<?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.Prosite.Pattern</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.Prosite-module.html">Package Prosite</a> :: Module Pattern </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.Prosite.Pattern-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Pattern</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html">source code</a></span></p> <!-- ==================== 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.Prosite.Pattern.PrositeAlphabet-class.html" class="summary-name">PrositeAlphabet</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.Prosite.Pattern.Prosite-class.html" class="summary-name">Prosite</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.Prosite.Pattern.PrositeTerm-class.html" class="summary-name">PrositeTerm</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.Prosite.Pattern.PrositeMatch-class.html" class="summary-name">PrositeMatch</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="prosite_to_re"></a><span class="summary-sig-name">prosite_to_re</span>(<span class="summary-sig-arg">pattern</span>)</span><br /> convert a valid Prosite pattern into an re string</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#prosite_to_re">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="prosite_to_grouped_re"></a><span class="summary-sig-name">prosite_to_grouped_re</span>(<span class="summary-sig-arg">pattern</span>)</span><br /> convert a valid Prosite pattern into an re with groups for each term</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#prosite_to_grouped_re">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="compile"></a><span class="summary-sig-name">compile</span>(<span class="summary-sig-arg">pattern</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#compile">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="pattern_mapping"></a><span class="summary-sig-name">pattern_mapping</span>(<span class="summary-sig-arg">prosite</span>, <span class="summary-sig-arg">mapping</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#pattern_mapping">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="find_terms"></a><span class="summary-sig-name">find_terms</span>(<span class="summary-sig-arg">pattern</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#find_terms">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="verify_pattern"></a><span class="summary-sig-name">verify_pattern</span>(<span class="summary-sig-arg">pattern</span>)</span><br /> returns 1 if the Prosite pattern is syntactically correct, else 0</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#verify_pattern">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 name="_verify_test"></a><span class="summary-sig-name">_verify_test</span>(<span class="summary-sig-arg">infile</span>)</span><br /> verify the patterns from a Prosite file handle</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Prosite.Pattern-pysrc.html#_verify_test">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 class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Prosite.Pattern-module.html#_prosite_trans" class="summary-name" onclick="show_private();">_prosite_trans</a> = <code title="'''\x00\x01\x02\x03\x04\x05\x06\x07\x08\t \x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\ \x1d\x1e\x1f !"#$%&\'{}*+,-./0123456789:;^=$?@ABCDEFGHIJKLMNOPQRSTUVW.\ YZ[\\]^_`ABCDEFGHIJKLMNOPQRSTUVW.YZ{|]~\x7f\x80\x81\x82\x83\x84\x85\x8\ 6\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\\ x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa\ 9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\\ xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xc\ ..."><code class="variable-quote">'</code><code class="variable-string">\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b</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="prosite_alphabet"></a><span class="summary-name">prosite_alphabet</span> = <code title="PrositeAlphabet()">PrositeAlphabet()</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.Prosite.Pattern-module.html#prosite_term_re" class="summary-name">prosite_term_re</a> = <code title="re.compile(r'(?x)(?:([ABCDEFGHIKLMNPQRSTVWXYZx])|\[(<?)([ABCDEFGHIKLMN\ PQRSTVWXYZ]+)(>?)\]|\{([ABCDEFGHIKLMNPQRSTVWXYZ]+)\})(?:\((\d+)(,\d+)?\ \))?$')">re.compile(r'<code class="re-flags">(?x)</code><code class="re-group">(?:</code><code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXY<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.Prosite.Pattern-module.html#prosite_re" class="summary-name">prosite_re</a> = <code title="re.compile(r'(?x)^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(\[<?[ABCDEFGHIKLMNPQR\ STVWXYZ]+>?\])|\{[ABCDEFGHIKLMNPQRSTVWXYZ]+\})(\(\d+(,\d+)?\))?(-([ABC\ DEFGHIKLMNPQRSTVWXYZx]|\[[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\]|\{[ABCDEFGHIKL\ MNPQRSTVWXYZ]+\})(\(\d+(,\d+)?\))?)*>?\.$')">re.compile(r'<code class="re-flags">(?x)</code>^<<code class="re-op">?</code><code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZx<code class="re-group">]</code><code class="re-op">|</code><code class="re-group">(</code><code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_prosite_trans"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_prosite_trans</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-quote">'''</code><code class="variable-string">\x00\x01\x02\x03\x04\x05\x06\x07\x08\t</code> <code class="variable-string">\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">\x1d\x1e\x1f !"#$%&\'{}*+,-./0123456789:;^=$?@ABCDEFGHIJKLMNOPQRSTUVW.</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">YZ[\\]^_`ABCDEFGHIJKLMNOPQRSTUVW.YZ{|]~\x7f\x80\x81\x82\x83\x84\x85\x8</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">6\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-string">xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xc</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="prosite_term_re"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">prosite_term_re</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'<code class="re-flags">(?x)</code><code class="re-group">(?:</code><code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZx<code class="re-group">]</code><code class="re-group">)</code><code class="re-op">|</code>\[<code class="re-group">(</code><<code class="re-op">?</code><code class="re-group">)</code><code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMN<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> PQRSTVWXYZ<code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code><code class="re-group">(</code>><code class="re-op">?</code><code class="re-group">)</code>\]<code class="re-op">|</code>\{<code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZ<code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code>\}<code class="re-group">)</code><code class="re-group">(?:</code>\(<code class="re-group">(</code>\d<code class="re-op">+</code><code class="re-group">)</code><code class="re-group">(</code>,\d<code class="re-op">+</code><code class="re-group">)</code><code class="re-op">?</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> \)<code class="re-group">)</code><code class="re-op">?</code>$') </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="prosite_re"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">prosite_re</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'<code class="re-flags">(?x)</code>^<<code class="re-op">?</code><code class="re-group">(</code><code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZx<code class="re-group">]</code><code class="re-op">|</code><code class="re-group">(</code>\[<<code class="re-op">?</code><code class="re-group">[</code>ABCDEFGHIKLMNPQR<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> STVWXYZ<code class="re-group">]</code><code class="re-op">+</code>><code class="re-op">?</code>\]<code class="re-group">)</code><code class="re-op">|</code>\{<code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZ<code class="re-group">]</code><code class="re-op">+</code>\}<code class="re-group">)</code><code class="re-group">(</code>\(\d<code class="re-op">+</code><code class="re-group">(</code>,\d<code class="re-op">+</code><code class="re-group">)</code><code class="re-op">?</code>\)<code class="re-group">)</code><code class="re-op">?</code><code class="re-group">(</code>-<code class="re-group">(</code><code class="re-group">[</code>ABC<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> DEFGHIKLMNPQRSTVWXYZx<code class="re-group">]</code><code class="re-op">|</code>\[<code class="re-group">[</code>ABCDEFGHIKLMNPQRSTVWXYZ<code class="re-group">]</code><code class="re-op">+</code>><code class="re-op">?</code>\]<code class="re-op">|</code>\{<code class="re-group">[</code>ABCDEFGHIKL<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> MNPQRSTVWXYZ<code class="re-group">]</code><code class="re-op">+</code>\}<code class="re-group">)</code><code class="re-group">(</code>\(\d<code class="re-op">+</code><code class="re-group">(</code>,\d<code class="re-op">+</code><code class="re-group">)</code><code class="re-op">?</code>\)<code class="re-group">)</code><code class="re-op">?</code><code class="re-group">)</code><code class="re-op">*</code>><code class="re-op">?</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 09:26:25 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>