def setUp(self):
self.instring = "A + B -2.0>\tC +\tB"
#this string includes:
# different kinds of whitespace
# disordered products
# floating-point rate
self.net = ReactionNetwork.from_string(self.instring)
self.othernet = ReactionNetwork.from_string(self.instring)
self.wrongstring = "A + B\t-3.0> C + B"
self.wrongnet = ReactionNetwork.from_string(self.wrongstring)
def setUp(self):
self.instring = "A + B -2.0>\tC +\tB"
#this string includes:
# different kinds of whitespace
# disordered products
# floating-point rate
self.net = ReactionNetwork.from_string(self.instring)
self.othernet = ReactionNetwork.from_string(self.instring)
self.wrongstring = "A + B\t-3.0> C + B"
self.wrongnet = ReactionNetwork.from_string(self.wrongstring)
def main():
parser = optparse.OptionParser(
description="Pretty-printer and syntax checker for .chem files.")
parser.add_option("-i",
"--infile",
dest="infile",
help="read from INFILE (if ommited, use stdin)",
metavar="INFILE")
parser.add_option(
"-o",
"--outfile",
dest="outfile",
help="write to OUTFILE in .chem format (if ommited, use stdout)",
metavar="OUTFILE")
(options, args) = parser.parse_args()
rn = None
if options.infile is None:
#read from standard in
rn = ReactionNetwork.from_string(sys.stdin.read())
else:
#read from provided filename
rn = ReactionNetwork.from_filename(options.infile)
chemstr = str(rn)
if options.outfile is None:
#print to standard out
sys.stdout.write(chemstr)
else:
#write to provided filename
outfile = open(options.outfile, "w")
outfile.write(chemstr)
outfile.close()
def main():
parser = optparse.OptionParser(description="Produces `.dot` output from `.chem` input.")
parser.add_option("-i", "--infile", dest="infile", help="read from INFILE in .chem format (if ommited, use stdin)", metavar="INFILE")
parser.add_option("-o", "--outfile", dest="outfile", help="write to OUTFILE in .dot format (if ommited, use stdout)", metavar="OUTFILE")
parser.add_option("-n", "--names", dest="names", help="style of molecular species naming. One of 'full', 'id', 'blank'", metavar="NAMES", default=None)
parser.add_option("-l", "--layout", dest="layout", help="layout to assign to the dot file")
(options, args) = parser.parse_args()
rn = None
if options.infile is None:
#read from standard in
rn = ReactionNetwork.from_string(sys.stdin.read())
else:
#read from provided filename
rn = ReactionNetwork.from_filename(options.infile)
dot = net_to_dot(rn, names=options.names)
if options.layout is not None:
dot["graph"]["layout"] = options.layout
dotstr = str(dot)
if options.outfile is None:
#print to standard out
sys.stdout.write(dotstr)
else:
#write to provided filename
outfile = open(options.outfile, "w")
outfile.write(dotstr)
outfile.close()
def main():
parser = optparse.OptionParser(description="Pretty-printer and syntax checker for .chem files.")
parser.add_option(
"-i", "--infile", dest="infile", help="read from INFILE (if ommited, use stdin)", metavar="INFILE"
)
parser.add_option(
"-o",
"--outfile",
dest="outfile",
help="write to OUTFILE in .chem format (if ommited, use stdout)",
metavar="OUTFILE",
)
(options, args) = parser.parse_args()
rn = None
if options.infile is None:
# read from standard in
rn = ReactionNetwork.from_string(sys.stdin.read())
else:
# read from provided filename
rn = ReactionNetwork.from_filename(options.infile)
chemstr = str(rn)
if options.outfile is None:
# print to standard out
sys.stdout.write(chemstr)
else:
# write to provided filename
outfile = open(options.outfile, "w")
outfile.write(chemstr)
outfile.close()
