Package Bio :: Package Restriction :: Module Restriction :: Class NoCut
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Type NoCut

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

Implement the methods specific to the enzymes that do not cut.

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.###).

When using search() with these enzymes the values returned are at the start of the restriction site.

Their catalyse() method returns a TypeError.

Unknown and NotDefined are also part of the base classes of these enzymes.

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]
 
cut_once(cls)
Return if the cutting pattern has one cut.
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cut_twice(cls)
Return if the cutting pattern has two cuts.
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_modify(cls, location)
Return a generator that moves the cutting position by 1 (PRIVATE).
source code
 
_rev_modify(cls, location)
Return a generator that moves the cutting position by 1 (PRIVATE).
source code
 
characteristic(cls)
Return a list of the enzyme's characteristics as tuple.
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Inherited from AbstractCut: all_suppliers, equischizomers, frequency, is_equischizomer, is_isoschizomer, is_neoschizomer, isoschizomers, neoschizomers, search

Properties [hide private]

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

Inherited from object: __class__

Method Details [hide private]

cut_once(cls)
Class Method

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Return if the cutting pattern has one cut.

True if the enzyme cut the sequence one time on each strand.

cut_twice(cls)
Class Method

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Return if the cutting pattern has two cuts.

True if the enzyme cut the sequence twice on each strand.

_modify(cls, location)
Class Method

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Return a generator that moves the cutting position by 1 (PRIVATE).

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.

_rev_modify(cls, location)
Class Method

source code 

Return a generator that moves the cutting position by 1 (PRIVATE).

For internal use only.

As _modify for site situated on the antiparallel strand when the enzyme is not palindromic.

characteristic(cls)
Class Method

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Return a list of the enzyme's characteristics as tuple.

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.