<?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.FragmentMapper'</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> ::
Module FragmentMapper'
</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.FragmentMapper%27-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module FragmentMapper'</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html">source code</a></span></p>
<p>Classify protein backbone structure according to Kolodny et al's
fragment libraries. It can be regarded as a form of objective secondary
structure classification. Only fragments of length 5 or 7 are supported
(ie. there is a 'central' residue).</p>
<p>Full reference:</p>
<p>Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein
fragments model native protein structures accurately. J Mol Biol. 2002
323(2):297-307.</p>
<p>The definition files of the fragments can be obtained from:</p>
<p><a href="http://csb.stanford.edu/~rachel/fragments/"
target="_top">http://csb.stanford.edu/~rachel/fragments/</a></p>
<p>You need these files to use this module.</p>
<p>The following example uses the library with 10 fragments of length 5.
The library files can be found in directory 'fragment_data'.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>model=structure[0]
<span class="py-prompt">>>> </span>fm=FragmentMapper(lsize=10, flength=5, dir=<span class="py-string">"fragment_data"</span>)
<span class="py-prompt">>>> </span>fm.map(model)
<span class="py-prompt">>>> </span>fragment=fm[residue]</pre>
<!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></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">Classes</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Classes"
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.FragmentMapper%27.Fragment-class.html" class="summary-name">Fragment</a><br />
Represent a polypeptide C-alpha fragment.
</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.FragmentMapper%27.FragmentMapper-class.html" class="summary-name">FragmentMapper</a><br />
Map polypeptides in a model to lists of representative fragments.
</td>
</tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></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">Functions</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Functions"
class="privatelink" onclick="toggle_private();"
>hide private</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.FragmentMapper%27-module.html#_make_fragment_list" class="summary-sig-name" onclick="show_private();">_make_fragment_list</a>(<span class="summary-sig-arg">pp</span>,
<span class="summary-sig-arg">length</span>)</span><br />
Dice up a peptide in fragments of length "length".</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_make_fragment_list">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.FragmentMapper%27-module.html#_map_fragment_list" class="summary-sig-name" onclick="show_private();">_map_fragment_list</a>(<span class="summary-sig-arg">flist</span>,
<span class="summary-sig-arg">reflist</span>)</span><br />
Map all frgaments in flist to the closest (in RMSD) fragment in
reflist.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_map_fragment_list">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.FragmentMapper%27-module.html#_read_fragments" class="summary-sig-name" onclick="show_private();">_read_fragments</a>(<span class="summary-sig-arg">size</span>,
<span class="summary-sig-arg">length</span>,
<span class="summary-sig-arg">dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span><br />
Read a fragment spec file (available from <a
href="http://csb.stanford.edu/rachel/fragments/"
target="_top">http://csb.stanford.edu/rachel/fragments/</a> and
return a list of Fragment objects.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_read_fragments">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== 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 name="Float0"></a><span class="summary-name">Float0</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="_FRAGMENT_FILE"></a><span class="summary-name">_FRAGMENT_FILE</span> = <code title="'lib_%s_z_%s.txt'"><code class="variable-quote">'</code><code class="variable-string">lib_%s_z_%s.txt</code><code class="variable-quote">'</code></code>
</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.FragmentMapper%27-module.html#standard_aa_names" class="summary-name">standard_aa_names</a> = <code title="['ALA',
'CYS',
'ASP',
'GLU',
'PHE',
'GLY',
'HIS',
'ILE',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code><code class="variable-ellipsis">...</code></code>
</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.FragmentMapper%27-module.html#to_one_letter_code" class="summary-name">to_one_letter_code</a> = <code title="{'2AS': 'D',
'3AH': 'H',
'5HP': 'E',
'ACL': 'R',
'AGM': 'R',
'AIB': 'A',
'ALA': 'A',
'ALM': 'A',
..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></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">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="_make_fragment_list"></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">_make_fragment_list</span>(<span class="sig-arg">pp</span>,
<span class="sig-arg">length</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_make_fragment_list">source code</a></span>
</td>
</tr></table>
<p>Dice up a peptide in fragments of length "length".</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>pp</code></strong> ([<a href="Bio.PDB.Residue-module.html" class="link">Residue</a>,
<a href="Bio.PDB.Residue-module.html" class="link">Residue</a>,
...]) - a list of residues (part of one peptide)</li>
<li><strong class="pname"><code>length</code></strong> (int) - fragment length</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="_map_fragment_list"></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">_map_fragment_list</span>(<span class="sig-arg">flist</span>,
<span class="sig-arg">reflist</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_map_fragment_list">source code</a></span>
</td>
</tr></table>
<p>Map all frgaments in flist to the closest (in RMSD) fragment in
reflist.</p>
<p>Returns a list of reflist indices.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>flist</code></strong> ([<a href="Bio.PDB.FragmentMapper%27.Fragment-class.html"
class="link">Fragment</a>, <a
href="Bio.PDB.FragmentMapper%27.Fragment-class.html"
class="link">Fragment</a>, ...]) - list of protein fragments</li>
<li><strong class="pname"><code>reflist</code></strong> ([<a href="Bio.PDB.FragmentMapper%27.Fragment-class.html"
class="link">Fragment</a>, <a
href="Bio.PDB.FragmentMapper%27.Fragment-class.html"
class="link">Fragment</a>, ...]) - list of reference (ie. library) fragments</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="_read_fragments"></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">_read_fragments</span>(<span class="sig-arg">size</span>,
<span class="sig-arg">length</span>,
<span class="sig-arg">dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#_read_fragments">source code</a></span>
</td>
</tr></table>
<p>Read a fragment spec file (available from <a
href="http://csb.stanford.edu/rachel/fragments/"
target="_top">http://csb.stanford.edu/rachel/fragments/</a> and return a
list of Fragment objects.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>size</code></strong> (int) - number of fragments in the library</li>
<li><strong class="pname"><code>length</code></strong> (int) - length of the fragments</li>
<li><strong class="pname"><code>dir</code></strong> (string) - directory where the fragment spec files can be found</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== 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="standard_aa_names"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">standard_aa_names</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">HIS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ILE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="to_one_letter_code"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">to_one_letter_code</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">AGM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">AIB</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ALM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</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>
