<?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.Restriction.Restriction.Defined</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.Restriction-module.html">Package Restriction</a> :: <a href="Bio.Restriction.Restriction-module.html">Module Restriction</a> :: Class Defined </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.Restriction.Restriction.Defined-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== TYPE DESCRIPTION ==================== --> <h1 class="epydoc">Type Defined</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined">source code</a></span></p> <pre class="base-tree"> object --+ | type --+ | <a href="Bio.Restriction.Restriction.RestrictionType-class.html">RestrictionType</a> --+ | <a href="Bio.Restriction.Restriction.AbstractCut-class.html">AbstractCut</a> --+ | <strong class="uidshort">Defined</strong> </pre> <hr /> <pre class="literalblock"> Implement the methods specific to the enzymes for which the overhang and the cut are not variable. Typical example : EcoRI -> G^AATT_C The overhang will always be AATT Notes : Blunt enzymes are always defined. even if there site is GGATCCNNN^_N There overhang is always the same : blunt! Internal use only. Not meant to be instantiated. </pre> <!-- ==================== 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 colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html">RestrictionType</a></code></b>: <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__add__">__add__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__div__">__div__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__eq__">__eq__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__floordiv__">__floordiv__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__ge__">__ge__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__gt__">__gt__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__init__">__init__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__le__">__le__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__len__">__len__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__lt__">__lt__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__mod__">__mod__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__ne__">__ne__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rdiv__">__rdiv__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__repr__">__repr__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rfloordiv__">__rfloordiv__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rshift__">__rshift__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__rtruediv__">__rtruediv__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__str__">__str__</a></code>, <code><a href="Bio.Restriction.Restriction.RestrictionType-class.html#__truediv__">__truediv__</a></code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>type</code></b>: <code>__call__</code>, <code>__cmp__</code>, <code>__delattr__</code>, <code>__getattribute__</code>, <code>__hash__</code>, <code>__new__</code>, <code>__setattr__</code>, <code>__subclasses__</code>, <code>mro</code> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__reduce__</code>, <code>__reduce_ex__</code> </p> </td> </tr> </table> <!-- ==================== CLASS METHODS ==================== --> <a name="section-ClassMethods"></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">Class Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassMethods" 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">list</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#_drop" class="summary-sig-name" onclick="show_private();">_drop</a>(<span class="summary-sig-arg">RE</span>)</span><br /> for internal use only.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined._drop">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">bool</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#is_defined" class="summary-sig-name">is_defined</a>(<span class="summary-sig-arg">RE</span>)</span><br /> True if the sequence recognised and cut is constant, i.e.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_defined">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">bool</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#is_ambiguous" class="summary-sig-name">is_ambiguous</a>(<span class="summary-sig-arg">RE</span>)</span><br /> True if the sequence recognised and cut is ambiguous, i.e.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_ambiguous">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">bool</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#is_unknown" class="summary-sig-name">is_unknown</a>(<span class="summary-sig-arg">RE</span>)</span><br /> True if the sequence is unknown, i.e.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_unknown">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type">str</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#elucidate" class="summary-sig-name">elucidate</a>(<span class="summary-sig-arg">RE</span>)</span><br /> return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.elucidate">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">bool</span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Defined-class.html#_mod2" class="summary-sig-name" onclick="show_private();">_mod2</a>(<span class="summary-sig-arg">RE</span>, <span class="summary-sig-arg">other</span>)</span><br /> for internal use only</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined._mod2">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html">AbstractCut</a></code></b>: <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#all_suppliers">all_suppliers</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#equischizomers">equischizomers</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#frequency">frequency</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_equischizomer">is_equischizomer</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_isoschizomer">is_isoschizomer</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#is_neoschizomer">is_neoschizomer</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#isoschizomers">isoschizomers</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#neoschizomers">neoschizomers</a></code>, <code><a href="Bio.Restriction.Restriction.AbstractCut-class.html#search">search</a></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 colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Properties</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Properties" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>type</code></b>: <code>__base__</code>, <code>__bases__</code>, <code>__basicsize__</code>, <code>__dictoffset__</code>, <code>__flags__</code>, <code>__itemsize__</code>, <code>__mro__</code>, <code>__name__</code>, <code>__weakrefoffset__</code> </p> <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 colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_drop"></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">_drop</span>(<span class="sig-arg">RE</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined._drop">source code</a></span> </td> </tr></table> <p>for internal use only.</p> <p>drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.</p> <dl class="fields"> <dt>Returns: list</dt> </dl> </td></tr></table> </div> <a name="is_defined"></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">is_defined</span>(<span class="sig-arg">RE</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_defined">source code</a></span> </td> </tr></table> <pre class="literalblock"> True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown() </pre> <dl class="fields"> <dt>Returns: bool</dt> </dl> </td></tr></table> </div> <a name="is_ambiguous"></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">is_ambiguous</span>(<span class="sig-arg">RE</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_ambiguous">source code</a></span> </td> </tr></table> <pre class="literalblock"> True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown() </pre> <dl class="fields"> <dt>Returns: bool</dt> </dl> </td></tr></table> </div> <a name="is_unknown"></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">is_unknown</span>(<span class="sig-arg">RE</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.is_unknown">source code</a></span> </td> </tr></table> <pre class="literalblock"> True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous() </pre> <dl class="fields"> <dt>Returns: bool</dt> </dl> </td></tr></table> </div> <a name="elucidate"></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">elucidate</span>(<span class="sig-arg">RE</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined.elucidate">source code</a></span> </td> </tr></table> <p>return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie : >>> EcoRI.elucidate() # 5' overhang 'G^AATT_C' >>> KpnI.elucidate() # 3' overhang 'G_GTAC^C' >>> EcoRV.elucidate() # blunt 'GAT^_ATC' >>> SnaI.elucidate() # NotDefined, cut profile unknown. '? GTATAC ?' >>></p> <dl class="fields"> <dt>Returns: str</dt> </dl> </td></tr></table> </div> <a name="_mod2"></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">_mod2</span>(<span class="sig-arg">RE</span>, <span class="sig-arg">other</span>)</span> <br /><em class="fname">Class Method</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Defined._mod2">source code</a></span> </td> </tr></table> <p>for internal use only</p> <p>test for the compatibility of restriction ending of RE and other.</p> <dl class="fields"> <dt>Returns: bool</dt> </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 09:26:37 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. 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