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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 AbstractCut
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<!-- ==================== TYPE DESCRIPTION ==================== -->
<h1 class="epydoc">Type AbstractCut</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut">source code</a></span></p>
<pre class="base-tree">
object --+
|
type --+
|
<a href="Bio.Restriction.Restriction.RestrictionType-class.html">RestrictionType</a> --+
|
<strong class="uidshort">AbstractCut</strong>
</pre>
<hr />
<p>Implement the methods that are common to all restriction enzymes.</p>
<p>All the methods are classmethod.</p>
<p>For internal use only. Not meant to be instantiate.</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>,
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<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>,
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<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>,
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<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>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__reduce__</code>,
<code>__reduce_ex__</code>
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<!-- ==================== CLASS METHODS ==================== -->
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<span class="summary-type">list</span>
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.AbstractCut-class.html#search" class="summary-sig-name">search</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">dna</span>,
<span class="summary-sig-arg">linear</span>=<span class="summary-sig-default">True</span>)</span><br />
return a list of all the site of RE in dna.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.search">source code</a></span>
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<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="all_suppliers"></a><span class="summary-sig-name">all_suppliers</span>(<span class="summary-sig-arg">self</span>)</span><br />
RE.all_suppliers -> print all the suppliers of R</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.all_suppliers">source code</a></span>
</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.AbstractCut-class.html#is_equischizomer" class="summary-sig-name">is_equischizomer</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">other</span>)</span><br />
True if other is an isoschizomer of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.is_equischizomer">source code</a></span>
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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.AbstractCut-class.html#is_neoschizomer" class="summary-sig-name">is_neoschizomer</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">other</span>)</span><br />
True if other is an isoschizomer of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.is_neoschizomer">source code</a></span>
</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.AbstractCut-class.html#is_isoschizomer" class="summary-sig-name">is_isoschizomer</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">other</span>)</span><br />
True if other is an isoschizomer of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.is_isoschizomer">source code</a></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">
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.AbstractCut-class.html#equischizomers" class="summary-sig-name">equischizomers</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">batch</span>=<span class="summary-sig-default">...</span>)</span><br />
return a tuple of all the isoschizomers of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.equischizomers">source code</a></span>
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">list</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.AbstractCut-class.html#neoschizomers" class="summary-sig-name">neoschizomers</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">batch</span>=<span class="summary-sig-default">...</span>)</span><br />
return a tuple of all the neoschizomers of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.neoschizomers">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">list</span>
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<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.AbstractCut-class.html#isoschizomers" class="summary-sig-name">isoschizomers</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">batch</span>=<span class="summary-sig-default">...</span>)</span><br />
return a tuple of all the equischizomers and neoschizomers of RE.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.isoschizomers">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">int</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="frequency"></a><span class="summary-sig-name">frequency</span>(<span class="summary-sig-arg">RE</span>)</span><br />
frequency of the site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#AbstractCut.frequency">source code</a></span>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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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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<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">search</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">dna</span>,
<span class="sig-arg">linear</span>=<span class="sig-default">True</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#AbstractCut.search">source code</a></span>
</td>
</tr></table>
<p>return a list of all the site of RE in dna. Compensate for circular
sequences and so on.</p>
<p>dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq
instance.</p>
<p>if linear is False, the restriction sites than span over the
boundaries will be included.</p>
<p>The positions are the first base of the 3' fragment, i.e. the first
base after the position the enzyme will cut.</p>
<dl class="fields">
<dt>Returns: list</dt>
</dl>
</td></tr></table>
</div>
<a name="is_equischizomer"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">is_equischizomer</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#AbstractCut.is_equischizomer">source code</a></span>
</td>
</tr></table>
<p>True if other is an isoschizomer of RE. False else.</p>
<p>equischizomer <=> same site, same position of restriction.</p>
<dl class="fields">
<dt>Returns: bool</dt>
</dl>
</td></tr></table>
</div>
<a name="is_neoschizomer"></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_neoschizomer</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#AbstractCut.is_neoschizomer">source code</a></span>
</td>
</tr></table>
<p>True if other is an isoschizomer of RE. False else.</p>
<p>neoschizomer <=> same site, different position of
restriction.</p>
<dl class="fields">
<dt>Returns: bool</dt>
</dl>
</td></tr></table>
</div>
<a name="is_isoschizomer"></a>
<div>
<table class="details" border="1" cellpadding="3"
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">is_isoschizomer</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#AbstractCut.is_isoschizomer">source code</a></span>
</td>
</tr></table>
<p>True if other is an isoschizomer of RE. False else.</p>
<p>isoschizomer <=> same site.</p>
<dl class="fields">
<dt>Returns: bool</dt>
</dl>
</td></tr></table>
</div>
<a name="equischizomers"></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">equischizomers</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">batch</span>=<span class="sig-default">...</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#AbstractCut.equischizomers">source code</a></span>
</td>
</tr></table>
<p>return a tuple of all the isoschizomers of RE. if batch is supplied it
is used instead of the default AllEnzymes.</p>
<p>equischizomer <=> same site, same position of restriction.</p>
<dl class="fields">
<dt>Returns: list</dt>
</dl>
</td></tr></table>
</div>
<a name="neoschizomers"></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">neoschizomers</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">batch</span>=<span class="sig-default">...</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#AbstractCut.neoschizomers">source code</a></span>
</td>
</tr></table>
<p>return a tuple of all the neoschizomers of RE. if batch is supplied it
is used instead of the default AllEnzymes.</p>
<p>neoschizomer <=> same site, different position of
restriction.</p>
<dl class="fields">
<dt>Returns: list</dt>
</dl>
</td></tr></table>
</div>
<a name="isoschizomers"></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">isoschizomers</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">batch</span>=<span class="sig-default">...</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#AbstractCut.isoschizomers">source code</a></span>
</td>
</tr></table>
<p>return a tuple of all the equischizomers and neoschizomers of RE. if
batch is supplied it is used instead of the default AllEnzymes.</p>
<dl class="fields">
<dt>Returns: list</dt>
</dl>
</td></tr></table>
</div>
<br />
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