<?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.Polypeptide._PPBuilder</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.Polypeptide-module.html">Module Polypeptide</a> :: Class _PPBuilder </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.Polypeptide._PPBuilder-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class _PPBuilder</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder">source code</a></span></p> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.PDB.Polypeptide.CaPPBuilder-class.html">CaPPBuilder</a></li><li>, <a href="Bio.PDB.Polypeptide.PPBuilder-class.html">PPBuilder</a></li> </ul> </dd></dl> <hr /> <p>Base class to extract polypeptides. It checks if two consecutive residues in a chain are connected. The connectivity test is implemented by a subclass.</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.Polypeptide._PPBuilder-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">radius</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder.__init__">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 name="_accept"></a><span class="summary-sig-name">_accept</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">residue</span>)</span><br /> Check if the residue is an amino acid.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder._accept">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.Polypeptide._PPBuilder-class.html#build_peptides" class="summary-sig-name">build_peptides</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">entity</span>, <span class="summary-sig-arg">aa_only</span>=<span class="summary-sig-default">1</span>)</span><br /> Build and return a list of Polypeptide objects.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder.build_peptides">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">radius</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder.__init__">source code</a></span> </td> </tr></table> <dl class="fields"> <dt>Parameters:</dt> <dd><ul class="nomargin-top"> <li><strong class="pname"><code>radius</code></strong> (float) - distance</li> </ul></dd> </dl> </td></tr></table> </div> <a name="build_peptides"></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">build_peptides</span>(<span class="sig-arg">self</span>, <span class="sig-arg">entity</span>, <span class="sig-arg">aa_only</span>=<span class="sig-default">1</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Polypeptide-pysrc.html#_PPBuilder.build_peptides">source code</a></span> </td> </tr></table> <p>Build and return a list of Polypeptide objects.</p> <dl class="fields"> <dt>Parameters:</dt> <dd><ul class="nomargin-top"> <li><strong class="pname"><code>entity</code></strong> (<a href="Bio.PDB.Structure-module.html" class="link">Structure</a>, <a href="Bio.PDB.Model-module.html" class="link">Model</a> or <a href="Bio.PDB.Chain-module.html" class="link">Chain</a>) - polypeptides are searched for in this object</li> <li><strong class="pname"><code>aa_only</code></strong> (int) - if 1, the residue needs to be a standard AA</li> </ul></dd> </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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