def test():
global lastSmiles
# test NCI data
file = open("data/NCI_aug00_SMI")
import time
t1 = time.time()
index = 0
for line in file.xreadlines():
smiles, id = line.split()
lastSmiles = smiles
mol1 = smilin(smiles, transform1)
mol2 = smilin(smiles, transform2)
if mol1.cansmiles() != mol2.cansmiles():
"%s different smiles->%s %s"%(smiles,
mol1.cansmiles(), mol2.cansmiles())
# check to see if the rings are the same
if len(mol1.cycles) != len(mol2.cycles):
print "%s number of rings are different"%smiles
rings1 = {}
keys = {}
cycles1 = mol1.cycles
for cycle in mol1.cycles:
rings1[len(cycle)] = rings1.get(len(cycle), 0) +1
atoms, bonds = cycle.atoms, cycle.bonds
atoms.sort()
bonds.sort()
keys[(tuple(atoms), tuple(bonds))] = 1
mol1 = RingDetection.sssr(mol1)
rings2 = {}
for cycle in mol1.cycles:
rings2[len(cycle)] = rings1.get(len(cycle), 0) +1
atoms, bonds = cycle.atoms, cycle.bonds
atoms.sort()
bonds.sort()
key = tuple(atoms), tuple(bonds)
if not keys.has_key(key):
print smiles, "->rings are different"
break
lengths1 = [len(cycle) for cycle in cycles1]
lengths2 = [len(cycle) for cycle in mol1.cycles]
lengths1.sort()
lengths2.sort()
if lengths1 != lengths2:
print "%s forms rings of different sizes"%smiles
print "\t",lengths1
print "\t",lengths2
index += 1
if max and index >= max:
break
t2 = time.time()
print "tot time", t2-t1
print "compound time", (t2-t1)/index
print "compounds/sec", index/(t2-t1)
from test_smiles import smilesStrings
from frowns.Smiles import smilin
import time
#smilesStrings = ["Cc1[nH]ccc1"]
#smilesStrings = ["c1ccc[nH]1"]
##smilesStrings = ["c1ccccc1",
#smilesStrings = ["C=1=CC=CC=1"]
#smilesStrings = ["c1ccccc1"]
t1 = time.time()
for smile in smilesStrings:
print "="*44
print smile
mol = smilin(smile)
out = mol.arbsmiles()
can = mol.cansmiles()
for bond in mol.bonds:
print bond.symbol, bond.bondorder, bond.bondtype, bond.fixed
for atom in mol.atoms:
print atom, atom.sumBondOrders()
print smile, out, can
t2 = time.time()
print (t2-t1)/len(smilesStrings)
print len(smilesStrings)/(t2-t1)
