class EnzymaticReaction(ExpressionReaction):
"""
Subclass to describe reactions that are catalyzed by an enzyme.
"""
def __init__(self, enzymes = None, scaled = False, *args, **kwargs):
ExpressionReaction.__init__(self, scaled, *args, **kwargs)
self.enzymes = DictList()
if enzymes:
self.add_enzymes(enzymes)
def add_enzymes(self, enzymes):
"""`
Method to add the enzymes to the reaction.
:param enzymes: iterable of or single Enzyme object
:return:
"""
if not hasattr(enzymes, '__iter__'):
enzymes = [enzymes]
for e in enzymes:
# Avoid duplicates
if e.id in self.enzymes:
self.enzymes._replace_on_id(e)
else:
self.enzymes += [e]
@property
def scaling_factor(self):
return self.enzyme.kcat_max * self.enzyme.scaling_factor
class EnzymaticReaction(ExpressionReaction):
"""
Subclass to describe reactions that are catalyzed by an enzyme.
"""
def __init__(self, enzymes = None, scaled = False, *args, **kwargs):
ExpressionReaction.__init__(self, scaled, *args, **kwargs)
self.enzymes = DictList()
if enzymes:
self.add_enzymes(enzymes)
@classmethod
def from_reaction(cls,reaction, gene_id = None, enzymes = None, scaled=False):
"""
This method clones a cobra.Reaction object into a transcription reaction,
and attaches enzymes to it
:param reaction: the reaction to reproduce
:type reaction: cobra.Reaction
:param enzymes: a(n iterable of the) enzyme(s) to be attached to the reaction
:return: an EnzymaticReaction object
"""
if gene_id is not None:
# it's a transcription or translation reaction
new = cls( id = reaction.id,
name= reaction.name,
gene_id= gene_id,
subsystem= reaction.subsystem,
lower_bound= reaction.lower_bound,
upper_bound= reaction.upper_bound,
enzymes= enzymes,
scaled=scaled)
else:
new = cls( id = reaction.id,
name= reaction.name,
subsystem= reaction.subsystem,
lower_bound= reaction.lower_bound,
upper_bound= reaction.upper_bound,
enzymes= enzymes,
scaled=scaled)
new.add_metabolites(reaction.metabolites, rescale = False)
new.gene_reaction_rule = reaction.gene_reaction_rule
return new
def add_enzymes(self, enzymes):
"""`
Method to add the enzymes to the reaction.
:param enzymes: iterable of or single Enzyme object
:return:
"""
if not hasattr(enzymes, '__iter__'):
enzymes = [enzymes]
for e in enzymes:
# Avoid duplicates
if e.id in self.enzymes:
self.enzymes._replace_on_id(e)
else:
self.enzymes += [e]
@property
def scaling_factor(self):
return self.enzyme.kcat_max * self.enzyme.scaling_factor
