def test():
import Smiles, time
h = BuildMol()
file = open("../test/data/NCI_aug00_SMI")
lines = file.readlines()
tests = []
for l in lines:
tests.append(l.split()[0])
tests = tests[:1]
## for smi in ["C1C([NH4+])(=O).C1.[235U].N[C@@H](C)C(=O)O",
## "c1cccc1"]:
t1 = time.time()
for smi in tests:
Smiles.tokenize(smi, h)
#print smi
for bond in h.mol.bonds:
print bond.symbol, bond.bondorder, bond.bondtype, bond.fixed
print h.mol.cansmiles() #.dump()
t2 = time.time()
delta = (t2 - t1) / len(tests)
print "Time per molecule with no transform", delta
print "molecules per second:",
if delta:
print 1 / delta
else:
print "very fast!"
def cleanup(s):
save_h = SilentSaveTokens()
Smiles.tokenize(s, save_h)
save = []
for name, pos, text in save_h:
save.append( (name, text) )
closures = {}
in_quote = 0
i = 0
for name, text in save:
if name == "open_bracket":
in_quote = 1
has_element = 0
pos = i
elif name == "close_bracket":
in_quote = 0
elif name == "element" and in_quote:
has_element = 1
i = i + 1
if in_quote:
if has_element:
save.append( ("close_bracket", "]") )
else:
del save[pos:]
i = 0
for name, text in save:
if name == "closure":
val = cleanup_closure(text)
if closures.has_key(val):
del closures[val]
else:
closures[val] = i
i = i + 1
for val, i in closures.items():
save[i] = ("fake", "[%d*]" % val)
# trim trailing '(', '.' and bond symbols
while save and (save[-1][0] == "close_branch" or
save[-1][0] == "dot" or
save[-1][0] == "bond"):
save.pop()
paren_count = 0
for name, text in save:
if name == "open_branch":
paren_count = paren_count + 1
elif name == "close_branch":
paren_count = paren_count - 1
assert paren_count >= 0, paren_count
save.extend( [("close_branch", ")")] * paren_count )
smi = ""
for name, text in save:
smi = smi + text
return smi
def test():
import Smiles, time
h = BuildMol()
file = open("../test/data/NCI_aug00_SMI")
lines = file.readlines()
tests = []
for l in lines:
tests.append(l.split()[0])
tests = tests[:1]
## for smi in ["C1C([NH4+])(=O).C1.[235U].N[C@@H](C)C(=O)O",
## "c1cccc1"]:
t1 = time.time()
for smi in tests:
Smiles.tokenize(smi, h)
#print smi
for bond in h.mol.bonds:
print bond.symbol, bond.bondorder, bond.bondtype, bond.fixed
print h.mol.cansmiles()#.dump()
t2 = time.time()
delta = (t2-t1) / len(tests)
print "Time per molecule with no transform", delta
print "molecules per second:",
if delta:
print 1/delta
else:
print "very fast!"
def cleanup(s):
save_h = SilentSaveTokens()
Smiles.tokenize(s, save_h)
save = []
for name, pos, text in save_h:
save.append((name, text))
closures = {}
in_quote = 0
i = 0
for name, text in save:
if name == "open_bracket":
in_quote = 1
has_element = 0
pos = i
elif name == "close_bracket":
in_quote = 0
elif name == "element" and in_quote:
has_element = 1
i = i + 1
if in_quote:
if has_element:
save.append(("close_bracket", "]"))
else:
del save[pos:]
i = 0
for name, text in save:
if name == "closure":
val = cleanup_closure(text)
if closures.has_key(val):
del closures[val]
else:
closures[val] = i
i = i + 1
for val, i in closures.items():
save[i] = ("fake", "[%d*]" % val)
# trim trailing '(', '.' and bond symbols
while save and (save[-1][0] == "close_branch" or save[-1][0] == "dot"
or save[-1][0] == "bond"):
save.pop()
paren_count = 0
for name, text in save:
if name == "open_branch":
paren_count = paren_count + 1
elif name == "close_branch":
paren_count = paren_count - 1
assert paren_count >= 0, paren_count
save.extend([("close_branch", ")")] * paren_count)
smi = ""
for name, text in save:
smi = smi + text
return smi
def test():
h = Handler.TokenHandler()
t1 = time.clock()
#h = Handler.WriteHandler() # uncomment to print
for line in lines:
#print "####", line
Smiles.tokenize(line, h)
t2 = time.clock()
print len(lines), "patt. in", t2 - t1, "s =>",
print (t2-t1)/len(lines), "s/patt. ==",
print len(lines)/(t2-t1), "patt./s"
def test():
h = Handler.TokenHandler()
t1 = time.clock()
#h = Handler.WriteHandler() # uncomment to print
for line in lines:
#print "####", line
Smiles.tokenize(line, h)
t2 = time.clock()
print len(lines), "patt. in", t2 - t1, "s =>",
print(t2 - t1) / len(lines), "s/patt. ==",
print len(lines) / (t2 - t1), "patt./s"
def test():
lines = test_Smiles.lines
h = BuildMol.BuildMol()
t1 = time.clock()
for line in lines:
#print line
Smiles.tokenize(line, h)
#s = h.mol.dump()
#print s
t2 = time.clock()
print len(lines), "patt. in", t2 - t1, "s =>",
print(t2 - t1) / len(lines), "s/patt. ==",
print len(lines) / (t2 - t1), "patt./s"
def test():
lines = test_Smiles.lines
h = BuildMol.BuildMol()
t1 = time.clock()
for line in lines:
#print line
Smiles.tokenize(line, h)
#s = h.mol.dump()
#print s
t2 = time.clock()
print len(lines), "patt. in", t2 - t1, "s =>",
print (t2-t1)/len(lines), "s/patt. ==",
print len(lines)/(t2-t1), "patt./s"
def Btn_Input_Clicked(self):
self.SmilesRunning(True, False)
self.top.ChildWindow = Smiles.Smiles(self, self.SmilesString,
self.SmilesName)
