def main():
parser = argparse.ArgumentParser(description="Generates `.chem` using Linear 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("-a", "--natoms", action="store", type=int, help="number of atoms", default=2)
parser.add_argument("-l", "--length", action="store", type=int, help="maximum number of atoms per molecule", default=5)
parser.add_argument("-f", "--pform", action="store", type=float, help="probability of bonding", default=0.25)
parser.add_argument("-b", "--pbreak", action="store", type=float, help="probability of breaking", default=0.1)
parser.add_argument("-u", "--undirected", action="store_false", dest="directed", help="undirected molecules")
parser.add_argument("-d", "--directed", action="store_true", help="directed molecules", default=True)
parser.add_argument("-t", "--rates", action="store", type=int, 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()
rates = [float(x) for x in args.rates]
#strip defaults
if len(rates) > 1:
rates = rates[1:]
rng = random.Random(args.seed)
#import cProfile
#cProfile.run("""
net = Linear(args.natoms, args.length, args.pform, args.pbreak, args.directed, rates, rng=rng)
#""".strip())
chemstr = """#Linear reaction network
# natoms = {0}
# length = {1}
# pform = {2}
# pbreak = {3}
# direct = {4}
# rates = {5}
# seed = {6}
""".format(args.natoms, args.length, args.pform, args.pbreak, args.directed, 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_undirected(self):
net = Linear(2, 3, 0.2, 0.2, False)
net = Linear(2, 3, 0.2, 0.2, False, rng=self.rng)
def test_directed(self):
net = Linear(2, 3, 0.2, 0.2, True)
net = Linear(2, 3, 0.2, 0.2, True, rng=self.rng)
def test_pform_tuple(self):
net = Linear(2, (3, 5), (0.2, 0.5), 0.2)
net = Linear(2, (3, 5), (0.2, 0.5), 0.2, rng=self.rng)
def test_pbreak_tuple(self):
net = Linear(2, (3, 5), 0.2, (0.2, 0.5))
net = Linear(2, (3, 5), 0.2, (0.2, 0.5), rng=self.rng)
def test_maxlengt_dict(self):
net = Linear(2, {3: 2, 5: 2.1}, 0.2, 0.2)
net = Linear(2, {3: 2, 5: 2.1}, 0.2, 0.2, rng=self.rng)
def test_maxlengt_tuple(self):
net = Linear(2, (3, 5), 0.2, 0.2)
net = Linear(2, (3, 5), 0.2, 0.2, rng=self.rng)
def test_natoms_dict(self):
net = Linear({2: 2, 3: 2.1}, 3, 0.2, 0.2)
net = Linear({2: 2, 3: 2.1}, 3, 0.2, 0.2, rng=self.rng)
def test_natoms_tuple(self):
net = Linear((2, 3), 3, 0.2, 0.2)
net = Linear((2, 3), 3, 0.2, 0.2, rng=self.rng)
def test_natoms_int(self):
net = Linear(2, 3, 0.2, 0.2)
net = Linear(2, 3, 0.2, 0.2, rng=self.rng)