<?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.Atom.DisorderedAtom</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.Atom-module.html">Module Atom</a> :: Class DisorderedAtom </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.Atom.DisorderedAtom-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class DisorderedAtom</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom">source code</a></span></p> <pre class="base-tree"> <a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html">Entity.DisorderedEntityWrapper</a> --+ | <strong class="uidshort">DisorderedAtom</strong> </pre> <hr /> <p>This class contains all Atom objects that represent the same disordered atom. One of these atoms is "selected" and all method calls not caught by DisorderedAtom are forwarded to the selected Atom object. In that way, a DisorderedAtom behaves exactly like a normal Atom. By default, the selected Atom object represents the Atom object with the highest occupancy, but a different Atom object can be selected by using the disordered_select(altloc) method.</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.PDB.Atom.DisorderedAtom-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Arguments: o id - string, atom name</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom.__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="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom.__repr__">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.Atom.DisorderedAtom-class.html#disordered_add" class="summary-sig-name">disordered_add</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">atom</span>)</span><br /> Add a disordered atom.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom.disordered_add">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html">Entity.DisorderedEntityWrapper</a></code></b>: <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__getattr__">__getattr__</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__setitem__">__setitem__</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#detach_parent">detach_parent</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_get">disordered_get</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_get_id_list">disordered_get_id_list</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_get_list">disordered_get_list</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_has_id">disordered_has_id</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_select">disordered_select</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_id">get_id</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_parent">get_parent</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#is_disordered">is_disordered</a></code>, <code><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#set_parent">set_parent</a></code> </p> </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">id</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom.__init__">source code</a></span> </td> </tr></table> <p>Arguments: o id - string, atom name</p> <dl class="fields"> <dt>Overrides: <a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__init__">Entity.DisorderedEntityWrapper.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="disordered_add"></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">disordered_add</span>(<span class="sig-arg">self</span>, <span class="sig-arg">atom</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#DisorderedAtom.disordered_add">source code</a></span> </td> </tr></table> <p>Add a disordered atom.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_add">Entity.DisorderedEntityWrapper.disordered_add</a> </dt> </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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