP.Scop</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.SCOP-module.html">Package SCOP</a> :: Class Scop </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.SCOP.Scop-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Scop</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop">source code</a></span></p> <p>The entire SCOP hierarchy.</p> <p>root -- The root node of the hierarchy</p> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SCOP.Scop-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">cla_handle</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">des_handle</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">hie_handle</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">dir_path</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">db_handle</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">version</span>=<span class="summary-sig-default">None</span>)</span><br /> Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getRoot"></a><span class="summary-sig-name">getRoot</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getRoot">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getDomainBySid"></a><span class="summary-sig-name">getDomainBySid</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sid</span>)</span><br /> Return a domain from its sid</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getDomainBySid">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getNodeBySunid"></a><span class="summary-sig-name">getNodeBySunid</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sunid</span>)</span><br /> Return a node from its sunid</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getNodeBySunid">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getDomains"></a><span class="summary-sig-name">getDomains</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns an ordered tuple of all SCOP Domains</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getDomains">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_hie"></a><span class="summary-sig-name">write_hie</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Build an HIE SCOP parsable file from this object</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_hie">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_des"></a><span class="summary-sig-name">write_des</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Build a DES SCOP parsable file from this object</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_des">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_cla"></a><span class="summary-sig-name">write_cla</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Build a CLA SCOP parsable file from this object</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_cla">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getDomainFromSQL"></a><span class="summary-sig-name">getDomainFromSQL</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sunid</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">sid</span>=<span class="summary-sig-default">None</span>)</span><br /> Load a node from the SQL backend using sunid or sid</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getDomainFromSQL">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="getAscendentFromSQL"></a><span class="summary-sig-name">getAscendentFromSQL</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>, <span class="summary-sig-arg">type</span>)</span><br /> Get ascendents using SQL backend</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getAscendentFromSQL">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SCOP.Scop-class.html#getDescendentsFromSQL" class="summary-sig-name">getDescendentsFromSQL</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>, <span class="summary-sig-arg">type</span>)</span><br /> Get descendents of a node using the database backend.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getDescendentsFromSQL">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_hie_sql"></a><span class="summary-sig-name">write_hie_sql</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Write HIE data to SQL database</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_hie_sql">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_cla_sql"></a><span class="summary-sig-name">write_cla_sql</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Write CLA data to SQL database</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_cla_sql">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write_des_sql"></a><span class="summary-sig-name">write_des_sql</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">handle</span>)</span><br /> Write DES data to SQL database</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.write_des_sql">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="__init__"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">cla_handle</span>=<span class="sig-default">None</span>, <span class="sig-arg">des_handle</span>=<span class="sig-default">None</span>, <span class="sig-arg">hie_handle</span>=<span class="sig-default">None</span>, <span class="sig-arg">dir_path</span>=<span class="sig-default">None</span>, <span class="sig-arg">db_handle</span>=<span class="sig-default">None</span>, <span class="sig-arg">version</span>=<span class="sig-default">None</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.__init__">source code</a></span> </td> </tr></table> <p>Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.</p> <p>If no file handles are given, then a Scop object with a single empty root node is returned.</p> <p>If a directory and version are given (with dir_path=.., version=...) or file handles for each file, the whole scop tree will be built in memory.</p> <p>If a MySQLdb database handle is given, the tree will be built as needed, minimising construction times. To build the SQL database to the methods write_xxx_sql to create the tables.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="getDescendentsFromSQL"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">getDescendentsFromSQL</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node</span>, <span class="sig-arg">type</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SCOP-pysrc.html#Scop.getDescendentsFromSQL">source code</a></span> </td> </tr></table> <p>Get descendents of a node using the database backend. This avoids repeated iteration of SQL calls and is therefore much quicker than repeatedly calling node.getChildren().</p> <dl class="fields"> </dl> </td></tr></table> </div> <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 09:26:38 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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