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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Load KEGG Pathway maps for use with the Biopython Pathway module.
The pathway maps are in the format::
RXXXXX:[X.X.X.X:] A + 2 B <=> C
RXXXXX:[X.X.X.X:] 3C <=> 2 D + E
...
where RXXXXX is a five-digit reaction id, and X.X.X.X is the optional
EC number of the enzyme that catalyze the reaction.
"""
from Bio.Pathway import Reaction
def parse(handle):
"""Parse a KEGG pathway map."""
for line in handle:
data, catalysts, reaction = line.split(":")
catalysts = [(catalysts,)]
reactants = {}
before, after = reaction.split("<=>")
compounds = before.split(" + ")
for compound in compounds:
compound = compound.strip()
try:
number, compound = compound.split()
number = -int(number)
except ValueError:
number = -1
reactants[compound] = number
compounds = after.split(" + ")
for compound in compounds:
compound = compound.strip()
try:
number, compound = compound.split()
number = int(number)
except ValueError:
number = +1
reactants[compound] = number
yield Reaction(reactants, catalysts, True, data)
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