def testOrderBug2(self):
from rdkit.Chem import Randomize
from rdkit import DataStructs
probes = ['Oc1nc(Oc2ncccc2)ccc1']
for smi in probes:
m1 = Chem.MolFromSmiles(smi)
#m1.Debug()
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
csmi = Chem.MolToSmiles(m1)
m2 = Chem.MolFromSmiles(csmi)
#m2.Debug()
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
self.failUnless(list(sig1.GetOnBits())==list(sig2.GetOnBits()),'%s %s'%(smi,csmi))
self.failUnlessEqual(DataStructs.DiceSimilarity(sig1,sig2),1.0)
self.failUnlessEqual(sig1,sig2)
for i in range(10):
m2 = Randomize.RandomizeMol(m1)
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
if sig2!=sig1:
Generate._verbose=True
print '----------------'
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
print '----------------'
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
print '----------------'
print Chem.MolToMolBlock(m1)
print '----------------'
print Chem.MolToMolBlock(m2)
print '----------------'
s1 = set(sig1.GetOnBits())
s2= set(sig2.GetOnBits())
print s1.difference(s2)
self.failUnlessEqual(sig1,sig2)
def TestMolecule(mol):
try:
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
except ValueError as msg:
return -1
except Exception:
import traceback
traceback.print_exc()
return -2
if mol.GetNumAtoms():
try:
Randomize.CheckCanonicalization(mol, 10)
except Exception:
import traceback
traceback.print_exc()
return -3
return 0
import sys
from rdkit.Chem import Randomize
def TestMolecule(mol):
try:
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
except ValueError,msg:
return -1
except:
import traceback
traceback.print_exc()
return -2
if mol.GetNumAtoms():
try:
Randomize.CheckCanonicalization(mol,10)
except:
import traceback
traceback.print_exc()
return -3
return 0
def TestSupplier(suppl,stopAfter=-1,reportInterval=100,reportTo=sys.stderr,
nameProp='_Name'):
nDone = 0
nFailed = 0
while 1:
try:
mol = suppl.next()
except StopIteration: