<?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.FSSP</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 FSSP </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.FSSP-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== PACKAGE DESCRIPTION ==================== --> <h1 class="epydoc">Package FSSP</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.FSSP-pysrc.html">source code</a></span></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.FSSP.FSSPTools-module.html">Bio.FSSP.FSSPTools</a></strong> </li> <li> <strong class="uidlink"><a href="Bio.FSSP.fssp_rec-module.html">Bio.FSSP.fssp_rec</a></strong> </li> </ul></td></tr> </table> <br /> <!-- ==================== 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.FSSP.FSSPHeader-class.html" class="summary-name">FSSPHeader</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.FSSP.PosAlign-class.html" class="summary-name">PosAlign</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.FSSP.FSSPSumRec-class.html" class="summary-name">FSSPSumRec</a><br /> Contains info from an FSSP summary record </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.FSSP.FSSPAlignRec-class.html" class="summary-name">FSSPAlignRec</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.FSSP.FSSPAlignDict-class.html" class="summary-name">FSSPAlignDict</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.FSSP.FSSPSumDict-class.html" class="summary-name">FSSPSumDict</a> </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> <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="read_fssp"></a><span class="summary-sig-name">read_fssp</span>(<span class="summary-sig-arg">fssp_handle</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.FSSP-pysrc.html#read_fssp">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 href="Bio.FSSP-module.html#header_records" class="summary-name">header_records</a> = <code title="{'author': re.compile(r'^AUTHOR'), 'compnd': re.compile(r'^COMPND'), 'database': re.compile(r'^DATABASE'), 'header': re.compile(r'^HEADER'), 'nalign': re.compile(r'^NALIGN'), 'pdbid': re.compile(r'^PDBID'), 'seqlength': re.compile(r'^SEQLENGTH'), 'source': re.compile(r'^SOURCE')}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">author</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^AUTHOR')<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">compnd</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 name="summary_title"></a><span class="summary-name">summary_title</span> = <code title="re.compile(r'## +SUMMARY')">re.compile(r'## <code class="re-op">+</code>SUMMARY')</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_rec"></a><span class="summary-name">summary_rec</span> = <code title="re.compile(r' *[0-9]+: +[1-9][0-9a-z]{3}')">re.compile(r' <code class="re-op">*</code><code class="re-group">[</code>0<code class="re-op">-</code>9<code class="re-group">]</code><code class="re-op">+</code>: <code class="re-op">+</code><code class="re-group">[</code>1<code class="re-op">-</code>9<code class="re-group">]</code><code class="re-group">[</code>0<code class="re-op">-</code>9a<code class="re-op">-</code>z<code class="re-group">]</code><code class="re-op">{3}</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="alignments_title"></a><span class="summary-name">alignments_title</span> = <code title="re.compile(r'## +ALIGNMENTS')">re.compile(r'## <code class="re-op">+</code>ALIGNMENTS')</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="alignments_rec"></a><span class="summary-name">alignments_rec</span> = <code title="re.compile(r' *[0-9]+ +-?[0-9]+')">re.compile(r' <code class="re-op">*</code><code class="re-group">[</code>0<code class="re-op">-</code>9<code class="re-group">]</code><code class="re-op">+</code> <code class="re-op">+</code>-<code class="re-op">?</code><code class="re-group">[</code>0<code class="re-op">-</code>9<code class="re-group">]</code><code class="re-op">+</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="equiv_title"></a><span class="summary-name">equiv_title</span> = <code title="re.compile(r'## +EQUIVALENCES')">re.compile(r'## <code class="re-op">+</code>EQUIVALENCES')</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="header_records"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">header_records</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">author</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^AUTHOR')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">compnd</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^COMPND')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">database</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^DATABASE')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">header</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^HEADER')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">nalign</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^NALIGN')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">pdbid</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^PDBID')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">seqlength</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^SEQLENGTH')<code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">source</code><code class="variable-quote">'</code><code class="variable-op">: </code>re.compile(r'^SOURCE')<code class="variable-group">}</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" 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