Package transsys :: Class PromoterElementLink

Class PromoterElementLink

     object --+    
              |    
PromoterElement --+
                  |
                 PromoterElementLink

Instance Methods

[hide private]

__init__(self, expr1, expr2, factor_list, dot_attrs=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

__str__(self)
str(x)

source code

resolve(self, tp)

source code

unresolved_copy(self)

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getValueNodes(self)
Get all constant value expressions involved in this promoter element.

source code

getSpecValueNodes(self)
Get the constant value expressions involved Michaelis-Menten spec parameter.

source code

getMaxValueNodes(self)
Get the constant value expressions involved Michaelis-Menten max parameter.

source code

getIdentifierNodes(self)
Get all identifier nodes that control this promoter element.

source code

canonicalise(self)
Clip the spec parameter to non-negative if it is a constant.

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write_dot_edge(self, f, target_name, display_factors, arrowhead, transsys)

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, expr1, expr2, factor_list, dot_attrs=None)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

getIdentifierNodes(self)

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Get all identifier nodes that control this promoter element. The list includes the factors mentioned in activate and repress as well as any identifier nodes that may appear in the parameters to the link element.

canonicalise(self)

source code

Clip the spec parameter to non-negative if it is a constant.

Notice that negative max parameters are permitted. These effectively invert activate to repress and vice versa, thus creating a degeneracy in representation, but this feature has proven unexpectedly useful in optimisation.

Future implementations of canonicalisation may convert links with negative max constants to their antagonistic counterparts.

Class PromoterElementLink

__init__(self, expr1, expr2, factor_list, dot_attrs=None) (Constructor)

__str__(self) (Informal representation operator)

getIdentifierNodes(self)

canonicalise(self)

init(self, expr1, expr2, factor_list, dot_attrs=None)
(Constructor)

str(self)
(Informal representation operator)