def _apply_min_growth(community, min_growth, atol=1e-6, rtol=1e-6):
"""Set minimum growth constraints on a model.
Will integrate with the context.
"""
context = get_context(community)
def reset(taxon, lb):
logger.info("resetting growth rate constraint for %s" % taxon)
community.constraints["objective_" + taxon].ub = None
community.constraints["objective_" + taxon].lb = lb
for sp in community.taxa:
logger.info("setting growth rate constraint for %s" % sp)
obj = community.constraints["objective_" + sp]
if context:
context(partial(reset, sp, obj.lb))
if min_growth[sp] > atol:
obj.lb = (1.0 - rtol) * min_growth[sp] - atol
else:
logger.info(
"minimal growth rate smaller than tolerance,"
" setting to zero."
)
obj.lb = 0
def add_cons_vars_to_problem(
model: "Model",
what: Union[List[CONS_VARS], Tuple[CONS_VARS], Components],
**kwargs,
) -> None:
"""Add variables and constraints to a model's solver object.
Useful for variables and constraints that can not be expressed with
reactions and lower/upper bounds. It will integrate with the model's
context manager in order to revert changes upon leaving the context.
Parameters
----------
model : cobra.Model
The model to which to add the variables and constraints.
what : list or tuple of optlang.interface.Variable or
optlang.interface.Constraint
The variables and constraints to add to the model.
**kwargs : keyword arguments
Keyword arguments passed to solver's add() method.
"""
model.solver.add(what, **kwargs)
context = get_context(model)
if context:
context(partial(model.solver.remove, what))
def add_proteins(self, protein_list: Iterator[Protein]):
"""Add proteins to the model, in the same fashion as `.add_metabollites`."""
if not hasattr(protein_list, "__iter__"):
protein_list = [protein_list]
if len(protein_list) == 0:
return None
# Take left difference
pruned = [x for x in protein_list if x.id not in self.proteins]
for prot in pruned:
prot._model = self
to_add = []
for prot in pruned:
if prot.id not in self.constraints:
constraint = self.problem.Constraint(Zero,
name=prot.id,
lb=0,
ub=0)
to_add += [constraint]
self.add_cons_vars(to_add)
context = get_context(self)
if context:
context(partial(self.proteins.__isub__, pruned))
for x in pruned:
context(partial(setattr, x, "_model", None))
self.proteins += pruned
self._populate_solver([], None, pruned)
def __imul__(self, coefficient):
"""Scale coefficients in a reaction by a given value
E.g. A -> B becomes 2A -> 2B.
If coefficient is less than zero, the reaction is reversed and the
bounds are swapped.
"""
self._metabolites = {
met: value * coefficient
for met, value in self._metabolites.items()
}
if coefficient < 0:
self.bounds = (-self.upper_bound, -self.lower_bound)
if self._model:
self._model._populate_solver([self])
context = get_context(self)
if context:
context(partial(self._model._populate_solver, [self]))
context(partial(self.__imul__, 1.0 / coefficient))
return self
def remove_reactions(self, reactions, remove_orphans=False):
"""Remove reactions from the model.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reactions : list
A list with reactions (`cobra.Reaction`), or their id's, to remove
remove_orphans : bool
Remove orphaned genes and metabolites from the model as well
"""
if isinstance(reactions, string_types) or hasattr(reactions, "id"):
warn("need to pass in a list")
reactions = [reactions]
context = get_context(self)
for reaction in reactions:
# Make sure the reaction is in the model
try:
reaction = self.reactions[self.reactions.index(reaction)]
except ValueError:
warn('%s not in %s' % (reaction, self))
else:
forward = reaction.forward_variable
reverse = reaction.reverse_variable
if context:
context(partial(self._populate_solver, [reaction]))
context(partial(setattr, reaction, '_model', self))
context(partial(self.reactions.add, reaction))
self.remove_cons_vars([forward, reverse])
self.reactions.remove(reaction)
reaction._model = None
for met in reaction._metabolites:
if reaction in met._reaction:
met._reaction.remove(reaction)
if context:
context(partial(met._reaction.add, reaction))
if remove_orphans and len(met._reaction) == 0:
self.remove_metabolites(met)
for gene in reaction._genes:
if reaction in gene._reaction:
gene._reaction.remove(reaction)
if context:
context(partial(gene._reaction.add, reaction))
if remove_orphans and len(gene._reaction) == 0:
self.genes.remove(gene)
if context:
context(partial(self.genes.add, gene))
def remove_reactions(self, reactions, remove_orphans=False):
"""Remove reactions from the model.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reactions : list
A list with reactions (`cobra.Reaction`), or their id's, to remove
remove_orphans : bool
Remove orphaned genes and metabolites from the model as well
"""
if isinstance(reactions, string_types) or hasattr(reactions, "id"):
warn("need to pass in a list")
reactions = [reactions]
context = get_context(self)
for reaction in reactions:
# Make sure the reaction is in the model
try:
reaction = self.reactions[self.reactions.index(reaction)]
except ValueError:
warn('%s not in %s' % (reaction, self))
else:
forward = reaction.forward_variable
reverse = reaction.reverse_variable
if context:
context(partial(self._populate_solver, [reaction]))
context(partial(setattr, reaction, '_model', self))
context(partial(self.reactions.add, reaction))
self.remove_cons_vars([forward, reverse])
self.reactions.remove(reaction)
reaction._model = None
for met in reaction._metabolites:
if reaction in met._reaction:
met._reaction.remove(reaction)
if context:
context(partial(met._reaction.add, reaction))
if remove_orphans and len(met._reaction) == 0:
self.remove_metabolites(met)
for gene in reaction._genes:
if reaction in gene._reaction:
gene._reaction.remove(reaction)
if context:
context(partial(gene._reaction.add, reaction))
if remove_orphans and len(gene._reaction) == 0:
self.genes.remove(gene)
if context:
context(partial(self.genes.add, gene))
def gene_reaction_rule(self, new_rule):
# TODO: Do this :)
if get_context(self):
warn("Context management not implemented for "
"gene reaction rules")
