def test_nprods_none_dict(self):
net = Uniform(10, 50, {(1, 1): 1, (2, 2): 2.0}, None)
net = Uniform(10, 50, {(1, 1): 1, (2, 2): 2.0}, None, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_rate_float(self):
net = Uniform(10, 50, 2, 2, 2.5)
net = Uniform(10, 50, 2, 2, 2.5, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nprods_dict(self):
net = Uniform(10, 50, 2, {1: 1, 2: 2})
net = Uniform(10, 50, 2, {1: 1, 2: 2}, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nprods_none_tuple(self):
net = Uniform(10, 50, ((1, 1), (2, 2), (2, 2)), None)
net = Uniform(10, 50, ((1, 1), (2, 2), (2, 2)), None, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nprods_tuple(self):
net = Uniform(10, 50, 2, (1, 2, 2))
net = Uniform(10, 50, 2, (1, 2, 2), rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nprods_list(self):
net = Uniform(10, 50, 2, [1, 2, 2])
net = Uniform(10, 50, 2, [1, 2, 2], rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nreacts_dict(self):
net = Uniform(10, 50, {1: 1, 2: 2.0}, 2)
net = Uniform(10, 50, {1: 1, 2: 2.0}, 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_rate_dict(self):
net = Uniform(10, 50, 2, 2, {1: 1, 1.0: 1, 2.5: 2.5})
net = Uniform(10, 50, 2, 2, {1: 1, 1.0: 1, 2.5: 2.5}, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nreacts_tuple(self):
net = Uniform(10, 50, (1, 2, 2), 2)
net = Uniform(10, 50, (1, 2, 2), 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nreacts_list(self):
net = Uniform(10, 50, [1, 2, 2], 2)
net = Uniform(10, 50, [1, 2, 2], 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nmols_dict(self):
mols = dict(list(zip(self.mols, list(range(1, len(self.mols) + 1)))))
net = Uniform(mols, 50, 2, 2)
net = Uniform(mols, 50, 2, 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nmols_list(self):
net = Uniform(list(self.mols), 50, 2, 2)
net = Uniform(list(self.mols), 50, 2, 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nmols_tuple(self):
net = Uniform(self.mols, 50, 2, 2)
net = Uniform(self.mols, 50, 2, 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_rate_list(self):
net = Uniform(10, 50, 2, 2, [1, 2.5, 3])
net = Uniform(10, 50, 2, 2, [1, 2.5, 3], rng=self.rng)
self.assertEqual(net.seen, self.mols)
def test_nprods_int(self):
net = Uniform(10, 50, 2, 2)
net = Uniform(10, 50, 2, 2, rng=self.rng)
self.assertEqual(net.seen, self.mols)
def main():
parser = argparse.ArgumentParser(
description="Generates `.chem` using Uniform algorithm.")
parser.add_argument(
"-o",
"--outfile",
action="store",
type=argparse.FileType('w'),
help="write to OUTFILE in .chem format (if ommited, use stdout)",
metavar="OUTFILE")
parser.add_argument("-n",
"--nmols",
action="store",
type=int,
help="number of molecules",
default=10)
parser.add_argument("-m",
"--nreactions",
action="store",
type=int,
help="number of reactions",
default=10)
parser.add_argument("-r",
"--nreactants",
action="append",
help="possible number of reactants",
default=[2])
parser.add_argument("-p",
"--nproducts",
action="append",
help="possible number of products",
default=[2])
parser.add_argument("-t",
"--rates",
action="append",
help="possible reaction rates",
default=[1.0])
parser.add_argument("-s",
"--seed",
action="store",
type=int,
help="pseudo-random seed",
default=None)
args = parser.parse_args()
nmols = args.nmols
nreactions = args.nreactions
nreactants = [int(x) for x in args.nreactants]
nproducts = [int(x) for x in args.nproducts]
rates = [float(x) for x in args.rates]
#strip defaults
if len(nreactants) > 1:
nreactants = nreactants[1:]
if len(nproducts) > 1:
nproducts = nproducts[1:]
if len(rates) > 1:
rates = rates[1:]
rng = random.Random(args.seed)
net = Uniform(nmols, nreactions, nreactants, nproducts, rates, rng=rng)
chemstr = """#Uniform reaction network
# nmols = {0}
# nreactions = {1}
# reactants = {2}
# products = {3}
# rates = {4}
# seed = {5}
""".format(repr(nmols), repr(nreactions), repr(nreactants), repr(nproducts),
repr(rates), args.seed)
chemstr += str(net)
chemstr += "\n"
if args.outfile is None:
#print to standard out
sys.stdout.write(chemstr)
else:
#write to provided filename
args.outfile.write(chemstr)
def test_rate_tuple(self):
net = Uniform(10, 50, 2, 2, (1, 2.5, 3))
net = Uniform(10, 50, 2, 2, (1, 2.5, 3), rng=self.rng)
self.assertEqual(net.seen, self.mols)