<?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.CDD.cdd_format</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.CDD-module.html">Package CDD</a> ::
Module cdd_format
</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.CDD.cdd_format-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module cdd_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.CDD.cdd_format-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Martel based parser to read CDD formatted files.
This is a huge regular regular expression for CDD, built using
the 'regular expressiona on steroids' capabilities of Martel.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "
|
?"
[\R] means "[
]"
This helps us have endlines be consistent across platforms.
# standard library
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
</pre>
<!-- ==================== 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="upper_alpha"></a><span class="summary-name">upper_alpha</span> = <code title="Any("ABCDEFGHIJKLMNOPQRSTUVWXYZ")">Any("ABCDEFGHIJKLMNOPQRSTUVWXYZ")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="white_space"></a><span class="summary-name">white_space</span> = <code title="Any("\t ")">Any("\t ")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="eols"></a><span class="summary-name">eols</span> = <code title="'''\r
'''"><code class="variable-quote">'</code><code class="variable-string">\r\n</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 name="white_spaces"></a><span class="summary-name">white_spaces</span> = <code title="Rep(white_space)">Rep(white_space)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="summary_line"></a><span class="summary-name">summary_line</span> = <code title="Str("CD summary")+ ToEol()">Str("CD summary")+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="cd_tag"></a><span class="summary-name">cd_tag</span> = <code title="Group("cd_tag", Str("CD:"))">Group("cd_tag", Str("CD:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="description_tag"></a><span class="summary-name">description_tag</span> = <code title="Group("description_tag", Str("Description:"))">Group("description_tag", Str("Description:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="status_tag"></a><span class="summary-name">status_tag</span> = <code title="Group("status_tag", Str("CD status:"))">Group("status_tag", Str("CD status:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="source_tag"></a><span class="summary-name">source_tag</span> = <code title="Group("source_tag", Str("Source:"))">Group("source_tag", Str("Source:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="date_tag"></a><span class="summary-name">date_tag</span> = <code title="Group("date_tag", Str("Created:"))">Group("date_tag", Str("Created:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reference_tag"></a><span class="summary-name">reference_tag</span> = <code title="Group("reference_tag", Str("References:"))">Group("reference_tag", Str("References:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="taxonomy_tag"></a><span class="summary-name">taxonomy_tag</span> = <code title="Group("taxonomy_tag", Str("Taxonomy spanned:"))">Group("taxonomy_tag", Str("Taxonomy spanned:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="aligned_tag"></a><span class="summary-name">aligned_tag</span> = <code title="Group("aligned_tag", Str("Aligned sequences:"))">Group("aligned_tag", Str("Aligned sequences:"))</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.CDD.cdd_format-module.html#representative_tag" class="summary-name">representative_tag</a> = <code title="Group("representative_tag", Str("Representative:"))">Group("representative_tag", Str("Represen<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 name="range_tag"></a><span class="summary-name">range_tag</span> = <code title="Group("range_tag", Str("Aligned range:"))">Group("range_tag", Str("Aligned range:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sequence_tag"></a><span class="summary-name">sequence_tag</span> = <code title="Group("sequence_tag", Str("Sequence:"))">Group("sequence_tag", Str("Sequence:"))</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.CDD.cdd_format-module.html#has_tag" class="summary-name">has_tag</a> = <code title="Alt(cd_tag, description_tag, status_tag, source_tag, date_tag, referen\
ce_tag, taxonomy_tag, aligned_tag, representative_tag, range_tag, sequ\
ence_tag)">Alt(cd_tag, description_tag, status_tag, source_tag,<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 name="cd_key_line"></a><span class="summary-name">cd_key_line</span> = <code title="cd_tag+ white_spaces+ AnyEol()">cd_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="description_key_line"></a><span class="summary-name">description_key_line</span> = <code title="description_tag+ white_spaces+ AnyEol()">description_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="status_key_line"></a><span class="summary-name">status_key_line</span> = <code title="status_tag+ white_spaces+ AnyEol()">status_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="source_key_line"></a><span class="summary-name">source_key_line</span> = <code title="source_tag+ white_spaces+ AnyEol()">source_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="date_key_line"></a><span class="summary-name">date_key_line</span> = <code title="date_tag+ white_spaces+ AnyEol()">date_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reference_key_line"></a><span class="summary-name">reference_key_line</span> = <code title="reference_tag+ white_spaces+ AnyEol()">reference_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="taxonomy_key_line"></a><span class="summary-name">taxonomy_key_line</span> = <code title="taxonomy_tag+ white_spaces+ AnyEol()">taxonomy_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="aligned_key_line"></a><span class="summary-name">aligned_key_line</span> = <code title="aligned_tag+ white_spaces+ AnyEol()">aligned_tag+ white_spaces+ AnyEol()</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.CDD.cdd_format-module.html#representative_key_line" class="summary-name">representative_key_line</a> = <code title="representative_tag+ white_spaces+ AnyEol()">representative_tag+ white_spaces+ An<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 name="range_key_line"></a><span class="summary-name">range_key_line</span> = <code title="range_tag+ white_spaces+ AnyEol()">range_tag+ white_spaces+ AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sequence_key_line"></a><span class="summary-name">sequence_key_line</span> = <code title="sequence_tag+ white_spaces+ AnyEol()">sequence_tag+ white_spaces+ AnyEol()</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.CDD.cdd_format-module.html#cd_contents_line" class="summary-name">cd_contents_line</a> = <code title="Group("cd_contents_line", AssertNot(has_tag)+ ToEol())">Group("cd_contents_line", AssertNot(has_tag<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 name="description_contents_line"></a><span class="summary-name">description_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="status_contents_line"></a><span class="summary-name">status_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="source_contents_line"></a><span class="summary-name">source_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="date_contents_line"></a><span class="summary-name">date_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reference_contents_line"></a><span class="summary-name">reference_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="taxonomy_contents_line"></a><span class="summary-name">taxonomy_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="aligned_contents_line"></a><span class="summary-name">aligned_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="representative_contents_line"></a><span class="summary-name">representative_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="range_contents_line"></a><span class="summary-name">range_contents_line</span> = <code title="AssertNot(has_tag)+ ToEol()">AssertNot(has_tag)+ ToEol()</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.CDD.cdd_format-module.html#sequence_contents_line" class="summary-name">sequence_contents_line</a> = <code title="Group("sequence_contents_line", white_spaces+ Rep1(upper_alpha)+ white\
