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csb.apps.csfrag.CSfrag-class.html
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<?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>csb.apps.csfrag.CSfrag</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">
<!-- Home link -->
<th> <a
href="csb-module.html">Home</a> </th>
<!-- 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>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
>CSB v1.2.5.d7fd331</th>
</tr></table></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="csb-module.html">Package csb</a> ::
<a href="csb.apps-module.html">Package apps</a> ::
<a href="csb.apps.csfrag-module.html">Module csfrag</a> ::
Class CSfrag
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="csb.apps.csfrag.CSfrag-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class CSfrag</h1><p class="nomargin-top"><span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">CSfrag</strong>
</pre>
<hr />
<!-- ==================== 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 align="left" colspan="2" class="table-header">
<span class="table-header">Instance Methods</span></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="csb.apps.csfrag.CSfrag-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">query</span>,
<span class="summary-sig-arg">cstable</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">window</span>=<span class="summary-sig-default">8</span>,
<span class="summary-sig-arg">logger</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><a href="csb.bio.fragments.rosetta.RosettaFragmentMap-class.html"
class="link">RosettaFragmentMap</a></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="build_filtered_map"></a><span class="summary-sig-name">build_filtered_map</span>(<span class="summary-sig-arg">self</span>)</span><br />
Build a filtered fragset of centroids.</td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.build_filtered_map">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><a href="csb.bio.fragments.rosetta.RosettaFragmentMap-class.html"
class="link">RosettaFragmentMap</a></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="build_fragment_map"></a><span class="summary-sig-name">build_fragment_map</span>(<span class="summary-sig-arg">self</span>)</span><br />
Build a full Rosetta fragset.</td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.build_fragment_map">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">tuple of <a href="csb.bio.fragments.ChemShiftAssignment-class.html"
class="link">ChemShiftAssignment</a>s</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="csb.apps.csfrag.CSfrag-class.html#extract_fragments" class="summary-sig-name">extract_fragments</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">top</span>=<span class="summary-sig-default">25</span>,
<span class="summary-sig-arg">cpu</span>=<span class="summary-sig-default">2</span>)</span><br />
Extract fragments with matching chemical shifts using a sliding
window.</td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.extract_fragments">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="log"></a><span class="summary-sig-name">log</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">*a</span>,
<span class="summary-sig-arg">**ka</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.log">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Properties</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="csb.apps.csfrag.CSfrag-class.html#database" class="summary-name">database</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="csb.apps.csfrag.CSfrag-class.html#query" class="summary-name">query</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="csb.apps.csfrag.CSfrag-class.html#window" class="summary-name">window</a>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</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 align="left" colspan="2" class="table-header">
<span class="table-header">Method Details</span></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">query</span>,
<span class="sig-arg">cstable</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">window</span>=<span class="sig-default">8</span>,
<span class="sig-arg">logger</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>query</code></strong> (str) - query FASTA sequence path and file name</li>
<li><strong class="pname"><code>cstable</code></strong> (str) - file, containing the table of assigned experimental chemical
shifts</li>
<li><strong class="pname"><code>database</code></strong> (str) - path to the PDBS25 directory</li>
<li><strong class="pname"><code>logger</code></strong> (<a href="csb.apps.Application-class.html"
class="link">Application</a>) - logging client (needs to have a <code>log</code> method)</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="extract_fragments"></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">extract_fragments</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">top</span>=<span class="sig-default">25</span>,
<span class="sig-arg">cpu</span>=<span class="sig-default">2</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="csb.apps.csfrag-pysrc.html#CSfrag.extract_fragments">source code</a></span>
</td>
</tr></table>
<p>Extract fragments with matching chemical shifts using a sliding
window.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>top</code></strong> (int) - <a href="csb.apps.csfrag.MatchTable-class.html"
class="link">MatchTable</a> capacity per starting position</li>
<li><strong class="pname"><code>cpu</code></strong> (int) - degree of parallelism</li>
</ul></dd>
<dt>Returns: tuple of <a href="csb.bio.fragments.ChemShiftAssignment-class.html"
class="link">ChemShiftAssignment</a>s</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Property Details</span></td>
</tr>
</table>
<a name="database"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">database</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.database(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.database(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.query(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="window"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">window</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.window(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.window(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<br />
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