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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 NoCut
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<!-- ==================== TYPE DESCRIPTION ==================== -->
<h1 class="epydoc">Type NoCut</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut">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">NoCut</strong>
</pre>
<hr />
<p>Implement the methods specific to the enzymes that do not cut.</p>
<p>These enzymes are generally enzymes that have been only partially
characterised and the way they cut the DNA is unknow or enzymes for which
the pattern of cut is to complex to be recorded in Rebase (ncuts values
of 0 in emboss_e.###).</p>
<p>When using search() with these enzymes the values returned are at the
start of the restriction site.</p>
<p>Their catalyse() method returns a TypeError.</p>
<p>Unknown and NotDefined are also part of the base classes of these
enzymes.</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">bool</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="cut_once"></a><span class="summary-sig-name">cut_once</span>(<span class="summary-sig-arg">RE</span>)</span><br />
True if the enzyme cut the sequence one time on each strand.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut.cut_once">source code</a></span>
</td>
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<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 name="cut_twice"></a><span class="summary-sig-name">cut_twice</span>(<span class="summary-sig-arg">RE</span>)</span><br />
True if the enzyme cut the sequence twice on each strand.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut.cut_twice">source code</a></span>
</td>
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<span class="summary-type">int</span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.NoCut-class.html#_modify" class="summary-sig-name" onclick="show_private();">_modify</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">location</span>)</span><br />
for internal use only.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut._modify">source code</a></span>
</td>
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<span class="summary-type">generator of int</span>
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<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.NoCut-class.html#_rev_modify" class="summary-sig-name" onclick="show_private();">_rev_modify</a>(<span class="summary-sig-arg">RE</span>,
<span class="summary-sig-arg">location</span>)</span><br />
for internal use only.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut._rev_modify">source code</a></span>
</td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">tuple</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="characteristic"></a><span class="summary-sig-name">characteristic</span>(<span class="summary-sig-arg">RE</span>)</span><br />
the tuple contains the attributes :
fst5 -> first 5' cut ((current strand) or None
fst3 -> first 3' cut (complementary strand) or None
scd5 -> second 5' cut (current strand) or None
scd5 -> second 3' cut (complementary strand) or None
site -> recognition site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#NoCut.characteristic">source code</a></span>
</td>
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<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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<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>
</p>
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<td align="left"><span class="table-header">Method Details</span></td>
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<a name="_modify"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_modify</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">location</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#NoCut._modify">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
for internal use only.
location is an integer corresponding to the location of the match for
the enzyme pattern in the sequence.
_modify returns the real place where the enzyme will cut.
example :
EcoRI pattern : GAATTC
EcoRI will cut after the G.
so in the sequence :
______
GAATACACGGAATTCGA
|
10
dna.finditer(GAATTC, 6) will return 10 as G is the 10th base
EcoRI cut after the G so :
EcoRI._modify(10) -> 11.
if the enzyme cut twice _modify will returns two integer corresponding
to each cutting site.
</pre>
<dl class="fields">
<dt>Returns: int</dt>
</dl>
</td></tr></table>
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<a name="_rev_modify"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_rev_modify</span>(<span class="sig-arg">RE</span>,
<span class="sig-arg">location</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#NoCut._rev_modify">source code</a></span>
</td>
</tr></table>
<p>for internal use only.</p>
<p>as _modify for site situated on the antiparallel strand when the
enzyme is not palindromic</p>
<dl class="fields">
<dt>Returns: generator of int</dt>
</dl>
</td></tr></table>
</div>
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