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<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 NotDefined
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<!-- ==================== TYPE DESCRIPTION ==================== -->
<h1 class="epydoc">Type NotDefined</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NotDefined">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">NotDefined</strong>
</pre>
<hr />
<p>Implement the methods specific to the enzymes for which the overhang
is not characterised.</p>
<p>Correspond to NoCut and Unknown.</p>
<p>Internal use only. Not meant to be instantiated.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<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>
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<!-- ==================== CLASS METHODS ==================== -->
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<td align="left"><span class="table-header">Class Methods</span></td>
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<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.NotDefined-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#NotDefined._drop">source code</a></span>
</td>
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<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.NotDefined-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#NotDefined.is_defined">source code</a></span>
</td>
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</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.NotDefined-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#NotDefined.is_ambiguous">source code</a></span>
</td>
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</td>
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<span class="summary-type">bool</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.NotDefined-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#NotDefined.is_unknown">source code</a></span>
</td>
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</td>
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<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.NotDefined-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#NotDefined._mod2">source code</a></span>
</td>
</tr>
</table>
</td>
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<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.NotDefined-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#NotDefined.elucidate">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>
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<!-- ==================== PROPERTIES ==================== -->
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class="privatelink" onclick="toggle_private();"
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<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>
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<td align="left"><span class="table-header">Method Details</span></td>
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class="privatelink" onclick="toggle_private();"
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cellspacing="0" width="100%" bgcolor="white">
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<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#NotDefined._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#NotDefined.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#NotDefined.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">
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<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#NotDefined.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="_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#NotDefined._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>
<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#NotDefined.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>
<br />
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