<?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.PDB.Entity.Entity</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.PDB-module.html">Package PDB</a> :: <a href="Bio.PDB.Entity-module.html">Module Entity</a> :: Class Entity </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.PDB.Entity.Entity-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Entity</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity">source code</a></span></p> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.PDB.Chain.Chain-class.html">Chain.Chain</a></li><li>, <a href="Bio.PDB.Model.Model-class.html">Model.Model</a></li><li>, <a href="Bio.PDB.Structure.Structure-class.html">Structure.Structure</a></li><li>, <a href="Bio.PDB.Residue.Residue-class.html">Residue.Residue</a></li> </ul> </dd></dl> <hr /> <p>Basic container object. Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup.</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 name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Return the child with given id.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__getitem__">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="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__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="__iter__"></a><span class="summary-sig-name">__iter__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Iterate over children.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__iter__">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="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return the number of children.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__len__">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="add"></a><span class="summary-sig-name">add</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">entity</span>)</span><br /> Add a child to the Entity.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.add">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="detach_child"></a><span class="summary-sig-name">detach_child</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Remove a child.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.detach_child">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="detach_parent"></a><span class="summary-sig-name">detach_parent</span>(<span class="summary-sig-arg">self</span>)</span><br /> Detach the parent.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.detach_parent">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.PDB.Entity.Entity-class.html#get_full_id" class="summary-sig-name">get_full_id</a>(<span class="summary-sig-arg">self</span>)</span><br /> Return the full id.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_full_id">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="get_id"></a><span class="summary-sig-name">get_id</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return the id.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_id">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="get_iterator"></a><span class="summary-sig-name">get_iterator</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return iterator over children.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_iterator">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.PDB.Entity.Entity-class.html#get_level" class="summary-sig-name">get_level</a>(<span class="summary-sig-arg">self</span>)</span><br /> Return level in hierarchy.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_level">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="get_list"></a><span class="summary-sig-name">get_list</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return a copy of the list of children.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_list">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="get_parent"></a><span class="summary-sig-name">get_parent</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return the parent Entity object.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_parent">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="has_id"></a><span class="summary-sig-name">has_id</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Return 1 if a child with given id exists, otherwise 0.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.has_id">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="set_parent"></a><span class="summary-sig-name">set_parent</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">entity</span>)</span><br /> Set the parent Entity object.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.set_parent">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="get_full_id"></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">get_full_id</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_full_id">source code</a></span> </td> </tr></table> <p>Return the full id.</p> <p>The full id is a tuple containing all id's starting from the top object (Structure) down to the current object. A full id for a Residue object e.g. is something like:</p> <p>("1abc", 0, "A", (" ", 10, "A"))</p> <p>This corresponds to:</p> <p>Structure with id "1abc" Model with id 0 Chain with id "A" Residue with id (" ", 10, "A")</p> <p>The Residue id indicates that the residue is not a hetero-residue (or a water) beacuse it has a blanc hetero field, that its sequence identifier is 10 and its insertion code "A".</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="get_level"></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">get_level</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_level">source code</a></span> </td> </tr></table> <p>Return level in hierarchy.</p> <p>A - atom R - residue C - chain M - model S - structure</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 09:26:36 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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