self._gene_reaction_rule = new_rule.strip()
try:
_, gene_names = parse_gpr(self._gene_reaction_rule)
except (SyntaxError, TypeError) as e:
if "AND" in new_rule or "OR" in new_rule:
warn("uppercase AND/OR found in rule '%s' for '%s'" %
(new_rule, repr(self)))
new_rule = uppercase_AND.sub("and", new_rule)
new_rule = uppercase_OR.sub("or", new_rule)
self.gene_reaction_rule = new_rule
return
warn("malformed gene_reaction_rule '%s' for %s" %
(new_rule, repr(self)))
tmp_str = and_or_search.sub("", self._gene_reaction_rule)
gene_names = set((gpr_clean.sub(" ", tmp_str).split(" ")))
if "" in gene_names:
gene_names.remove("")
old_genes = self._genes
if self._model is None:
self._genes = {Gene(i) for i in gene_names}
else:
model_genes = self._model.genes
self._genes = set()
for id in gene_names:
if model_genes.has_id(id):
self._genes.add(model_genes.get_by_id(id))
else:
new_gene = Gene(id)
new_gene._model = self._model
self._genes.add(new_gene)
model_genes.append(new_gene)
# Make the genes aware that it is involved in this reaction
for g in self._genes:
g._reaction.add(self)
# make the old genes aware they are no longer involved in this reaction
for g in old_genes:
if g not in self._genes: # if an old gene is not a new gene
try:
g._reaction.remove(self)
except KeyError:
warn("could not remove old gene %s from reaction %s" %
(g.id, self.id))
def gene_reaction_rule(self, new_rule):
# TODO: Do this :)
if get_context(self):
warn("Context management not implemented for "
"gene reaction rules")
self._gene_reaction_rule = new_rule.strip()
try:
_, gene_names = parse_gpr(self._gene_reaction_rule)
except (SyntaxError, TypeError) as e:
if "AND" in new_rule or "OR" in new_rule:
warn("uppercase AND/OR found in rule '%s' for '%s'" %
(new_rule, repr(self)))
new_rule = uppercase_AND.sub("and", new_rule)
new_rule = uppercase_OR.sub("or", new_rule)
self.gene_reaction_rule = new_rule
return
warn("malformed gene_reaction_rule '%s' for %s" %
(new_rule, repr(self)))
tmp_str = and_or_search.sub('', self._gene_reaction_rule)
gene_names = set((gpr_clean.sub(' ', tmp_str).split(' ')))
if '' in gene_names:
gene_names.remove('')
old_genes = self._genes
if self._model is None:
self._genes = {Gene(i) for i in gene_names}
else:
model_genes = self._model.genes
self._genes = set()
for id in gene_names:
if model_genes.has_id(id):
self._genes.add(model_genes.get_by_id(id))
else:
new_gene = Gene(id)
new_gene._model = self._model
self._genes.add(new_gene)
model_genes.append(new_gene)
# Make the genes aware that it is involved in this reaction
for g in self._genes:
g._reaction.add(self)
# make the old genes aware they are no longer involved in this reaction
for g in old_genes:
if g not in self._genes: # if an old gene is not a new gene
try:
g._reaction.remove(self)
except:
warn("could not remove old gene %s from reaction %s" %
(g.id, self.id))
def add_metabolites(self, metabolite_list):
"""Will add a list of metabolites to the model object and add new
constraints accordingly.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolite_list : A list of `cobra.core.Metabolite` objects
"""
if not hasattr(metabolite_list, "__iter__"):
metabolite_list = [metabolite_list]
if len(metabolite_list) == 0:
return None
# First check whether the metabolites exist in the model
metabolite_list = [
x for x in metabolite_list if x.id not in self.metabolites
]
bad_ids = [
m for m in metabolite_list
if not isinstance(m.id, string_types) or len(m.id) < 1
]
if len(bad_ids) != 0:
raise ValueError("invalid identifiers in {}".format(repr(bad_ids)))
for x in metabolite_list:
x._model = self
self.metabolites += metabolite_list
# from cameo ...
to_add = []
for met in metabolite_list:
if met.id not in self.constraints:
constraint = self.problem.Constraint(Zero,
name=met.id,
lb=0,
ub=0)
to_add += [constraint]
self.add_cons_vars(to_add)
context = get_context(self)
if context:
context(partial(self.metabolites.__isub__, metabolite_list))
for x in metabolite_list:
# Do we care?
context(partial(setattr, x, "_model", None))
def remove_metabolites(self, metabolite_list, destructive=False):
"""Remove a list of metabolites from the the object.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolite_list : list
A list with `cobra.Metabolite` objects as elements.
destructive : bool
If False then the metabolite is removed from all
associated reactions. If True then all associated
reactions are removed from the Model.
"""
if not hasattr(metabolite_list, "__iter__"):
metabolite_list = [metabolite_list]
# Make sure metabolites exist in model
metabolite_list = [
x for x in metabolite_list if x.id in self.metabolites
]
for x in metabolite_list:
x._model = None
# remove reference to the metabolite in all groups
associated_groups = self.get_associated_groups(x)
for group in associated_groups:
group.remove_members(x)
if not destructive:
for the_reaction in list(x._reaction):
the_coefficient = the_reaction._metabolites[x]
the_reaction.subtract_metabolites({x: the_coefficient})
else:
for x in list(x._reaction):
x.remove_from_model()
self.metabolites -= metabolite_list
to_remove = [self.solver.constraints[m.id] for m in metabolite_list]
self.remove_cons_vars(to_remove)
context = get_context(self)
if context:
context(partial(self.metabolites.__iadd__, metabolite_list))
for x in metabolite_list:
context(partial(setattr, x, "_model", self))
def add_metabolites(self, metabolite_list):
"""Will add a list of metabolites to the model object and add new
constraints accordingly.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolite_list : A list of `cobra.core.Metabolite` objects
"""
if not hasattr(metabolite_list, '__iter__'):
metabolite_list = [metabolite_list]
if len(metabolite_list) == 0:
return None
# First check whether the metabolites exist in the model
metabolite_list = [x for x in metabolite_list
if x.id not in self.metabolites]
bad_ids = [m for m in metabolite_list
if not isinstance(m.id, string_types) or len(m.id) < 1]
if len(bad_ids) != 0:
raise ValueError('invalid identifiers in {}'.format(repr(bad_ids)))
for x in metabolite_list:
