class Metabolism2glpk(object):
"""docstring for metabolism2glpk"""
def __init__(self, metabolism):
super(Metabolism2glpk, self).__init__()
self.metabolism = metabolism
self.stoich = StoichiometricMatrix()
self.stoich.make_new_from_system(self.metabolism)
def __stoich_to_sparse_triplet(self):
"""docstring for fname"""
non_zero = self.stoich.matrix.nonzero()
num_non_zero = len(non_zero[0])
non_zero_elements = self.stoich.matrix[non_zero]
ia = intArray(num_non_zero)
ja = intArray(num_non_zero)
ar = doubleArray(num_non_zero)
print non_zero
for i in range(0, num_non_zero):
ia[i+1] = int(non_zero[0][i] + 1.)
ja[i+1] = non_zero[1][i] + 1
ar[i+1] = non_zero_elements[i]
print num_non_zero
print ia[1]
return (num_non_zero, ia, ja, ar)
def convert_to_ifba_metabolism(self):
"""docstring for convert_to_ifba_metabolism"""
lp = glp_create_prob()
(num_non_zero, ia, ja, ar) = self.__stoich_to_sparse_triplet()
glp_add_rows(lp, self.stoich.num_compounds)
glp_add_cols(lp, self.stoich.num_reactions)
glp_load_matrix(lp, num_non_zero, ia, ja, ar)
for i in range(self.stoich.num_compounds):
rev_compound_map = dict((v,k) for k, v in self.stoich.compound_map.iteritems())
glp_set_row_name(lp, i+1, rev_compound_map[i].identifier+"_"+rev_compound_map[i].compartment.name)
for i in range(self.stoich.num_reactions):
rev_reaction_map = dict((v,k) for k, v in self.stoich.reaction_map.iteritems())
glp_set_col_name(lp, i+1, rev_reaction_map[i].identifier)
fba_object = ifba.Metabolism(lp)
col_bounds = dict()
for r in self.metabolism:
if r.reversible:
print r
col_bounds[r.identifier] = (-1000, 1000)
else:
col_bounds[r.identifier] = (0, 1000)
fba_object.modifyColumnBounds(col_bounds)
fba_object.modifyRowBounds(dict([(r, (0., 0.)) for r in fba_object.getRowIDs()]))
return fba_object
def convert_to_ifba_glpk(self):
"""docstring for convert_to_ifba_metabolism"""
pass
def convert_to_ifba_glpk(self):
"""docstring for convert_to_ifba_metabolism"""
pass
if __name__ == '__main__':
import re
smallModel = '../test_data/Ec_core_flux1.xml'
bigModel = '../test_data/iAF1260.xml'
parser = SBMLParser(smallModel, rprefix='R_', rsuffix='', cprefix='M_', csuffix=re.compile('_.$'))
metbol = parser.get_metabolic_system()
print metbol[0]
s = StoichiometricMatrix()
s.make_new_from_system(metbol)
print s.matrix
converter = Metabolism2glpk(metbol)
lp = converter.convert_to_ifba_metabolism()
print lp
print lp.getColumnIDs()
print lp.getObjectiveFunction()
lp.simplex()
print lp
extra_mets = [m.get_id() for m in metbol.compounds if m.compartment == 'Extra_organism']
lp.freeMetabolites(extra_mets)
lp.setOptFlag('Max')
lp.setReactionObjective('Biomass_Ecoli_core_N__w_GAM_')
print lp.getObjectiveFunction()
print lp.fba()
print lp
