def create_modelFromReactionsAndMetabolitesTables(self,rxns_table_I,mets_table_I):
'''generate a cobra model from isotopomer_modelReactions and isotopomer_modelMetabolites tables'''
cobra_model = Model(rxns_table_I[0]['model_id']);
for rxn_cnt,rxn_row in enumerate(rxns_table_I):
#if rxn_row['rxn_id'] == 'HEX1':
# print 'check'
mets = {}
print(rxn_row['rxn_id'])
# parse the reactants
for rxn_met_cnt,rxn_met in enumerate(rxn_row['reactants_ids']):
for met_cnt,met_row in enumerate(mets_table_I):
if met_row['met_id']==rxn_met:# and met_row['balanced']:
compartment = met_row['compartment']
if not compartment:
met_id_tmp = met_row['met_id'].split('.')[0]
compartment = met_id_tmp.split('_')[-1];
met_tmp = Metabolite(met_row['met_id'],met_row['formula'],met_row['met_name'],compartment)
met_tmp.charge = met_row['charge']
# check for duplicate metabolites
met_keys = list(mets.keys());
met_keys_ids = {};
if met_keys:
for cnt,met in enumerate(met_keys):
met_keys_ids[met.id]=cnt;
if met_tmp.id in list(met_keys_ids.keys()):
mets[met_keys[met_keys_ids[met_tmp.id]]]-=1
else:
mets[met_tmp] = rxn_row['reactants_stoichiometry'][rxn_met_cnt];
break;
# parse the products
for rxn_met_cnt,rxn_met in enumerate(rxn_row['products_ids']):
for met_cnt,met_row in enumerate(mets_table_I):
if met_row['met_id']==rxn_met:# and met_row['balanced']:
compartment = met_row['compartment']
if not compartment:
met_id_tmp = met_row['met_id'].split('.')[0]
compartment = met_id_tmp.split('_')[-1];
met_tmp = Metabolite(met_row['met_id'],met_row['formula'],met_row['met_name'],compartment)
met_tmp.charge = met_row['charge']
# check for duplicate metabolites
met_keys = list(mets.keys());
met_keys_ids = {};
if met_keys:
for cnt,met in enumerate(met_keys):
met_keys_ids[met.id]=cnt;
if met_tmp.id in list(met_keys_ids.keys()):
mets[met_keys[met_keys_ids[met_tmp.id]]]+=1
else:
mets[met_tmp] = rxn_row['products_stoichiometry'][rxn_met_cnt];
break;
rxn = None;
rxn = Reaction(rxn_row['rxn_id']);
rxn.add_metabolites(mets);
rxn.lower_bound=rxn_row['lower_bound'];
rxn.upper_bound=rxn_row['upper_bound'];
rxn.subsystem=rxn_row['subsystem'];
rxn.gpr=rxn_row['gpr'];
rxn.objective_coefficient=rxn_row['objective_coefficient'];
cobra_model.add_reactions([rxn]);
cobra_model.repair();
return cobra_model