x._model = self
self.metabolites += metabolite_list
# from cameo ...
to_add = []
for met in metabolite_list:
if met.id not in self.constraints:
constraint = self.problem.Constraint(
Zero, name=met.id, lb=0, ub=0)
to_add += [constraint]
self.add_cons_vars(to_add)
context = get_context(self)
if context:
context(partial(self.metabolites.__isub__, metabolite_list))
for x in metabolite_list:
# Do we care?
context(partial(setattr, x, '_model', None))
def remove_metabolites(self, metabolite_list, destructive=False):
"""Remove a list of metabolites from the the object.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolite_list : list
A list with `cobra.Metabolite` objects as elements.
destructive : bool
If False then the metabolite is removed from all
associated reactions. If True then all associated
reactions are removed from the Model.
"""
if not hasattr(metabolite_list, '__iter__'):
metabolite_list = [metabolite_list]
# Make sure metabolites exist in model
metabolite_list = [x for x in metabolite_list
if x.id in self.metabolites]
for x in metabolite_list:
x._model = None
if not destructive:
for the_reaction in list(x._reaction):
the_coefficient = the_reaction._metabolites[x]
the_reaction.subtract_metabolites({x: the_coefficient})
else:
for x in list(x._reaction):
x.remove_from_model()
self.metabolites -= metabolite_list
to_remove = [self.solver.constraints[m.id] for m in metabolite_list]
self.remove_cons_vars(to_remove)
context = get_context(self)
if context:
context(partial(self.metabolites.__iadd__, metabolite_list))
for x in metabolite_list:
context(partial(setattr, x, '_model', self))
def add_metabolites(self, metabolite_list):
"""Will add a list of metabolites to the model object and add new
constraints accordingly.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolite_list : A list of `cobra.core.Metabolite` objects
"""
if not hasattr(metabolite_list, '__iter__'):
metabolite_list = [metabolite_list]
if len(metabolite_list) == 0:
return None
# First check whether the metabolites exist in the model
metabolite_list = [
x for x in metabolite_list if x.id not in self.metabolites
]
for x in metabolite_list:
x._model = self
self.metabolites += metabolite_list
# from cameo ...
to_add = []
for met in metabolite_list:
if met.id not in self.constraints:
constraint = self.problem.Constraint(S.Zero,
name=met.id,
lb=0,
ub=0)
to_add += [constraint]
self.add_cons_vars(to_add)
context = get_context(self)
if context:
context(partial(self.metabolites.__isub__, metabolite_list))
for x in metabolite_list:
# Do we care?
context(partial(setattr, x, '_model', None))
def remove_cons_vars_from_problem(model, what):
"""Remove variables and constraints from a Model's solver object.
Useful to temporarily remove variables and constraints from a Models's
solver object.
Parameters
----------
model : a cobra model
The model from which to remove the variables and constraints.
what : list or tuple of optlang variables or constraints.
The variables or constraints to remove from the model. Must be of
class `model.problem.Variable` or
`model.problem.Constraint`.
"""
context = get_context(model)
model.solver.remove(what)
if context:
context(partial(model.solver.add, what))
def remove_cons_vars_from_problem(model, what):
"""Remove variables and constraints from a Model's solver object.
Useful to temporarily remove variables and constraints from a Models's
solver object.
Parameters
----------
model : a cobra model
The model from which to remove the variables and constraints.
what : list or tuple of optlang variables or constraints.
The variables or constraints to remove from the model. Must be of
class `model.problem.Variable` or
`model.problem.Constraint`.
"""
context = get_context(model)
model.solver.remove(what)
if context:
context(partial(model.solver.add, what))
def _apply_min_growth(community, min_growth):
"""Set minimum growth constraints on a model.
Will integrate with the context.
"""
context = get_context(community)
def reset(species, lb):
logger.info("resetting growth rate constraint for %s" % species)
community.constraints["objective_" + species].ub = None
community.constraints["objective_" + species].lb = lb
for sp in community.species:
logger.info("setting growth rate constraint for %s" % sp)
obj = community.constraints["objective_" + sp]
if context:
context(partial(reset, sp, obj.lb))
if min_growth[sp] > 1e-6:
obj.lb = min_growth[sp]
else:
logger.info("minimal growth rate smaller than tolerance,"
" setting to zero.")
obj.lb = 0
def remove_cons_vars_from_problem(
model: "Model",
what: Union[List[CONS_VARS], Tuple[CONS_VARS], Components],
) -> None:
"""Remove variables and constraints from a model's solver object.
Useful to temporarily remove variables and constraints from a model's
solver object.
Parameters
----------
model : cobra.Model
The model from which to remove the variables and constraints.
what : list or tuple of optlang.interface.Variable or
optlang.interface.Constraint
The variables and constraints to remove from the model.
"""
model.solver.remove(what)
context = get_context(model)
if context:
context(partial(model.solver.add, what))
def add_cons_vars_to_problem(model, what, **kwargs):
"""Add variables and constraints to a Model's solver object.
Useful for variables and constraints that can not be expressed with
reactions and lower/upper bounds. Will integrate with the Model's context
manager in order to revert changes upon leaving the context.
Parameters
----------
model : a cobra model
The model to which to add the variables and constraints.
what : list or tuple of optlang variables or constraints.
The variables or constraints to add to the model. Must be of class
`model.problem.Variable` or
`model.problem.Constraint`.
**kwargs : keyword arguments
passed to solver.add()
"""
context = get_context(model)
model.solver.add(what, **kwargs)
if context:
context(partial(model.solver.remove, what))
def add_cons_vars_to_problem(model, what, **kwargs):
"""Add variables and constraints to a Model's solver object.
