def __init__(self, id=None, name="", subsystem="", lower_bound=0.0, upper_bound=None): Object.__init__(self, id, name) self._gene_reaction_rule = "" self.subsystem = subsystem # The cobra.Genes that are used to catalyze the reaction self._genes = set() # A dictionary of metabolites and their stoichiometric coefficients in # this reaction. self._metabolites = {} # self.model is None or refers to the cobra.Model that # contains self self._model = None # from cameo ... self._lower_bound = (lower_bound if lower_bound is not None else config.lower_bound) self._upper_bound = (upper_bound if upper_bound is not None else config.upper_bound)
def __init__(self, list_of_models=[], identifier=None, name=None): Object.__init__(self, identifier, name) if len(list_of_models) > 1: if not all(isinstance(x, Model) for x in list_of_models): raise AttributeError( "list_of_models may only contain cobra.core.Model objects") if len([model.id for model in list_of_models]) > \ len(set([model.id for model in list_of_models])): raise AssertionError( "Ensemble members cannot have duplicate model ids.") self.features = DictList() self._populate_features_base(list_of_models) self.members = DictList() self._populate_members(list_of_models) else: if len(list_of_models) == 0: self.base_model = Model(id_or_model=identifier+'_base_model',\ name=name) else: if not isinstance(list_of_models[0], Model): raise AttributeError( "list_of_models may only contain cobra.core.Model objects" ) self.base_model = list_of_models[0]
def __init__(self, id_or_model=None, name=None): if isinstance(id_or_model, Model): Object.__init__(self, name=name) self.__setstate__(id_or_model.__dict__) if not hasattr(self, "name"): self.name = None self._solver = id_or_model.solver else: Object.__init__(self, id_or_model, name=name) self._trimmed = False self._trimmed_genes = [] self._trimmed_reactions = {} self.genes = DictList() self.reactions = DictList() # A list of cobra.Reactions self.metabolites = DictList() # A list of cobra.Metabolites # genes based on their ids {Gene.id: Gene} self.compartments = dict() self._contexts = [] # from cameo ... # if not hasattr(self, '_solver'): # backwards compatibility # with older cobrapy pickles? interface = solvers[get_solver_name()] self._solver = interface.Model() self._solver.objective = interface.Objective(S.Zero) self._populate_solver(self.reactions, self.metabolites)
def __init__(self, id_or_model=None, name=None): if isinstance(id_or_model, Model): Object.__init__(self, name=name) self.__setstate__(id_or_model.__dict__) if not hasattr(self, "name"): self.name = None self._solver = id_or_model.solver else: Object.__init__(self, id_or_model, name=name) self._trimmed = False self._trimmed_genes = [] self._trimmed_reactions = {} self.genes = DictList() self.reactions = DictList() # A list of cobra.Reactions self.metabolites = DictList() # A list of cobra.Metabolites # genes based on their ids {Gene.id: Gene} self._compartments = dict() self._contexts = [] # from cameo ... # if not hasattr(self, '_solver'): # backwards compatibility # with older cobrapy pickles? interface = solvers[get_solver_name()] self._solver = interface.Model() self._solver.objective = interface.Objective(Zero) self._populate_solver(self.reactions, self.metabolites)
def __init__(self, id=None, name='', subsystem='', lower_bound=0.0, upper_bound=None, objective_coefficient=0.0): Object.__init__(self, id, name) self._gene_reaction_rule = '' self.subsystem = subsystem # The cobra.Genes that are used to catalyze the reaction self._genes = set() # A dictionary of metabolites and their stoichiometric coefficients in # this reaction. self._metabolites = {} # The set of compartments that partaking metabolites are in. self._compartments = None # self.model is None or refers to the cobra.Model that # contains self self._model = None if objective_coefficient != 0: raise NotImplementedError('setting objective coefficient when ' 'creating reaction is no longer ' 'supported. Use the model.objective ' 'setter') # from cameo ... self._lower_bound = lower_bound if lower_bound is not None else \ CONFIGURATION.lower_bound self._upper_bound = upper_bound if upper_bound is not None else \ CONFIGURATION.upper_bound
def __init__(self, identifier=None, name=None,ensemble=None,\ base_component=None, component_attribute=None, states=None): Object.__init__(self, identifier, name) self.ensemble = ensemble self.base_component = base_component self.component_attribute = component_attribute self.states = states
def __init__(self, id, name='', members=None, kind=None): Object.__init__(self, id, name) self._members = set() if members is None else set(members) self._kind = None self.kind = "collection" if kind is None else kind # self.model is None or refers to the cobra.Model that # contains self self._model = None
def __init__(self, id, name="", members=None, kind=None): Object.__init__(self, id, name) self._members = DictList() if members is None else DictList(members) self._kind = None self.kind = "collection" if kind is None else kind # self.model is None or refers to the cobra.Model that # contains self self._model = None
def __init__(self, id=None, name='', subsystem='', lower_bound=0., upper_bound=1000., objective_coefficient=0.): Object.__init__(self, id, name) self._gene_reaction_rule = '' self.subsystem = subsystem # The cobra.Genes that are used to catalyze the reaction self._genes = set() # A dictionary of metabolites and their stoichiometric coefficients in # this reaction. self._metabolites = {} # The set of compartments that partaking metabolites are in. self._compartments = None # self.model is None or refers to the cobra.Model that # contains self self._model = None if objective_coefficient != 0: raise NotImplementedError('setting objective coefficient when ' 'creating reaction is no longer ' 'supported. Use the model.objective ' 'setter') # Used during optimization. Indicates whether the # variable is modeled as continuous, integer, binary, semicontinous, or # semiinteger. self.variable_kind = 'continuous' # from cameo ... self._lower_bound = lower_bound self._upper_bound = upper_bound self._reverse_variable = None self._forward_variable = None
def __init__(self, id=None, name='', subsystem='', lower_bound=0., upper_bound=1000., objective_coefficient=0.): Object.__init__(self, id, name) self._gene_reaction_rule = '' self.subsystem = subsystem # The cobra.Genes that are used to catalyze the reaction self._genes = set() # A dictionary of metabolites and their stoichiometric coefficients in # this reaction. self._metabolites = dict() # The set of compartments that partaking metabolites are in. self._compartments = None # self.model is None or refers to the cobra.Model that # contains self self._model = None if objective_coefficient != 0: raise NotImplementedError('setting objective coefficient when ' 'creating reaction is no longer ' 'supported. Use the model.objective ' 'setter') # Used during optimization. Indicates whether the # variable is modeled as continuous, integer, binary, semicontinous, or # semiinteger. self.variable_kind = 'continuous' # from cameo ... self._lower_bound = lower_bound self._upper_bound = upper_bound self._reverse_variable = None self._forward_variable = None
def __init__(self, formula=None): Object.__init__(self, formula) self.formula = formula self.elements = {} if self.formula is not None: self.parse_composition()
def __init__(self, id=None, name=None): Object.__init__(self, id, name) self._model = None # references to reactions that operate on this species self._reaction = set()
def __init__(self,ensemble=None, identifier=None, name=None, states=None): Object.__init__(self,identifier,name) self.ensemble = ensemble self.states = states