def __init__(self, model, name):
"""
Very much model specific
"""
Model.__init__(self, model.copy(), name)
self._cons_queue = list()
self._var_queue = list()
def __init__(self, model, name, sloppy=False):
"""
Very much model specific
"""
Model.__init__(self, model.copy(), name)
self._cons_queue = list()
self._var_queue = list()
self._var_dict = dict()
self._cons_dict = dict()
self.sloppy = sloppy
def __init__(self, *args):
Model.__init__(self, *args)
self.global_info = {}
self.process_data = DictList()
# create the biomass/dilution constraint
self._biomass = Constraint("biomass")
self._biomass_dilution = SummaryVariable("biomass_dilution")
self._biomass_dilution.add_metabolites({self._biomass: -1})
self.add_reactions([self._biomass_dilution])
self._biomass_dilution.upper_bound = mu
self._biomass_dilution.lower_bound = mu
# maintenance energy
self._gam = 0.
self._ngam = 0.
# Unmodeled protein is handled by converting protein_biomass to
# biomass, and requiring production of the appropriate amount of dummy
# protein
self._unmodeled_protein_fraction = None
def __init__(self, *args):
Model.__init__(self, *args)
self.global_info = {}
self.stoichiometric_data = DictList()
self.complex_data = DictList()
self.modification_data = DictList()
self.translation_data = DictList()
self.transcription_data = DictList()
self.generic_data = DictList()
self.tRNA_data = DictList()
self.translocation_data = DictList()
self.posttranslation_data = DictList()
self.subreaction_data = DictList()
self.process_data = DictList()
# create the biomass/dilution constraint
self._biomass = Constraint("biomass")
self._biomass_dilution = SummaryVariable("biomass_dilution")
self._biomass_dilution.add_metabolites({self._biomass: -1})
self.add_reaction(self._biomass_dilution)
self._biomass_dilution.upper_bound = mu
self._biomass_dilution.lower_bound = mu
# maintenance energy
self._gam = 0.
self._ngam = 0.
# Unmodeled protein is handled by converting protein_biomass to
# biomass, and requiring production of the appropriate amount of dummy
# protein
self._unmodeled_protein_fraction = None
self._protein_biomass = Constraint("protein_biomass")
self._protein_biomass_dilution = SummaryVariable(
"protein_biomass_dilution")
self._protein_biomass_dilution.add_metabolites({
self._protein_biomass:
-1,
self._biomass:
1,
})
self._mRNA_biomass = Constraint("mRNA_biomass")
self._mRNA_biomass_dilution = SummaryVariable("mRNA_biomass_dilution")
self._mRNA_biomass_dilution.add_metabolites({
self._mRNA_biomass: -1,
self._biomass: 1,
})
self._tRNA_biomass = Constraint("tRNA_biomass")
self._tRNA_biomass_dilution = SummaryVariable("tRNA_biomass_dilution")
self._tRNA_biomass_dilution.add_metabolites({
self._tRNA_biomass: -1,
self._biomass: 1,
})
self._rRNA_biomass = Constraint("rRNA_biomass")
self._rRNA_biomass_dilution = SummaryVariable("rRNA_biomass_dilution")
self._rRNA_biomass_dilution.add_metabolites({
self._rRNA_biomass: -1,
self._biomass: 1,
})
self._ncRNA_biomass = Constraint("ncRNA_biomass")
self._ncRNA_biomass_dilution = SummaryVariable(
"ncRNA_biomass_dilution")
self._ncRNA_biomass_dilution.add_metabolites({
self._ncRNA_biomass: -1,
self._biomass: 1,
})
self._DNA_biomass = Constraint("DNA_biomass")
self._DNA_biomass_dilution = SummaryVariable("DNA_biomass_dilution")
self._DNA_biomass_dilution.add_metabolites({
self._DNA_biomass: -1,
self._biomass: 1,
})
self.add_reactions(
(self._protein_biomass_dilution, self._mRNA_biomass_dilution,
self._tRNA_biomass_dilution, self._rRNA_biomass_dilution,
self._ncRNA_biomass_dilution, self._DNA_biomass_dilution))
def __init__(self, *args):
Model.__init__(self, *args)
self.global_info = {}
self.stoichiometric_data = DictList()
self.complex_data = DictList()
self.modification_data = DictList()
self.translation_data = DictList()
self.transcription_data = DictList()
self.generic_data = DictList()
self.tRNA_data = DictList()
self.translocation_data = DictList()
self.posttranslation_data = DictList()
self.subreaction_data = DictList()
self.process_data = DictList()
# create the biomass/dilution constraint
self._biomass = Constraint("biomass")
self._biomass_dilution = SummaryVariable("biomass_dilution")
self._biomass_dilution.add_metabolites({self._biomass: -1})
self.add_reaction(self._biomass_dilution)
self._biomass_dilution.upper_bound = mu
self._biomass_dilution.lower_bound = mu
# Unmodeled protein is handled by converting protein_biomass to
# biomass, and requiring production of the appropriate amount of dummy
# protein
self._unmodeled_protein_fraction = None
self._protein_biomass = Constraint("protein_biomass")
self._protein_biomass_dilution = SummaryVariable("protein_biomass_dilution")
self._protein_biomass_dilution.add_metabolites({
self._protein_biomass: -1,
self._biomass: 1,
})
self._mRNA_biomass = Constraint("mRNA_biomass")
self._mRNA_biomass_dilution = SummaryVariable("mRNA_biomass_dilution")
self._mRNA_biomass_dilution.add_metabolites({
self._mRNA_biomass: -1,
self._biomass: 1,
})
self._tRNA_biomass = Constraint("tRNA_biomass")
self._tRNA_biomass_dilution = SummaryVariable("tRNA_biomass_dilution")
self._tRNA_biomass_dilution.add_metabolites({
self._tRNA_biomass: -1,
self._biomass: 1,
})
self._rRNA_biomass = Constraint("rRNA_biomass")
self._rRNA_biomass_dilution = SummaryVariable("rRNA_biomass_dilution")
self._rRNA_biomass_dilution.add_metabolites({
self._rRNA_biomass: -1,
self._biomass: 1,
})
self._ncRNA_biomass = Constraint("ncRNA_biomass")
self._ncRNA_biomass_dilution = SummaryVariable("ncRNA_biomass_dilution")
self._ncRNA_biomass_dilution.add_metabolites({
self._ncRNA_biomass: -1,
self._biomass: 1,
})
self.add_reactions((self._protein_biomass_dilution,
self._mRNA_biomass_dilution,
self._tRNA_biomass_dilution,
self._rRNA_biomass_dilution,
self._ncRNA_biomass_dilution))
self._DNA_biomass = Constraint("DNA_biomass")
self._DNA_biomass_dilution = SummaryVariable("DNA_biomass_dilution")
self._DNA_biomass_dilution.add_metabolites({
self._DNA_biomass: -1e-3,
self._biomass: 1e-3,
})
self._DNA_biomass_dilution.lower_bound = mu
self._DNA_biomass_dilution.upper_bound = mu
