Package Bio :: Package Restriction :: Module Restriction :: Class NotDefined
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Type NotDefined

source code

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

Implement methods for enzymes with non-characterized overhangs.

Correspond to NoCut and Unknown.

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]
 
_drop(cls)
Remove cuts that are outsite of the sequence (PRIVATE).
source code
 
is_defined(cls)
Return if recognition sequence and cut are defined.
source code
 
is_ambiguous(cls)
Return if recognition sequence and cut may be ambiguous.
source code
 
is_unknown(cls)
Return if recognition sequence is unknown.
source code
 
_mod2(cls, other)
Test if other enzyme produces compatible ends for enzyme (PRIVATE).
source code
 
elucidate(cls)
Return a string representing the recognition site and cuttings.
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]

_drop(cls)
Class Method

source code 

Remove cuts that are outsite of the sequence (PRIVATE).

For internal use only.

Drop the site that are situated outside the sequence in linear sequence. Modify the index for site in circular sequences.

is_defined(cls)
Class Method

source code 

Return if recognition sequence and cut are defined.

True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site.

Related methods:
  • RE.is_ambiguous()
  • RE.is_unknown()

is_ambiguous(cls)
Class Method

source code 

Return if recognition sequence and cut may be ambiguous.

True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site.

Related methods:
  • RE.is_defined()
  • RE.is_unknown()

is_unknown(cls)
Class Method

source code 

Return if recognition sequence is unknown.

True if the sequence is unknown, i.e. the recognition site has not been characterised yet.

Related methods:
  • RE.is_defined()
  • RE.is_ambiguous()

_mod2(cls, other)
Class Method

source code 

Test if other enzyme produces compatible ends for enzyme (PRIVATE).

For internal use only.

Test for the compatibility of restriction ending of RE and other.

elucidate(cls)
Class Method

source code 

Return a string representing the recognition site and cuttings.

Return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie:

>>> EcoRI.elucidate()   # 5' overhang
'G^AATT_C'
>>> KpnI.elucidate()    # 3' overhang
'G_GTAC^C'
>>> EcoRV.elucidate()   # blunt
'GAT^_ATC'
>>> SnaI.elucidate()     # NotDefined, cut profile unknown.
'? GTATAC ?'
>>>