Useful for variables and constraints that can not be expressed with
reactions and lower/upper bounds. Will integrate with the Model's context
manager in order to revert changes upon leaving the context.
Parameters
----------
model : a cobra model
The model to which to add the variables and constraints.
what : list or tuple of optlang variables or constraints.
The variables or constraints to add to the model. Must be of class
`model.problem.Variable` or
`model.problem.Constraint`.
**kwargs : keyword arguments
passed to solver.add()
"""
context = get_context(model)
model.solver.add(what, **kwargs)
if context:
context(partial(model.solver.remove, what))
def __imul__(self, coefficient):
"""Scale coefficients in a reaction by a given value
E.g. A -> B becomes 2A -> 2B.
If coefficient is less than zero, the reaction is reversed and the
bounds are swapped.
"""
self._metabolites = {
met: value * coefficient
for met, value in iteritems(self._metabolites)}
if coefficient < 0:
self.bounds = (-self.upper_bound, -self.lower_bound)
if self._model:
self._model._populate_solver([self])
context = get_context(self)
if context:
context(partial(self._model._populate_solver, [self]))
context(partial(self.__imul__, 1./coefficient))
return self
def add_reactions(self, reaction_list):
"""Add reactions to the model.
Reactions with identifiers identical to a reaction already in the
model are ignored.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reaction_list : list
A list of `cobra.Reaction` objects
"""
def existing_filter(rxn):
if rxn.id in self.reactions:
LOGGER.warning(
"Ignoring reaction '%s' since it already exists.", rxn.id)
return False
return True
# First check whether the reactions exist in the model.
pruned = DictList(filter(existing_filter, reaction_list))
context = get_context(self)
# Add reactions. Also take care of genes and metabolites in the loop.
for reaction in pruned:
reaction._model = self
# Build a `list()` because the dict will be modified in the loop.
for metabolite in list(reaction.metabolites):
# TODO: Should we add a copy of the metabolite instead?
if metabolite not in self.metabolites:
self.add_metabolites(metabolite)
# A copy of the metabolite exists in the model, the reaction
# needs to point to the metabolite in the model.
else:
# FIXME: Modifying 'private' attributes is horrible.
stoichiometry = reaction._metabolites.pop(metabolite)
model_metabolite = self.metabolites.get_by_id(
metabolite.id)
reaction._metabolites[model_metabolite] = stoichiometry
model_metabolite._reaction.add(reaction)
if context:
context(partial(
model_metabolite._reaction.remove, reaction))
for gene in list(reaction._genes):
# If the gene is not in the model, add it
if not self.genes.has_id(gene.id):
self.genes += [gene]
gene._model = self
if context:
# Remove the gene later
context(partial(self.genes.__isub__, [gene]))
context(partial(setattr, gene, '_model', None))
# Otherwise, make the gene point to the one in the model
else:
model_gene = self.genes.get_by_id(gene.id)
if model_gene is not gene:
reaction._dissociate_gene(gene)
reaction._associate_gene(model_gene)
self.reactions += pruned
if context:
context(partial(self.reactions.__isub__, pruned))
# from cameo ...
self._populate_solver(pruned)
def add_reactions(self, reaction_list: Iterator[Reaction]):
"""Add reactions to the model.
Reactions with identifiers identical to a reaction already in the
model are ignored.
The change is reverted upon exit when using the model as a context.
Enzyme Constrained changes: avoid adding proteins as metabolites.
Parameters
----------
reaction_list : list
A list of `cobra.Reaction` objects
"""
def existing_filter(rxn):
if rxn.id in self.reactions:
LOGGER.warning(
f"Ignoring reaction '{rxn.id}' since it already exists.")
return False
return True
# First check whether the reactions exist in the model.
pruned = DictList(filter(existing_filter, reaction_list))
context = get_context(self)
# Add reactions. Also take care of genes and metabolites in the loop.
for reaction in pruned:
reaction._model = self
# Build a `list()` because the dict will be modified in the loop.
for metabolite in list(reaction.metabolites):
is_prot = isinstance(metabolite, Protein)
target = self.proteins if is_prot else self.metabolites
if metabolite not in target:
if is_prot:
self.add_proteins([metabolite])
else:
self.add_metabolites(metabolite)
# A copy of the metabolite exists in the model, the reaction
# needs to point to the metabolite in the model.
else:
stoichiometry = reaction._metabolites.pop(metabolite)
model_metabolite = target.get_by_id(metabolite.id)
reaction._metabolites[model_metabolite] = stoichiometry
model_metabolite._reaction.add(reaction)
if context:
context(
partial(model_metabolite._reaction.remove,
reaction))
for gene in list(reaction._genes):
# If the gene is not in the model, add it
if not self.genes.has_id(gene.id):
self.genes += [gene]
gene._model = self
if context:
# Remove the gene later
context(partial(self.genes.__isub__, [gene]))
context(partial(setattr, gene, "_model", None))
# Otherwise, make the gene point to the one in the model
else:
model_gene = self.genes.get_by_id(gene.id)
if model_gene is not gene:
reaction._dissociate_gene(gene)
reaction._associate_gene(model_gene)
self.reactions += pruned
if context:
context(partial(self.reactions.__isub__, pruned))
# from cameo ...
self._populate_solver(pruned)
def set_objective(model, value, additive=False):
"""Set the model objective.
Parameters
----------
model : cobra model
The model to set the objective for
value : model.problem.Objective,
e.g. optlang.glpk_interface.Objective, sympy.Basic or dict
If the model objective is linear, the value can be a new Objective
object or a dictionary with linear coefficients where each key is a
reaction and the element the new coefficient (float).
If the objective is not linear and `additive` is true, only values
of class Objective.
additive : boolmodel.reactions.Biomass_Ecoli_core.bounds = (0.1, 0.1)
If true, add the terms to the current objective, otherwise start with
an empty objective.
