<?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.Residue.Residue</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.Residue-module.html">Module Residue</a> :: Class Residue </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.Residue.Residue-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Residue</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue">source code</a></span></p> <pre class="base-tree"> <a href="Bio.PDB.Entity.Entity-class.html">Entity.Entity</a> --+ | <strong class="uidshort">Residue</strong> </pre> <hr /> <p>Represents a residue. A Residue object stores atoms.</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.Residue.Residue-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>, <span class="summary-sig-arg">resname</span>, <span class="summary-sig-arg">segid</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.__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.Residue-pysrc.html#Residue.__repr__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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.Residue.Residue-class.html#_sort" class="summary-sig-name" onclick="show_private();">_sort</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">a1</span>, <span class="summary-sig-arg">a2</span>)</span><br /> Sort the Atom objects.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue._sort">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.Residue.Residue-class.html#add" class="summary-sig-name">add</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">atom</span>)</span><br /> Add an Atom object.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.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="sort"></a><span class="summary-sig-name">sort</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.sort">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="flag_disordered"></a><span class="summary-sig-name">flag_disordered</span>(<span class="summary-sig-arg">self</span>)</span><br /> Set the disordered flag.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.flag_disordered">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="is_disordered"></a><span class="summary-sig-name">is_disordered</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return 1 if the residue contains disordered atoms.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.is_disordered">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_resname"></a><span class="summary-sig-name">get_resname</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.get_resname">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_unpacked_list"></a><span class="summary-sig-name">get_unpacked_list</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns the list of all atoms, unpack DisorderedAtoms."</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.get_unpacked_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_segid"></a><span class="summary-sig-name">get_segid</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.get_segid">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.Entity-class.html">Entity.Entity</a></code></b>: <code><a href="Bio.PDB.Entity.Entity-class.html#__getitem__">__getitem__</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#__iter__">__iter__</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#__len__">__len__</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#detach_child">detach_child</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#detach_parent">detach_parent</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_full_id">get_full_id</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_id">get_id</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_iterator">get_iterator</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_level">get_level</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_list">get_list</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#get_parent">get_parent</a></code>, <code><a href="Bio.PDB.Entity.Entity-class.html#has_id">has_id</a></code>, <code><a href="Bio.PDB.Entity.Entity-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 class="sig-arg">resname</span>, <span class="sig-arg">segid</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue.__init__">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Overrides: <a href="Bio.PDB.Entity.Entity-class.html#__init__">Entity.Entity.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="_sort"></a> <div class="private"> <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">_sort</span>(<span class="sig-arg">self</span>, <span class="sig-arg">a1</span>, <span class="sig-arg">a2</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Residue-pysrc.html#Residue._sort">source code</a></span> </td> </tr></table> <p>Sort the Atom objects.</p> <p>Atoms are sorted alphabetically according to their name, but N, CA, C, O always come first.</p> <p>Arguments: o a1, a2 - Atom objects</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="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">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.Residue-pysrc.html#Residue.add">source code</a></span> </td> </tr></table> <p>Add an Atom object.</p> <p>Checks for adding duplicate atoms, and raises a PDBConstructionException if so.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.PDB.Entity.Entity-class.html#add">Entity.Entity.add</a> </dt> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" 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