def escapes(self, escapes_file, readquiet):
#read and define escape metabolites.
if not readquiet:
print 'escapes from', escapes_file
escapes = {}
file = open(escapes_file)
while True:
line = file.readline()
if line == '': break
line = line.rstrip()
if line == '': continue
if line[0] == '#': continue
col = line.split('\t')
rawmet = col[0]
if not readquiet:
print ' ', rawmet
#convert metabolites from forms like 'leu-L[c]' to 'M_leu_DASH_L_c'...
met = eq_current.convert_metabolite_ext2int(rawmet)
escapes[met] = 1
escapelist = escapes.keys()
cb.set_escapes(self, escapelist)
if not readquiet:
print
def exchanges(self, exchanges_file, readquiet):
#read and define exchange metabolites.
if not readquiet:
print 'exchanges from', exchanges_file
exchanges = {}
file = open(exchanges_file)
while True:
line = file.readline()
if line == '': break
line = line.rstrip()
if line == '': continue
if line[0] == '#': continue
col = line.split() ## starting here, some changes here to cope with MM2 output
try:
lb, ub = col[1], col[2]
except:
lb, ub = '-1000', '1000'
rawmet = col[0]
if not readquiet:
print ' ', rawmet
#convert metabolites from forms like 'leu-L[c]' to 'M_leu_DASH_L_c'...
met = eq_current.convert_metabolite_ext2int(rawmet)
exchanges[(met, lb, ub)] = 1
exchangelist = exchanges.keys()
cb.set_exchanges(self, exchangelist)
if not readquiet:
print
def biomass(self, biomass_file, readquiet):
#read and define biomass equation...
if not readquiet:
print 'biomass from', biomass_file
biomass_equation = [[], []]
file = open(biomass_file)
while True:
line = file.readline()
if line == '': break
line = line.rstrip()
if line == '': continue
if line[0] == '#': continue
col = line.split('\t')
[rawmet, coef, side] = col[0:3]
#convert metabolites from forms like 'leu-L[c]' to 'M_leu_DASH_L_c'...
met = eq_current.convert_metabolite_ext2int(rawmet)
if 'reactant' in side:
biomass_equation[0].append((met, coef))
self.NOTSOURCES.append(met)
elif 'product' in side:
biomass_equation[1].append((met, coef))
self.NOTSOURCES.append(met)
else:
print 'Warning: biomass component skipped because cannot be idenified as reactant or product-->', line
#add biomass equation to model, and set this as the objective...
cb.add_reaction(self, 'R_biomass_target', 'BiomassRxn', False, {'SUBSYSTEM: BiomassObjective':1, 'EC: .':1}, biomass_equation)
cb.set_objective(self, 'Maximize', 'R_biomass_target')
#cb.set_constraint(self, 'R_biomass_target', '0.0', str(float(self.VMAX)) )
if not readquiet:
print eq_current.makestring(biomass_equation, False)
print