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 instantiate.

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]
list

search(RE, dna, linear=True)
return a list of all the site of RE in dna.
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all_suppliers(self)
RE.all_suppliers -> print all the suppliers of R
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bool

is_equischizomer(RE, other)
True if other is an isoschizomer of RE.
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bool

is_neoschizomer(RE, other)
True if other is an isoschizomer of RE.
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bool

is_isoschizomer(RE, other)
True if other is an isoschizomer of RE.
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list

equischizomers(RE, batch=...)
return a tuple of all the isoschizomers of RE.
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list

neoschizomers(RE, batch=...)
return a tuple of all the neoschizomers of RE.
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list

isoschizomers(RE, batch=...)
return a tuple of all the equischizomers and neoschizomers of RE.
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int

frequency(RE)
frequency of the site.
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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(RE, dna, linear=True)
Class Method

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return a list of all the site of RE in dna. 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 than 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. 

Returns:
list

is_equischizomer(RE, other)
Class Method

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True if other is an isoschizomer of RE.
False else.

equischizomer <=> same site, same position of restriction.

Returns:
bool

is_neoschizomer(RE, other)
Class Method

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True if other is an isoschizomer of RE.
False else.

neoschizomer <=> same site, different position of restriction.

Returns:
bool

is_isoschizomer(RE, other)
Class Method

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True if other is an isoschizomer of RE.
False else.

isoschizomer <=> same site.

Returns:
bool

equischizomers(RE, batch=...)
Class Method

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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.

Returns:
list

neoschizomers(RE, batch=...)
Class Method

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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.

Returns:
list

isoschizomers(RE, batch=...)
Class Method

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

Returns:
list