"""
interface = model.problem
reverse_value = model.solver.objective.expression
reverse_value = interface.Objective(
reverse_value, direction=model.solver.objective.direction,
sloppy=True)
if isinstance(value, dict):
if not model.objective.is_Linear:
raise ValueError('can only update non-linear objectives '
'additively using object of class '
'model.problem.Objective, not %s' %
type(value))
if not additive:
model.solver.objective = interface.Objective(
Zero, direction=model.solver.objective.direction)
for reaction, coef in value.items():
model.solver.objective.set_linear_coefficients(
{reaction.forward_variable: coef,
reaction.reverse_variable: -coef})
elif isinstance(value, (Basic, optlang.interface.Objective)):
if isinstance(value, Basic):
value = interface.Objective(
value, direction=model.solver.objective.direction,
sloppy=False)
# Check whether expression only uses variables from current model
# clone the objective if not, faster than cloning without checking
if not _valid_atoms(model, value.expression):
value = interface.Objective.clone(value, model=model.solver)
if not additive:
model.solver.objective = value
else:
model.solver.objective += value.expression
else:
raise TypeError(
'%r is not a valid objective for %r.' % (value, model.solver))
context = get_context(model)
if context:
def reset():
model.solver.objective = reverse_value
model.solver.objective.direction = reverse_value.direction
context(reset)
def remove_reactions(self, reactions, delete=True, remove_orphans=False):
"""Remove reactions from the model.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reactions : list
A list with reactions (`cobra.Reaction`), or their id's, to remove
delete : bool
Whether or not the reactions should be deleted after removal.
If the reactions are not deleted, those objects will be
recreated with new metabolite and gene objects.
remove_orphans : bool
Remove orphaned genes and metabolites from the model as well
"""
if isinstance(reactions, string_types) or hasattr(reactions, "id"):
warn("need to pass in a list")
reactions = [reactions]
context = get_context(self)
for reaction in reactions:
try:
reaction = self.reactions[self.reactions.index(reaction)]
except ValueError:
warn('%s not in %s' % (reaction, self))
else:
forward = reaction.forward_variable
reverse = reaction.reverse_variable
self.remove_cons_vars([forward, reverse])
self.reactions.remove(reaction)
reaction._model = None
if context:
context(partial(setattr, reaction, '_model', self))
context(partial(self.reactions.add, reaction))
for x in reaction._metabolites:
if reaction in x._reaction:
x._reaction.remove(reaction)
if context:
context(partial(x._reaction.add, reaction))
if remove_orphans and len(x._reaction) == 0:
self.remove_metabolites(x)
for x in reaction._genes:
if reaction in x._reaction:
x._reaction.remove(reaction)
if context:
context(partial(x._reaction.add, reaction))
if remove_orphans and len(x._reaction) == 0:
self.genes.remove(x)
if context:
context(partial(self.genes.add, x))
reaction._metabolites = {}
reaction._genes = set()
def add_reactions(self, reaction_list):
"""Will add a cobra.Reaction object to the model, if
reaction.id is not in self.reactions.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reaction_list : list
A list of `cobra.Reaction` objects
"""
try:
reaction_list = DictList(reaction_list)
except TypeError:
reaction_list = DictList([reaction_list])
# Only add the reaction if one with the same ID is not already
# present in the model.
reactions_in_model = [
i.id for i in reaction_list if i.id in self.reactions
]
if len(reactions_in_model) > 0:
raise Exception("Reactions already in the model: " +
", ".join(reactions_in_model))
context = get_context(self)
# Add reactions. Also take care of genes and metabolites in the loop
for reaction in reaction_list:
reaction._reset_var_cache()
reaction._model = self # the reaction now points to the model
# keys() is necessary because the dict will be modified during
# the loop
for metabolite in list(reaction._metabolites.keys()):
# if the metabolite is not in the model, add it
# should we be adding a copy instead.
if metabolite not in self.metabolites:
self.add_metabolites(metabolite)
# A copy of the metabolite exists in the model, the reaction
# needs to point to the metabolite in the model.
else:
stoichiometry = reaction._metabolites.pop(metabolite)
model_metabolite = self.metabolites.get_by_id(
metabolite.id)
reaction._metabolites[model_metabolite] = stoichiometry
model_metabolite._reaction.add(reaction)
if context:
context(
partial(model_metabolite._reaction.remove,
reaction))
for gene in list(reaction._genes):
# If the gene is not in the model, add it
if not self.genes.has_id(gene.id):
self.genes += [gene]
gene._model = self
if context:
# Remove the gene later
context(partial(self.genes.__isub__, [gene]))
context(partial(setattr, gene, '_model', None))
# Otherwise, make the gene point to the one in the model
else:
model_gene = self.genes.get_by_id(gene.id)
if model_gene is not gene:
reaction._dissociate_gene(gene)
reaction._associate_gene(model_gene)
self.reactions += reaction_list
if context:
context(partial(self.reactions.__isub__, reaction_list))
# from cameo ...
self._populate_solver(reaction_list)
def add_metabolites(self,
metabolites_to_add,
combine=True,
reversibly=True):
"""Add metabolites and stoichiometric coefficients to the reaction.
If the final coefficient for a metabolite is 0 then it is removed
from the reaction.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolites_to_add : dict
Dictionary with metabolite objects or metabolite identifiers as
keys and coefficients as values.
combine : bool
Describes behavior a metabolite already exists in the reaction.
True causes the coefficients to be added.
False causes the coefficient to be replaced.
reversibly : bool
Whether to add the change to the context to make the change
reversibly or not (primarily intended for internal use).