_spaces+ AnyEol())">Group("sequence_contents_line", white<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.CDD.cdd_format-module.html#sentinel_line" class="summary-name">sentinel_line</a> = <code title="white_spaces+ Str("Definition")+ white_spaces+ AnyEol()">white_spaces+ Str("Definition")+ white_spaces+<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 name="boiler_plate"></a><span class="summary-name">boiler_plate</span> = <code title="AssertNot(sentinel_line)+ ToEol()">AssertNot(sentinel_line)+ ToEol()</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.CDD.cdd_format-module.html#definition_line" class="summary-name">definition_line</a> = <code title="Group("definition_line", Rep(AnyBut(eols+ '['))+ Str('[CD]')+ white_sp\
aces+ AnyEol())">Group("definition_line", Rep(AnyBut(eols+ '[<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 name="pdb_id_line"></a><span class="summary-name">pdb_id_line</span> = <code title="AssertNot(definition_line)+ ToEol()">AssertNot(definition_line)+ ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="pdb_id_multiline"></a><span class="summary-name">pdb_id_multiline</span> = <code title="Group("pdb_id_multiline", Rep1(pdb_id_line))">Group("pdb_id_multiline", Rep1(pdb_id_line))</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.CDD.cdd_format-module.html#table_entry" class="summary-name">table_entry</a> = <code title="Group("table_entry", pdb_id_multiline+ definition_line)">Group("table_entry", pdb_id_multiline+ definitio<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 name="table"></a><span class="summary-name">table</span> = <code title="Group("table", Rep1(table_entry))">Group("table", Rep1(table_entry))</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.CDD.cdd_format-module.html#cd_contents_multiline" class="summary-name">cd_contents_multiline</a> = <code title="Group("cd_contents_multiline", Rep(cd_contents_line))">Group("cd_contents_multiline", Rep(cd_<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.CDD.cdd_format-module.html#description_contents_multiline" class="summary-name">description_contents_multiline</a> = <code title="Group("description_contents_multiline", Rep(description_contents_line)\
)">Group("description_contents_m<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.CDD.cdd_format-module.html#status_contents_multiline" class="summary-name">status_contents_multiline</a> = <code title="Group("status_contents_multiline", Rep(status_contents_line))">Group("status_contents_multiline",<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.CDD.cdd_format-module.html#source_contents_multiline" class="summary-name">source_contents_multiline</a> = <code title="Group("source_contents_multiline", Rep(source_contents_line))">Group("source_contents_multiline",<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.CDD.cdd_format-module.html#date_contents_multiline" class="summary-name">date_contents_multiline</a> = <code title="Group("date_contents_multiline", Rep(date_contents_line))">Group("date_contents_multiline", Rep<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.CDD.cdd_format-module.html#reference_contents_multiline" class="summary-name">reference_contents_multiline</a> = <code title="Group("reference_contents_multiline", Rep(reference_contents_line))">Group("reference_contents_multi<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.CDD.cdd_format-module.html#taxonomy_contents_multiline" class="summary-name">taxonomy_contents_multiline</a> = <code title="Group("taxonomy_contents_multiline", Rep(taxonomy_contents_line))">Group("taxonomy_contents_multili<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.CDD.cdd_format-module.html#aligned_contents_multiline" class="summary-name">aligned_contents_multiline</a> = <code title="Group("aligned_contents_multiline", Rep(aligned_contents_line))">Group("aligned_contents_multiline<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.CDD.cdd_format-module.html#representative_contents_multiline" class="summary-name">representative_contents_multiline</a> = <code title="Group("representative_contents_multiline", Rep(representative_contents\
_line))">Group("representative_cont<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.CDD.cdd_format-module.html#range_contents_multiline" class="summary-name">range_contents_multiline</a> = <code title="Group("range_contents_multiline", Rep(range_contents_line))">Group("range_contents_multiline", R<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.CDD.cdd_format-module.html#sequence_contents_multiline" class="summary-name">sequence_contents_multiline</a> = <code title="Group("sequence_contents_multiline", Rep(sequence_contents_line))">Group("sequence_contents_multili<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 name="cd_block"></a><span class="summary-name">cd_block</span> = <code title="cd_key_line+ cd_contents_multiline">cd_key_line+ cd_contents_multiline</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.CDD.cdd_format-module.html#description_block" class="summary-name">description_block</a> = <code title="description_key_line+ description_contents_multiline">description_key_line+ description_contents<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 name="status_block"></a><span class="summary-name">status_block</span> = <code title="status_key_line+ status_contents_multiline">status_key_line+ status_contents_multiline</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="source_block"></a><span class="summary-name">source_block</span> = <code title="source_key_line+ source_contents_multiline">source_key_line+ source_contents_multiline</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="date_block"></a><span class="summary-name">date_block</span> = <code title="date_key_line+ date_contents_multiline">date_key_line+ date_contents_multiline</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.CDD.cdd_format-module.html#reference_block" class="summary-name">reference_block</a> = <code title="Assert(reference_tag)+ reference_key_line+ reference_contents_multilin\
