def load_database(self):
self.logger.info("Test loading Database")
user_defined_export_rxns_Sji = {
'EX_glc': {
'C00031': -1.0
},
'EX_nad': {
'C00003': -1.0
},
'EX_adp': {
'C00008': -1.0
},
'EX_phosphate': {
'C00009': -1.0
},
'EX_pyruvate': {
'C00022': -1.0
},
'EX_nadh': {
'C00004': -1.0
},
'EX_atp': {
'C00002': -1.0
},
'EX_h2o': {
'C00001': -1.0
},
'EX_hplus': {
'C00080': -1.0
},
'EX_nadp': {
'C00006': -1.0
},
'EX_nadph': {
'C00005': -1.0
}
}
DB = load_db_v3(
reduce_model_size=True,
user_defined_export_rxns_Sji=user_defined_export_rxns_Sji)
DB.validate()
# assert_equal(len(DB.metabolites), 5969)
# assert_equal(len(DB.reactions), 7175)
return DB
def __init__(self,
objective='MinFlux',
zlb=10,
nATP=1,
add_loopless_constraints=True,
max_iteration=1,
pulp_solver=None,
result_filepath=None,
M=1000,
logger=None):
"""An example of the optStoic model for identifying glycolytic pathways
generating n ATP.
Args:
objective (str, optional): Description
zlb (int, optional): Description
nATP (int, optional): nATP (int, optional): The number of ATP
add_loopless_constraints (bool, optional): Description
max_iteration (int, optional): Description
pulp_solver (None, optional): Description
result_filepath (None, optional): Description
M (int, optional): Description
logger (None, optional): Description
"""
self.DBV3 = database.load_db_v3(
reduce_model_size=True,
user_defined_export_rxns_Sji=self.EXPORT_RXNS_SJI
)
super(OptStoicGlycolysis, self).__init__(
database=self.DBV3,
objective='MinFlux',
zlb=zlb,
specific_bounds=self.GLYCOLYSIS_BOUNDS,
custom_flux_constraints=self.CUSTOM_REDOX_CONSTRAINTS,
add_loopless_constraints=add_loopless_constraints,
max_iteration=max_iteration,
pulp_solver=pulp_solver,
result_filepath=result_filepath,
M=1000,
logger=logger)
self.nATP = nATP
def test_optstoic():
"""An alternative to the nosetest due to issue with PULP/SCIP_CMD
"""
logger = create_logger(name='optstoicpy.script.optstoic.main')
logger.info("Test generalized optstoic")
# Set the following reactions as allowable export reactions
db3 = load_db_v3(reduce_model_size=True,
user_defined_export_rxns_Sji={
'EX_glc': {
'C00031': -1.0
},
'EX_nad': {
'C00003': -1.0
},
'EX_adp': {
'C00008': -1.0
},
'EX_phosphate': {
'C00009': -1.0
},
'EX_pyruvate': {
'C00022': -1.0
},
'EX_nadh': {
'C00004': -1.0
},
'EX_atp': {
'C00002': -1.0
},
'EX_h2o': {
'C00001': -1.0
},
'EX_hplus': {
'C00080': -1.0
},
'EX_nadp': {
'C00006': -1.0
},
'EX_nadph': {
'C00005': -1.0
}
})
#logger.debug('Testing optstoic output filepath: %s', res_dir)
pulp_solver = load_pulp_solver(solver_names=[
'SCIP_CMD', 'GUROBI', 'GUROBI_CMD', 'CPLEX_CMD', 'GLPK_CMD'
],
logger=logger)
# How to add custom flux constraints:
# E.g.,
# v('EX_nadph') + v('EX_nadh') = 2;
# v('EX_nadp') + v('EX_nad') = -2;
# v('EX_nadh') + v('EX_nad') = 0;
# v('EX_nadph') + v('EX_nadp') = 0;
# became
# lp_prob += v['EX_nadph'] + v['EX_nadh'] == 2, 'nadphcons1'
# lp_prob += v['EX_nadp'] + v['EX_nad'] == -2, 'nadphcons2'
# lp_prob += v['EX_nadh'] + v['EX_nad'] == 0, 'nadphcons3'
# lp_prob += v['EX_nadph'] + v['EX_nadp'] == 0, 'nadphcons4'
custom_flux_constraints = [{
'constraint_name': 'nadphcons1',
'reactions': ['EX_nadph', 'EX_nadh'],
'UB': 2,
'LB': 2
}, {
'constraint_name': 'nadphcons2',
'reactions': ['EX_nadp', 'EX_nad'],
'UB': -2,
'LB': -2
}, {
'constraint_name': 'nadphcons3',
'reactions': ['EX_nadh', 'EX_nad'],
'UB': 0,
'LB': 0
}, {
'constraint_name': 'nadphcons4',
'reactions': ['EX_nadph', 'EX_nadp'],
'UB': 0,
'LB': 0
}]
specific_bounds = {
'EX_glc': {
'LB': -1,
'UB': -1
},
'EX_pyruvate': {
'LB': 2,
'UB': 2
},
'EX_nad': {
'LB': -2,
'UB': 0
},
'EX_nadh': {
'LB': 0,
'UB': 2
},
'EX_nadp': {
'LB': -2,
'UB': 0
},
'EX_nadph': {
'LB': 0,
'UB': 2
},
'EX_adp': {
'LB': -1,
'UB': -1
},
'EX_phosphate': {
'LB': -1,
'UB': -1
},
'EX_atp': {
'LB': 1,
'UB': 1
},
'EX_h2o': {
'LB': 1,
'UB': 1
},
'EX_hplus': {
'LB': -10,
'UB': 10
}
} # pulp/gurobi has issue with "h+"
test = OptStoic(database=db3,
objective='MinFlux',
zlb=None,
specific_bounds=specific_bounds,
custom_flux_constraints=custom_flux_constraints,
add_loopless_constraints=True,
max_iteration=2,
pulp_solver=pulp_solver,
result_filepath='./result/',
M=1000,
logger=logger)
if sys.platform == 'cygwin':
lp_prob, pathways = test.solve_gurobi_cl(
outputfile='test_optstoic_cyg.txt', cleanup=False)
#test.max_iteration = test.max_iteration + 2
#lp_prob, pathways = test.solve_gurobi_cl(outputfile='test_optstoic_cyg.txt', exclude_existing_solution=True, cleanup=False)
else:
lp_prob, pathways = test.solve(outputfile='test_optstoic.txt')
#test.max_iteration = test.max_iteration + 1
#lp_prob, pathways = test.solve(outputfile='test_optstoic.txt', exclude_existing_solution=True)
return lp_prob, pathways