"""
old_coefficients = self.metabolites
new_metabolites = []
_id_to_metabolites = dict([(x.id, x) for x in self._metabolites])
for metabolite, coefficient in iteritems(metabolites_to_add):
met_id = str(metabolite)
# If a metabolite already exists in the reaction then
# just add them.
if met_id in _id_to_metabolites:
reaction_metabolite = _id_to_metabolites[met_id]
if combine:
self._metabolites[reaction_metabolite] += coefficient
else:
self._metabolites[reaction_metabolite] = coefficient
else:
# If the reaction is in a model, ensure we aren't using
# a duplicate metabolite.
if self._model:
try:
metabolite = \
self._model.metabolites.get_by_id(met_id)
except KeyError as e:
if isinstance(metabolite, Metabolite):
new_metabolites.append(metabolite)
else:
# do we want to handle creation here?
raise e
elif isinstance(metabolite, string_types):
# if we want to handle creation, this should be changed
raise ValueError(
"reaction '%s' does not belong to a model" % self.id)
self._metabolites[metabolite] = coefficient
# make the metabolite aware that it is involved in this
# reaction
metabolite._reaction.add(self)
for metabolite, the_coefficient in list(self._metabolites.items()):
if the_coefficient == 0:
# make the metabolite aware that it no longer participates
# in this reaction
metabolite._reaction.remove(self)
self._metabolites.pop(metabolite)
# from cameo ...
model = self.model
if model is not None:
model.add_metabolites(new_metabolites)
for metabolite, coefficient in metabolites_to_add.items():
if isinstance(metabolite,
str): # support metabolites added as strings.
metabolite = model.metabolites.get_by_id(metabolite)
if combine:
try:
old_coefficient = old_coefficients[metabolite]
except KeyError:
pass
else:
coefficient = coefficient + old_coefficient
model.constraints[metabolite.id].set_linear_coefficients({
self.forward_variable:
coefficient,
self.reverse_variable:
-coefficient
})
context = get_context(self)
if context and reversibly:
# Just subtract the metabolites that were added
context(
partial(self.subtract_metabolites,
metabolites_to_add,
combine=True,
reversibly=False))
def add_reactions(self, reaction_list):
"""Add reactions to the model.
Reactions with identifiers identical to a reaction already in the
model are ignored.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reaction_list : list
A list of `cobra.Reaction` objects
"""
try:
reaction_list = DictList(reaction_list)
except TypeError:
reaction_list = DictList([reaction_list])
# First check whether the metabolites exist in the model
existing = [rxn for rxn in reaction_list if rxn.id in self.reactions]
for rxn in existing:
LOGGER.info('skip adding reaction %s as already existing', rxn.id)
reaction_list = [
rxn for rxn in reaction_list if rxn.id not in existing
]
context = get_context(self)
# Add reactions. Also take care of genes and metabolites in the loop
for reaction in reaction_list:
reaction._reset_var_cache()
reaction._model = self # the reaction now points to the model
# keys() is necessary because the dict will be modified during
# the loop
for metabolite in list(reaction._metabolites.keys()):
# if the metabolite is not in the model, add it
# should we be adding a copy instead.
if metabolite not in self.metabolites:
self.add_metabolites(metabolite)
# A copy of the metabolite exists in the model, the reaction
# needs to point to the metabolite in the model.
else:
stoichiometry = reaction._metabolites.pop(metabolite)
model_metabolite = self.metabolites.get_by_id(
metabolite.id)
reaction._metabolites[model_metabolite] = stoichiometry
model_metabolite._reaction.add(reaction)
if context:
context(
partial(model_metabolite._reaction.remove,
reaction))
for gene in list(reaction._genes):
# If the gene is not in the model, add it
if not self.genes.has_id(gene.id):
self.genes += [gene]
gene._model = self
if context:
# Remove the gene later
context(partial(self.genes.__isub__, [gene]))
context(partial(setattr, gene, '_model', None))
# Otherwise, make the gene point to the one in the model
else:
model_gene = self.genes.get_by_id(gene.id)
if model_gene is not gene:
reaction._dissociate_gene(gene)
reaction._associate_gene(model_gene)
self.reactions += reaction_list
if context:
context(partial(self.reactions.__isub__, reaction_list))
# from cameo ...
self._populate_solver(reaction_list)
def set_objective(model, value, additive=False):
"""Set the model objective.
Parameters
----------
model : cobra model
The model to set the objective for
value : model.problem.Objective,
e.g. optlang.glpk_interface.Objective, sympy.Basic or dict
If the model objective is linear, the value can be a new Objective
object or a dictionary with linear coefficients where each key is a
reaction and the element the new coefficient (float).
If the objective is not linear and `additive` is true, only values
of class Objective.
additive : boolmodel.reactions.Biomass_Ecoli_core.bounds = (0.1, 0.1)
If true, add the terms to the current objective, otherwise start with
an empty objective.
"""
interface = model.problem
reverse_value = model.solver.objective.expression
reverse_value = interface.Objective(
reverse_value, direction=model.solver.objective.direction,
sloppy=True)
if isinstance(value, dict):
if not model.objective.is_Linear:
raise ValueError('can only update non-linear objectives '
'additively using object of class '
'model.problem.Objective, not %s' %
type(value))
if not additive:
model.solver.objective = interface.Objective(
Zero, direction=model.solver.objective.direction)
for reaction, coef in value.items():
model.solver.objective.set_linear_coefficients(
{reaction.forward_variable: coef,
reaction.reverse_variable: -coef})
elif isinstance(value, (Basic, optlang.interface.Objective)):
if isinstance(value, Basic):
value = interface.Objective(
value, direction=model.solver.objective.direction,
sloppy=False)
# Check whether expression only uses variables from current model
# clone the objective if not, faster than cloning without checking
if not _valid_atoms(model, value.expression):
value = interface.Objective.clone(value, model=model.solver)
if not additive:
model.solver.objective = value
else:
model.solver.objective += value.expression
else:
raise TypeError(
'%r is not a valid objective for %r.' % (value, model.solver))
context = get_context(model)
if context:
def reset():
model.solver.objective = reverse_value
model.solver.objective.direction = reverse_value.direction
context(reset)
def set_objective(
model: "Model",
value: Union[optlang.interface.Objective, optlang.symbolics.Basic,
Dict["Reaction", float], ],
additive: bool = False,
) -> None:
"""Set the model objective.