e">Assert(reference_tag)+ reference_key_line+ r<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 name="taxonomy_block"></a><span class="summary-name">taxonomy_block</span> = <code title="taxonomy_key_line+ taxonomy_contents_multiline">taxonomy_key_line+ taxonomy_contents_multiline</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="aligned_block"></a><span class="summary-name">aligned_block</span> = <code title="aligned_key_line+ aligned_contents_multiline">aligned_key_line+ aligned_contents_multiline</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.CDD.cdd_format-module.html#representative_block" class="summary-name">representative_block</a> = <code title="representative_key_line+ representative_contents_multiline">representative_key_line+ representative<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 name="range_block"></a><span class="summary-name">range_block</span> = <code title="range_key_line+ range_contents_multiline">range_key_line+ range_contents_multiline</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sequence_block"></a><span class="summary-name">sequence_block</span> = <code title="sequence_key_line+ sequence_contents_multiline">sequence_key_line+ sequence_contents_multiline</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="trailer_line"></a><span class="summary-name">trailer_line</span> = <code title="ToEol()">ToEol()</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.CDD.cdd_format-module.html#cdd_record" class="summary-name">cdd_record</a> = <code title="summary_line+ cd_block+ description_block+ status_block+ source_block+\
date_block+ Opt(reference_block)+ taxonomy_block+ aligned_block+ repr\
esentative_block+ range_block+ sequence_block+ Rep(boiler_plate)+ sent\
inel_line+ table">summary_line+ cd_block+ description_block+ status<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="representative_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">representative_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("representative_tag", Str("Representative:"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="has_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">has_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Alt(cd_tag, description_tag, status_tag, source_tag, date_tag, referen<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ce_tag, taxonomy_tag, aligned_tag, representative_tag, range_tag, sequ<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ence_tag)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="representative_key_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">representative_key_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
representative_tag+ white_spaces+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="cd_contents_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">cd_contents_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("cd_contents_line", AssertNot(has_tag)+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence_contents_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence_contents_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("sequence_contents_line", white_spaces+ Rep1(upper_alpha)+ white<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_spaces+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sentinel_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sentinel_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
white_spaces+ Str("Definition")+ white_spaces+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="definition_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">definition_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("definition_line", Rep(AnyBut(eols+ '['))+ Str('[CD]')+ white_sp<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
aces+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="table_entry"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">table_entry</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("table_entry", pdb_id_multiline+ definition_line)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="cd_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">cd_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("cd_contents_multiline", Rep(cd_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="description_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">description_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("description_contents_multiline", Rep(description_contents_line)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="status_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">status_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("status_contents_multiline", Rep(status_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="source_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">source_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("source_contents_multiline", Rep(source_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="date_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">date_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("date_contents_multiline", Rep(date_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reference_contents_multiline", Rep(reference_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="taxonomy_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">taxonomy_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("taxonomy_contents_multiline", Rep(taxonomy_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="aligned_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">aligned_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("aligned_contents_multiline", Rep(aligned_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="representative_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">representative_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("representative_contents_multiline", Rep(representative_contents<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="range_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">range_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("range_contents_multiline", Rep(range_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence_contents_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence_contents_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("sequence_contents_multiline", Rep(sequence_contents_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="description_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">description_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
description_key_line+ description_contents_multiline
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Assert(reference_tag)+ reference_key_line+ reference_contents_multilin<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="representative_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">representative_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
representative_key_line+ representative_contents_multiline
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="cdd_record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">cdd_record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
summary_line+ cd_block+ description_block+ status_block+ source_block+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
date_block+ Opt(reference_block)+ taxonomy_block+ aligned_block+ repr<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
esentative_block+ range_block+ sequence_block+ Rep(boiler_plate)+ sent<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
inel_line+ table
</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 09:26:23 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>
