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

source code

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

Implement the methods specific to the enzymes for which the overhang is not characterised.

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__, __new__, __setattr__, __subclasses__, mro

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

Class Methods [hide private]
list
_drop(RE)
for internal use only.
source code
bool
is_defined(RE)
True if the sequence recognised and cut is constant, i.e.
source code
bool
is_ambiguous(RE)
True if the sequence recognised and cut is ambiguous, i.e.
source code
bool
is_unknown(RE)
True if the sequence is unknown, i.e.
source code
bool
_mod2(RE, other)
for internal use only
source code
str
elucidate(RE)
return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'.
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__, __instancecheck__, __itemsize__, __mro__, __name__, __subclasscheck__, __weakrefoffset__

Inherited from object: __class__

Method Details [hide private]

_drop(RE)
Class Method

source code 

for internal use only.

drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.

Returns: list

is_defined(RE)
Class Method

source code 

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

see also:
RE.is_ambiguous() RE.is_unknown()
Returns: bool

is_ambiguous(RE)
Class Method

source code 

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

see also:
RE.is_defined() RE.is_unknown()
Returns: bool

is_unknown(RE)
Class Method

source code 

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

see also:
RE.is_defined() RE.is_ambiguous()
Returns: bool

_mod2(RE, other)
Class Method

source code 

for internal use only

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

Returns: bool

elucidate(RE)
Class Method

source code 
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 ?' >>>
Returns: str