Parameters
----------
model : cobra.Model
The model to set the objective for.
value : optlang.interface.Objective, optlang.symbolics.Basic, dict
If the model objective is linear, then the value can be a new
optlang.interface.Objective or a dictionary with linear
coefficients where each key is a reaction and the corresponding
value is the new coefficient (float).
If the objective is non-linear and `additive` is True, then only
values of class optlang.interface.Objective, are accepted.
additive : bool
If True, add the terms to the current objective, otherwise start with
an empty objective.
Raises
------
ValueError
If model objective is non-linear and the `value` is a dict.
TypeError
If the type of `value` is not one of the accepted ones.
"""
interface = model.problem
reverse_value = model.solver.objective.expression
reverse_value = interface.Objective(
reverse_value, direction=model.solver.objective.direction, sloppy=True)
if isinstance(value, dict):
if not model.objective.is_Linear:
raise ValueError(
"You can only update non-linear objectives additively using object of "
f"class optlang.interface.Objective, not of {type(value)}")
if not additive:
model.solver.objective = interface.Objective(
Zero, direction=model.solver.objective.direction)
for reaction, coef in value.items():
model.solver.objective.set_linear_coefficients({
reaction.forward_variable:
coef,
reaction.reverse_variable:
-coef
})
elif isinstance(value, (Basic, optlang.interface.Objective)):
if isinstance(value, Basic):
value = interface.Objective(
value,
direction=model.solver.objective.direction,
sloppy=False)
# Check whether expression only uses variables from current model;
# clone the objective if not, faster than cloning without checking
if not _valid_atoms(model, value.expression):
value = interface.Objective.clone(value, model=model.solver)
if not additive:
model.solver.objective = value
else:
model.solver.objective += value.expression
else:
raise TypeError(
f"{value} is not a valid objective for {model.solver}.")
context = get_context(model)
if context:
def reset():
model.solver.objective = reverse_value
model.solver.objective.direction = reverse_value.direction
context(reset)
def remove_reactions(self, reactions, remove_orphans=False):
"""Remove reactions from the model.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reactions : list
A list with reactions (`cobra.Reaction`), or their id's, to remove
remove_orphans : bool
Remove orphaned genes and metabolites from the model as well
"""
if isinstance(reactions, string_types) or hasattr(reactions, "id"):
warn("need to pass in a list")
reactions = [reactions]
context = get_context(self)
for reaction in reactions:
# Make sure the reaction is in the model
try:
reaction = self.reactions[self.reactions.index(reaction)]
except ValueError:
warn("%s not in %s" % (reaction, self))
else:
forward = reaction.forward_variable
reverse = reaction.reverse_variable
if context:
obj_coef = reaction.objective_coefficient
if obj_coef != 0:
context(
partial(
self.solver.objective.set_linear_coefficients,
{
forward: obj_coef,
reverse: -obj_coef
},
))
context(partial(self._populate_solver, [reaction]))
context(partial(setattr, reaction, "_model", self))
context(partial(self.reactions.add, reaction))
self.remove_cons_vars([forward, reverse])
self.reactions.remove(reaction)
reaction._model = None
for met in reaction._metabolites:
if reaction in met._reaction:
met._reaction.remove(reaction)
if context:
context(partial(met._reaction.add, reaction))
if remove_orphans and len(met._reaction) == 0:
self.remove_metabolites(met)
for gene in reaction._genes:
if reaction in gene._reaction:
gene._reaction.remove(reaction)
if context:
context(partial(gene._reaction.add, reaction))
if remove_orphans and len(gene._reaction) == 0:
self.genes.remove(gene)
if context:
context(partial(self.genes.add, gene))
# remove reference to the reaction in all groups
associated_groups = self.get_associated_groups(reaction)
for group in associated_groups:
group.remove_members(reaction)
def add_reactions(self, reaction_list):
"""Add reactions to the model.
Reactions with identifiers identical to a reaction already in the
model are ignored.
The change is reverted upon exit when using the model as a context.
Parameters
----------
reaction_list : list
A list of `cobra.Reaction` objects
"""
def existing_filter(rxn):
if rxn.id in self.reactions:
logger.warning(
"Ignoring reaction '%s' since it already exists.", rxn.id)
return False
return True
# First check whether the reactions exist in the model.
pruned = DictList(filter(existing_filter, reaction_list))
context = get_context(self)
# Add reactions. Also take care of genes and metabolites in the loop.
for reaction in pruned:
reaction._model = self
# Build a `list()` because the dict will be modified in the loop.
for metabolite in list(reaction.metabolites):
# TODO: Should we add a copy of the metabolite instead?
if metabolite not in self.metabolites:
self.add_metabolites(metabolite)
# A copy of the metabolite exists in the model, the reaction
# needs to point to the metabolite in the model.
else:
# FIXME: Modifying 'private' attributes is horrible.
stoichiometry = reaction._metabolites.pop(metabolite)
model_metabolite = self.metabolites.get_by_id(
metabolite.id)
reaction._metabolites[model_metabolite] = stoichiometry
model_metabolite._reaction.add(reaction)
if context:
context(
partial(model_metabolite._reaction.remove,
reaction))
for gene in list(reaction._genes):
# If the gene is not in the model, add it
if not self.genes.has_id(gene.id):
self.genes += [gene]
gene._model = self
if context:
# Remove the gene later
context(partial(self.genes.__isub__, [gene]))
context(partial(setattr, gene, "_model", None))
# Otherwise, make the gene point to the one in the model
else:
model_gene = self.genes.get_by_id(gene.id)
if model_gene is not gene:
reaction._dissociate_gene(gene)
reaction._associate_gene(model_gene)
self.reactions += pruned
if context:
context(partial(self.reactions.__isub__, pruned))
def add_metabolites(self,
metabolites_to_add,
combine=True,
reversibly=True):
"""Add metabolites and stoichiometric coefficients to the reaction.
If the final coefficient for a metabolite is 0 then it is removed
from the reaction.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolites_to_add : dict
Dictionary with metabolite objects or metabolite identifiers as
keys and coefficients as values. If keys are strings (name of a
metabolite) the reaction must already be part of a model and a
metabolite with the given name must exist in the model.
combine : bool
Describes behavior a metabolite already exists in the reaction.
