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, formula=None):
Object.__init__(self, formula)
self.formula = formula
self.elements = {}
if self.formula is not None:
self.parse_composition()
def __init__(self,ensemble=None, identifier=None, name=None, states=None):
Object.__init__(self,identifier,name)
self.ensemble = ensemble
self.states = states
