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