True causes the coefficients to be added.
False causes the coefficient to be replaced.
reversibly : bool
Whether to add the change to the context to make the change
reversibly or not (primarily intended for internal use).
"""
old_coefficients = self.metabolites
new_metabolites = []
_id_to_metabolites = dict([(x.id, x) for x in self._metabolites])
for metabolite, coefficient in metabolites_to_add.items():
# Make sure metabolites being added belong to the same model, or
# else copy them.
if isinstance(metabolite, Metabolite):
if (metabolite.model is not None) and (metabolite.model
is not self._model):
metabolite = metabolite.copy()
met_id = str(metabolite)
# If a metabolite already exists in the reaction then
# just add them.
if met_id in _id_to_metabolites:
reaction_metabolite = _id_to_metabolites[met_id]
if combine:
self._metabolites[reaction_metabolite] += coefficient
else:
self._metabolites[reaction_metabolite] = coefficient
else:
# If the reaction is in a model, ensure we aren't using
# a duplicate metabolite.
if self._model:
try:
metabolite = self._model.metabolites.get_by_id(met_id)
except KeyError as e:
if isinstance(metabolite, Metabolite):
new_metabolites.append(metabolite)
else:
# do we want to handle creation here?
raise e
elif isinstance(metabolite, str):
# if we want to handle creation, this should be changed
raise ValueError("Reaction '%s' does not belong to a "
"model. Either add the reaction to a "
"model or use Metabolite objects instead "
"of strings as keys." % self.id)
self._metabolites[metabolite] = coefficient
# make the metabolite aware that it is involved in this
# reaction
metabolite._reaction.add(self)
# from cameo ...
model = self.model
if model is not None:
model.add_metabolites(new_metabolites)
for metabolite, coefficient in self._metabolites.items():
model.constraints[metabolite.id].set_linear_coefficients({
self.forward_variable:
coefficient,
self.reverse_variable:
-coefficient,
})
for metabolite, the_coefficient in list(self._metabolites.items()):
if the_coefficient == 0:
# make the metabolite aware that it no longer participates
# in this reaction
metabolite._reaction.remove(self)
self._metabolites.pop(metabolite)
context = get_context(self)
if context and reversibly:
if combine:
# Just subtract the metabolites that were added
context(
partial(
self.subtract_metabolites,
metabolites_to_add,
combine=True,
reversibly=False,
))
else:
# Reset them with add_metabolites
mets_to_reset = {
key: old_coefficients[model.metabolites.get_by_any(key)[0]]
for key in metabolites_to_add.keys()
}
context(
partial(
self.add_metabolites,
mets_to_reset,
combine=False,
reversibly=False,
))
def add_metabolites(self, metabolites_to_add, combine=True,
reversibly=True):
"""Add metabolites and stoichiometric coefficients to the reaction.
If the final coefficient for a metabolite is 0 then it is removed
from the reaction.
The change is reverted upon exit when using the model as a context.
Parameters
----------
metabolites_to_add : dict
Dictionary with metabolite objects or metabolite identifiers as
keys and coefficients as values. If keys are strings (name of a
metabolite) the reaction must already be part of a model and a
metabolite with the given name must exist in the model.
combine : bool
Describes behavior a metabolite already exists in the reaction.
True causes the coefficients to be added.
False causes the coefficient to be replaced.
reversibly : bool
Whether to add the change to the context to make the change
reversibly or not (primarily intended for internal use).
"""
old_coefficients = self.metabolites
new_metabolites = []
_id_to_metabolites = dict([(x.id, x) for x in self._metabolites])
for metabolite, coefficient in iteritems(metabolites_to_add):
met_id = str(metabolite)
# If a metabolite already exists in the reaction then
# just add them.
if met_id in _id_to_metabolites:
reaction_metabolite = _id_to_metabolites[met_id]
if combine:
self._metabolites[reaction_metabolite] += coefficient
else:
self._metabolites[reaction_metabolite] = coefficient
else:
# If the reaction is in a model, ensure we aren't using
# a duplicate metabolite.
if self._model:
try:
metabolite = \
self._model.metabolites.get_by_id(met_id)
except KeyError as e:
if isinstance(metabolite, Metabolite):
new_metabolites.append(metabolite)
else:
# do we want to handle creation here?
raise e
elif isinstance(metabolite, string_types):
# if we want to handle creation, this should be changed
raise ValueError("Reaction '%s' does not belong to a "
"model. Either add the reaction to a "
"model or use Metabolite objects instead "
"of strings as keys."
% self.id)
self._metabolites[metabolite] = coefficient
# make the metabolite aware that it is involved in this
# reaction
metabolite._reaction.add(self)
for metabolite, the_coefficient in list(self._metabolites.items()):
if the_coefficient == 0:
# make the metabolite aware that it no longer participates
# in this reaction
metabolite._reaction.remove(self)
self._metabolites.pop(metabolite)
# from cameo ...
model = self.model
if model is not None:
model.add_metabolites(new_metabolites)
for metabolite, coefficient in metabolites_to_add.items():
if isinstance(metabolite,
str): # support metabolites added as strings.
metabolite = model.metabolites.get_by_id(metabolite)
if combine:
try:
old_coefficient = old_coefficients[metabolite]
except KeyError:
pass
else:
coefficient = coefficient + old_coefficient
model.constraints[
metabolite.id].set_linear_coefficients(
{self.forward_variable: coefficient,
self.reverse_variable: -coefficient
})
context = get_context(self)
if context and reversibly:
if combine:
# Just subtract the metabolites that were added
context(partial(
self.subtract_metabolites, metabolites_to_add,
combine=True, reversibly=False))
else:
# Reset them with add_metabolites
mets_to_reset = {
key: old_coefficients[model.metabolites.get_by_any(key)[0]]
for key in iterkeys(metabolites_to_add)}
context(partial(
self.add_metabolites, mets_to_reset,
combine=False, reversibly=False))