Package Bio :: Package Restriction :: Module Restriction :: Class AbstractCut
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Type AbstractCut

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 object --+        
          |        
       type --+    
              |    
RestrictionType --+
                  |
                 AbstractCut
Known Subclasses:

Implement the methods that are common to all restriction enzymes.

All the methods are classmethod.

For internal use only. Not meant to be instantiated.

Instance Methods [hide private]

Inherited from RestrictionType: __add__, __div__, __eq__, __floordiv__, __ge__, __gt__, __hash__, __init__, __le__, __len__, __lt__, __mod__, __ne__, __rdiv__, __repr__, __rfloordiv__, __rshift__, __rtruediv__, __str__, __truediv__

Inherited from type: __call__, __delattr__, __getattribute__, __instancecheck__, __new__, __setattr__, __subclasscheck__, __subclasses__, mro

Inherited from object: __format__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Class Methods [hide private]
 
search(cls, dna, linear=True)
Return a list of cutting sites of the enzyme in the sequence.
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all_suppliers(cls)
Print all the suppliers of restriction enzyme.
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is_equischizomer(cls, other)
Test for real isoschizomer.
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is_neoschizomer(cls, other)
Test for neoschizomer.
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is_isoschizomer(cls, other)
Test for same recognition site.
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equischizomers(cls, batch=None)
List equischizomers of the enzyme.
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neoschizomers(cls, batch=None)
List neoschizomers of the enzyme.
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isoschizomers(cls, batch=None)
List all isoschizomers of the enzyme.
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frequency(cls)
Return the theoretically cutting frequency of the enzyme.
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Properties [hide private]

Inherited from type: __abstractmethods__, __base__, __bases__, __basicsize__, __dictoffset__, __flags__, __itemsize__, __mro__, __name__, __weakrefoffset__

Inherited from object: __class__

Method Details [hide private]

search(cls, dna, linear=True)
Class Method

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Return a list of cutting sites of the enzyme in the sequence.

Compensate for circular sequences and so on.

dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance.

If linear is False, the restriction sites that span over the boundaries will be included.

The positions are the first base of the 3' fragment, i.e. the first base after the position the enzyme will cut.

is_equischizomer(cls, other)
Class Method

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Test for real isoschizomer.

True if other is an isoschizomer of RE, but not an neoschizomer, else False.

Equischizomer: same site, same position of restriction. >>> SacI.is_equischizomer(SstI) True >>> SmaI.is_equischizomer(XmaI) False

is_neoschizomer(cls, other)
Class Method

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Test for neoschizomer.

True if other is an isoschizomer of RE, else False. Neoschizomer: same site, different position of restriction.

is_isoschizomer(cls, other)
Class Method

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Test for same recognition site.

True if other has the same recognition site, else False.

Isoschizomer: same site. >>> SacI.is_isoschizomer(SstI) True >>> SmaI.is_isoschizomer(XmaI) True

equischizomers(cls, batch=None)
Class Method

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List equischizomers of the enzyme.

Return a tuple of all the isoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

Equischizomer: same site, same position of restriction.

neoschizomers(cls, batch=None)
Class Method

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List neoschizomers of the enzyme.

Return a tuple of all the neoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

Neoschizomer: same site, different position of restriction.

isoschizomers(cls, batch=None)
Class Method

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List all isoschizomers of the enzyme.

Return a tuple of all the equischizomers and neoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

frequency(cls)
Class Method

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Return the theoretically cutting frequency of the enzyme.

Frequency of the site, given as 'one cut per x bases' (int).