def density_functions(self, cytoplasm, external, other):
cytoplasm_density = 4.8972
cytoplasm_fraction = 0.7
external_fraction = 0.1
other_fraction = 0.2 / len(other)
fns = [
Function(
'amino_acid_concentration', 'linear', {
'LINEAR_COEF': -0.9757,
'LINEAR_CONSTANT': 6.3138,
'X_MIN': 0.25,
'X_MAX': 1.6,
'Y_MIN': float('-Inf'),
'Y_MAX': float('Inf')
})
]
# protein fraction
fns.append(self.protein_fraction(cytoplasm, cytoplasm_fraction))
fns.append(self.protein_fraction(external, external_fraction))
fns += [self.protein_fraction(c, other_fraction) for c in other]
# non enzymatic fraction
fns.append(self.non_enzymatic_fraction_cytoplasm(cytoplasm))
fns.append(self.non_enzymatic_fraction_secreted(external))
fns += [self.non_enzymatic_fraction_other(c) for c in other]
# total density
fns.append(
Function(cytoplasm + '_density', 'constant',
{'CONSTANT': cytoplasm_density}))
return fns
def transport_functions(self, reaction, metabolites):
return [
Function(self._transport_fn_id(reaction, met), 'michaelisMenten', {
'Km': 0.8,
'kmax': 1
}, met) for met in metabolites
]
def non_enzymatic_fraction_other(self, compartment_id):
"""
Return xml structure containing generic non-enzymatic fraction.
"""
params = {
'LINEAR_COEF': -0.0496,
'LINEAR_CONSTANT': 0.8965,
'X_MIN': 0.25,
'X_MAX': 1.6,
'Y_MIN': 0,
'Y_MAX': 1
}
return Function(self.non_enzymatic_fraction_id(compartment_id),
'linear', params)
def non_enzymatic_fraction_cytoplasm(self, compartment_id):
"""
Return xml structure containing non-enzymatic fraction in cytosol.
"""
params = {
'LINEAR_COEF': -0.0502,
'LINEAR_CONSTANT': 0.3526,
'X_MIN': 0.25,
'X_MAX': 1.6,
'Y_MIN': 0,
'Y_MAX': 1
}
return Function(self.non_enzymatic_fraction_id(compartment_id),
'linear', params)
def process_functions(self):
return [
# zero function
Function('zero', 'constant', {'CONSTANT': 0}),
# efficiencies
Function('ribosome_efficiency_MM', 'michaelisMenten', {
'kmax': 97200,
'Km': 0.5,
'Y_MIN': 32400
}),
Function('ribosome_efficiency_CM', 'constant',
{'CONSTANT': 97200}),
Function('fraction_active_ribosomes', 'exponential',
{'RATE': -0.083333}),
Function(
'chaperone_efficiency_LM', 'linear', {
'LINEAR_COEF': 36044.48,
'LINEAR_CONSTANT': -2888.0051,
'X_MIN': 0.25,
'X_MAX': 1.6,
'Y_MIN': float('-Inf'),
'Y_MAX': float('Inf')
}),
# targets
Function('mrna_degradation_flux', 'constant',
{'CONSTANT': 0.15996}),
Function('mrna_concentration', 'constant', {'CONSTANT': 0.01}),
Function('dna_concentration', 'constant', {'CONSTANT': 0.0807}),
Function(
'maintenance_atp', 'linear', {
'LINEAR_COEF': 12.1595,
'LINEAR_CONSTANT': -3.1595,
'X_MIN': 1,
'X_MAX': float('Inf'),
'Y_MIN': float('-Inf'),
'Y_MAX': float('Inf')
})
]
def transport_function(self):
return Function(self.transport_id, 'constant', {'CONSTANT': 2e6},
GROWTH_RATE)
def efficiency_function(self):
return Function(self.efficiency_id, 'constant', {'CONSTANT': 200000},
GROWTH_RATE)
def metabolite_concentration_function(self, id_, concentration):
return Function(self.metabolite_concentration(id_), 'constant',
{'CONSTANT': concentration})
def non_enzymatic_fraction_secreted(self, compartment_id):
"""
Return xml structure containing external non-enzymatic fraction.
"""
return Function(self.non_enzymatic_fraction_id(compartment_id),
'constant', {'CONSTANT': 1})
def protein_fraction(self, compartment_id, fraction):
"""
Return xml structure containing protein fraction in given compartment.
"""
return Function(self.protein_fraction_id(compartment_id), 'constant',
{'CONSTANT': fraction})
def inverse_average_protein_length(length):
"""
Return xml structure containing average protein length.
"""
return Function('inverse_average_protein_length', 'constant',
{'CONSTANT': 1.0 / length})