def test1(self):
" testing first 200 mols from NCI "
suppl = Chem.SDMolSupplier(self.inFileName)
idx = 1
oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
OldDonorCount = lambda x,y=oldDonorSmarts:Lipinski._NumMatches(x,y)
oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
OldAcceptorCount = lambda x,y=oldAcceptorSmarts:Lipinski._NumMatches(x,y)
for m in suppl:
if m:
calc = Lipinski.NHOHCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NOCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHDonors(m)
orig = int(m.GetProp('NUM_HDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHAcceptors(m)
orig = int(m.GetProp('NUM_HACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHeteroatoms(m)
orig = int(m.GetProp('NUM_HETEROATOMS'))
assert calc==orig,'bad num heteroatoms for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumRotatableBonds(m)
orig = int(m.GetProp('NUM_ROTATABLEBONDS'))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
idx += 1
def test1(self):
" testing first 200 mols from NCI "
# figure out which rotor version we are using
m = Chem.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")
if Lipinski.NumRotatableBonds(m) == 2:
rot_prop = NonStrict
else:
rot_prop = Strict
suppl = Chem.SDMolSupplier(self.inFileName)
idx = 1
oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
OldDonorCount = lambda x,y=oldDonorSmarts:Lipinski._NumMatches(x,y)
oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
OldAcceptorCount = lambda x,y=oldAcceptorSmarts:Lipinski._NumMatches(x,y)
for m in suppl:
if m:
calc = Lipinski.NHOHCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NOCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHDonors(m)
orig = int(m.GetProp('NUM_HDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHAcceptors(m)
orig = int(m.GetProp('NUM_HACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHeteroatoms(m)
orig = int(m.GetProp('NUM_HETEROATOMS'))
assert calc==orig,'bad num heteroatoms for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumRotatableBonds(m)
orig = int(m.GetProp(rot_prop))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
# test the underlying numrotatable bonds
calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.NonStrict)
orig = int(m.GetProp(NonStrict))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.Strict)
orig = int(m.GetProp(Strict))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
idx += 1
def test1(self):
" testing first 200 mols from NCI "
suppl = Chem.SDMolSupplier(self.inFileName)
idx = 1
oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
OldDonorCount = lambda x, y=oldDonorSmarts: Lipinski._NumMatches(x, y)
oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
OldAcceptorCount = lambda x, y=oldAcceptorSmarts: Lipinski._NumMatches(
x, y)
for m in suppl:
if m:
calc = Lipinski.NHOHCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NOCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHDonors(m)
orig = int(m.GetProp('NUM_HDONORS'))
assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHAcceptors(m)
orig = int(m.GetProp('NUM_HACCEPTORS'))
assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHeteroatoms(m)
orig = int(m.GetProp('NUM_HETEROATOMS'))
assert calc == orig, 'bad num heteroatoms for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumRotatableBonds(m)
orig = int(m.GetProp('NUM_ROTATABLEBONDS'))
assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
idx += 1
def test1(self):
" testing first 200 mols from NCI "
# figure out which rotor version we are using
m = Chem.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")
if Lipinski.NumRotatableBonds(m) == 2:
rot_prop = NonStrict
else:
rot_prop = Strict
suppl = Chem.SDMolSupplier(self.inFileName)
idx = 1
oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
OldDonorCount = lambda x, y=oldDonorSmarts: Lipinski._NumMatches(x, y)
oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
OldAcceptorCount = lambda x, y=oldAcceptorSmarts: Lipinski._NumMatches(
x, y)
for m in suppl:
if m:
calc = Lipinski.NHOHCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NOCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHDonors(m)
orig = int(m.GetProp('NUM_HDONORS'))
assert calc == orig, 'bad num h donors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHAcceptors(m)
orig = int(m.GetProp('NUM_HACCEPTORS'))
assert calc == orig, 'bad num h acceptors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumHeteroatoms(m)
orig = int(m.GetProp('NUM_HETEROATOMS'))
assert calc == orig, 'bad num heteroatoms for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = Lipinski.NumRotatableBonds(m)
orig = int(m.GetProp(rot_prop))
assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
# test the underlying numrotatable bonds
calc = rdMolDescriptors.CalcNumRotatableBonds(
m, rdMolDescriptors.NumRotatableBondsOptions.NonStrict)
orig = int(m.GetProp(NonStrict))
assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
calc = rdMolDescriptors.CalcNumRotatableBonds(
m, rdMolDescriptors.NumRotatableBondsOptions.Strict)
orig = int(m.GetProp(Strict))
assert calc == orig, 'bad num rotors for mol %d (%s): %d != %d' % (
idx, m.GetProp('SMILES'), calc, orig)
idx += 1
