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

source code

 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]
bool

cut_once(RE)
True if the enzyme cut the sequence one time on each strand.
source code
bool

cut_twice(RE)
True if the enzyme cut the sequence twice on each strand.
source code
int

_modify(RE, location)
for internal use only.
source code
generator of int

_rev_modify(RE, location)
for internal use only.
source code
tuple

characteristic(RE)
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.
source code

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]

_modify(RE, location)
Class Method

source code 
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.

Returns:
int

_rev_modify(RE, location)
Class Method

source code 
for internal use only.

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

Returns:
generator of int