def ParseReactionFormula(name, formula):
""" parse a two-sided formula such as: 2 C00001 = C00002 + C00003
return the set of substrates, products and the direction of the reaction
"""
try:
left, right = formula.split(' = ', 1)
except ValueError:
raise KeggParseException("There should be exactly one '=' sign")
sparse_reaction = {}
for cid, amount in NistRowData.ParseReactionFormulaSide(
left).iteritems():
sparse_reaction[cid] = -amount
for cid, amount in NistRowData.ParseReactionFormulaSide(
right).iteritems():
if (cid in sparse_reaction):
raise KeggParseException(
"C%05d appears on both sides of this formula" % cid)
sparse_reaction[cid] = amount
reaction = Reaction([name], sparse_reaction, None, '=>')
kegg = Kegg.getInstance()
rid = kegg.reaction2rid(reaction) or kegg.reaction2rid(
reaction.reverse())
reaction.rid = rid
return reaction
def ParseReactionFormula(name, formula):
""" parse a two-sided formula such as: 2 C00001 = C00002 + C00003
return the set of substrates, products and the direction of the reaction
"""
try:
left, right = formula.split(' = ', 1)
except ValueError:
raise KeggParseException("There should be exactly one '=' sign")
sparse_reaction = {}
for cid, amount in NistRowData.ParseReactionFormulaSide(left).iteritems():
sparse_reaction[cid] = -amount
for cid, amount in NistRowData.ParseReactionFormulaSide(right).iteritems():
if (cid in sparse_reaction):
raise KeggParseException("C%05d appears on both sides of this formula" % cid)
sparse_reaction[cid] = amount
reaction = Reaction([name], sparse_reaction, None, '=>')
kegg = Kegg.getInstance()
rid = kegg.reaction2rid(reaction) or kegg.reaction2rid(reaction.reverse())
reaction.rid = rid
return reaction
