<?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</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> ::
Package PDB
</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-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package PDB</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB-pysrc.html">source code</a></span></p>
<p>Classes that deal with macromolecular crystal structures. (eg. PDB and
mmCIF parsers, a Structure class, a module to keep a local copy of the
PDB up-to-date, selective IO of PDB files, etc.). Author: Thomas
Hamelryck. Additional code by Kristian Rother.</p>
<!-- ==================== SUBMODULES ==================== -->
<a name="section-Submodules"></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">Submodules</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Submodules"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr><td class="summary">
<ul class="nomargin">
<li> <strong class="uidlink"><a href="Bio.PDB.AbstractPropertyMap-module.html">Bio.PDB.AbstractPropertyMap</a></strong>: <em class="summary">Class that maps (chain_id, residue_id) to a residue property</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Atom-module.html">Bio.PDB.Atom</a></strong>: <em class="summary">Atom class, used in Structure objects.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Chain-module.html">Bio.PDB.Chain</a></strong>: <em class="summary">Chain class, used in Structure objects.</em> </li>
<li> <strong class="uidlink">Bio.PDB.DSSP</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.DSSP%27-module.html">Bio.PDB.DSSP'</a></strong>: <em class="summary">Use the DSSP program to calculate secondary structure and
accessibility.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Dice-module.html">Bio.PDB.Dice</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Entity-module.html">Bio.PDB.Entity</a></strong>: <em class="summary">Base class for Residue, Chain, Model and Structure classes.</em> </li>
<li> <strong class="uidlink">Bio.PDB.FragmentMapper</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.FragmentMapper%27-module.html">Bio.PDB.FragmentMapper'</a></strong>: <em class="summary">Classify protein backbone structure according to Kolodny et al's
fragment libraries.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure-module.html">Bio.PDB.HSExposure</a></strong>: <em class="summary">Half sphere exposure and coordination number calculation.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIF2Dict-module.html">Bio.PDB.MMCIF2Dict</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIFParser-module.html">Bio.PDB.MMCIFParser</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Model-module.html">Bio.PDB.Model</a></strong>: <em class="summary">Model class, used in Structure objects.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.NACCESS-module.html">Bio.PDB.NACCESS</a></strong>: <em class="summary">Interface for the program NACCESS - http://wolf.bms.umist.ac.uk/naccess/</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.NeighborSearch-module.html">Bio.PDB.NeighborSearch</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBExceptions-module.html">Bio.PDB.PDBExceptions</a></strong>: <em class="summary">Some Bio.PDB specific exceptions.</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBIO</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBIO%27-module.html">Bio.PDB.PDBIO'</a></strong>: <em class="summary">Output of PDB files.</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBList</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBList%27-module.html">Bio.PDB.PDBList'</a></strong>: <em class="summary">Access the PDB over the internet (for example to download
structures).</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBParser</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBParser%27-module.html">Bio.PDB.PDBParser'</a></strong>: <em class="summary">Parser for PDB files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PSEA-module.html">Bio.PDB.PSEA</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide-module.html">Bio.PDB.Polypeptide</a></strong>: <em class="summary">Polypeptide related classes (construction and representation).</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Residue-module.html">Bio.PDB.Residue</a></strong>: <em class="summary">Residue class, used by Structure objects.</em> </li>
<li> <strong class="uidlink">Bio.PDB.ResidueDepth</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.ResidueDepth%27-module.html">Bio.PDB.ResidueDepth'</a></strong>: <em class="summary">Calculation of residue depth (using Michel Sanner's MSMS program for the
surface calculation).</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Selection-module.html">Bio.PDB.Selection</a></strong>: <em class="summary">Selection of atoms, residues, etc.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Structure-module.html">Bio.PDB.Structure</a></strong>: <em class="summary">The structure class, representing a macromolecular structure.</em> </li>
<li> <strong class="uidlink">Bio.PDB.StructureAlignment</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureAlignment%27-module.html">Bio.PDB.StructureAlignment'</a></strong>: <em class="summary">Map the residues of two structures to each other based on a FASTA
alignment file.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureBuilder-module.html">Bio.PDB.StructureBuilder</a></strong>: <em class="summary">Consumer class that builds a Structure object.</em> </li>
<li> <strong class="uidlink">Bio.PDB.Superimposer</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Superimposer%27-module.html">Bio.PDB.Superimposer'</a></strong>: <em class="summary">Superimpose two structures.</em> </li>
<li> <strong class="uidlink">Bio.PDB.Vector</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Vector%27-module.html">Bio.PDB.Vector'</a></strong>: <em class="summary">Vector class, including rotation-related functions.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.mmCIF-module.html">Bio.PDB.mmCIF</a></strong> </li>
<li> <strong class="uidlink">Bio.PDB.parse_pdb_header</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.parse_pdb_header%27-module.html">Bio.PDB.parse_pdb_header'</a></strong>: <em class="summary">Parse the header of a PDB file.</em> </li>
</ul></td></tr>
</table>
<br />
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></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">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
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">
<a href="Bio.PDB-module.html#__doc__" class="summary-name">__doc__</a> = <code title=""""
Classes that deal with macromolecular crystal structures. (eg.
PDB and mmCIF parsers, a Structure class, a module to keep
a local copy of the PDB up-to-date, selective IO of PDB files,
etc.). Author: Thomas Hamelryck. Additional code by Kristian
Rother.
""""><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></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">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__doc__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">__doc__</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
"""
Classes that deal with macromolecular crystal structures. (eg.
PDB and mmCIF parsers, a Structure class, a module to keep
a local copy of the PDB up-to-date, selective IO of PDB files,
etc.). Author: Thomas Hamelryck. Additional code by Kristian
Rother.
"""
</pre></td></tr></table>
</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 09:26:24 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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
