def update(self, value_dict):
"""update matrix without propagating to model"""
if len(value_dict) < 100: # TODO benchmark for heuristic
for index, value in iteritems(value_dict):
lil_matrix.__setitem__(self, index, value)
else:
matrix = lil_matrix.todok(self)
matrix.update(value_dict)
self = SMatrix_lil(matrix.tolil(), model=self._model)
self._model._S = self
def update(self, value_dict):
"""update matrix without propagating to model"""
if len(value_dict) < 100: # TODO benchmark for heuristic
for index, value in iteritems(value_dict):
lil_matrix.__setitem__(self, index, value)
else:
matrix = lil_matrix.todok(self)
matrix.update(value_dict)
self = SMatrix_lil(matrix.tolil(), model=self._model)
self._model._S = self
def __setitem__(self, index, value):
lil_matrix.__setitem__(self, index, value)
if isinstance(index[0], int):
metabolites = [self._model.metabolites[index[0]]]
else:
metabolites = self._model.metabolites[index[0]]
if isinstance(index[1], int):
reactions = [self._model.reactions[index[1]]]
else:
reactions = self._model.reactions[index[1]]
if value == 0: # remove_metabolites
met_set = set(metabolites)
for reaction in reactions:
to_remove = met_set.intersection(reaction._metabolites)
for i in to_remove:
reaction.pop(i)
else: # add metabolites
met_dict = {met: value for met in metabolites}
for reaction in reactions:
reaction.add_metabolites(met_dict, combine=False)
def __setitem__(self, index, value):
lil_matrix.__setitem__(self, index, value)
if isinstance(index[0], int):
metabolites = [self._model.metabolites[index[0]]]
else:
metabolites = self._model.metabolites[index[0]]
if isinstance(index[1], int):
reactions = [self._model.reactions[index[1]]]
else:
reactions = self._model.reactions[index[1]]
if value == 0: # remove_metabolites
met_set = set(metabolites)
for reaction in reactions:
to_remove = met_set.intersection(reaction._metabolites)
for i in to_remove:
reaction.pop(i)
else: # add metabolites
met_dict = {met: value for met in metabolites}
for reaction in reactions:
reaction.add_metabolites(met_dict, combine=False)
