def CalculateTorsionLists(mol, maxDev='equal', symmRadius=2, ignoreColinearBonds=True):
""" Calculate a list of torsions for a given molecule. For each torsion
the four atom indices are determined and stored in a set.
Arguments:
- mol: the molecule of interest
- maxDev: maximal deviation used for normalization
'equal': all torsions are normalized using 180.0 (default)
'spec': each torsion is normalized using its specific
maximal deviation as given in the paper
- symmRadius: radius used for calculating the atom invariants
(default: 2)
- ignoreColinearBonds: if True (default), single bonds adjacent to
triple bonds are ignored
if False, alternative not-covalently bound
atoms are used to define the torsion
Return: two lists of torsions: non-ring and ring torsions
"""
if maxDev not in ['equal', 'spec']:
raise ValueError("maxDev must be either equal or spec")
# get non-terminal, non-cyclic bonds
bonds = _getBondsForTorsions(mol, ignoreColinearBonds)
# get atom invariants
if symmRadius > 0:
inv = _getAtomInvariantsWithRadius(mol, symmRadius)
else:
inv = rdMolDescriptors.GetConnectivityInvariants(mol)
# get the torsions
tors_list = [] # to store the atom indices of the torsions
for a1, a2, nb1, nb2 in bonds:
d1 = _getIndexforTorsion(nb1, inv)
d2 = _getIndexforTorsion(nb2, inv)
if len(d1) == 1 and len(d2) == 1: # case 1, 2, 4, 5, 7, 10, 16, 12, 17, 19
tors_list.append(([(d1[0].GetIdx(), a1, a2, d2[0].GetIdx())], 180.0))
elif len(d1) == 1: # case 3, 6, 8, 13, 20
if len(nb2) == 2: # two neighbors
tors_list.append(([(d1[0].GetIdx(), a1, a2, nb.GetIdx()) for nb in d2], 90.0))
else: # three neighbors
tors_list.append(([(d1[0].GetIdx(), a1, a2, nb.GetIdx()) for nb in d2], 60.0))
elif len(d2) == 1: # case 3, 6, 8, 13, 20
if len(nb1) == 2:
tors_list.append(([(nb.GetIdx(), a1, a2, d2[0].GetIdx()) for nb in d1], 90.0))
else: # three neighbors
tors_list.append(([(nb.GetIdx(), a1, a2, d2[0].GetIdx()) for nb in d1], 60.0))
else: # both symmetric
tmp = []
for n1 in d1:
for n2 in d2:
tmp.append((n1.GetIdx(), a1, a2, n2.GetIdx()))
if len(nb1) == 2 and len(nb2) == 2: # case 9
tors_list.append((tmp, 90.0))
elif len(nb1) == 3 and len(nb2) == 3: # case 21
tors_list.append((tmp, 60.0))
else: # case 15
tors_list.append((tmp, 30.0))
# maximal possible deviation for non-cyclic bonds
if maxDev == 'equal':
tors_list = [(t, 180.0) for t, d in tors_list]
# rings
rings = Chem.GetSymmSSSR(mol)
tors_list_rings = []
for r in rings:
# get the torsions
tmp = []
num = len(r)
maxdev = 180.0 * math.exp(-0.025 * (num - 14) * (num - 14))
for i in range(len(r)):
tmp.append((r[i], r[(i + 1) % num], r[(i + 2) % num], r[(i + 3) % num]))
tors_list_rings.append((tmp, maxdev))
return tors_list, tors_list_rings
def testMorganFingerprints(self):
mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
mol = Chem.MolFromSmiles('CC')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
self.assertTrue(list(fp.GetNonzeroElements().values())[0] == 2)
fp = rdMD.GetMorganFingerprint(mol, 0, useCounts=False)
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
self.assertTrue(list(fp.GetNonzeroElements().values())[0] == 1)
mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C')
fp = rdMD.GetHashedMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetHashedMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetMorganFingerprint(mol, 2)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
mol = Chem.MolFromSmiles('CC(F)(Cl)[C@](F)(Cl)C')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetMorganFingerprint(mol, 2)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
fp = rdMD.GetMorganFingerprint(mol, 0, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
fp = rdMD.GetMorganFingerprint(mol, 2, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 10)
mol = Chem.MolFromSmiles('CCCCC')
fp = rdMD.GetMorganFingerprint(mol, 0, fromAtoms=(0, ))
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
mol = Chem.MolFromSmiles('CC1CC1')
vs1 = rdMD.GetConnectivityInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
fp1 = rdMD.GetMorganFingerprint(mol, 2, invariants=vs1)
fp2 = rdMD.GetMorganFingerprint(mol, 2)
self.assertEqual(fp1, fp2)
vs2 = rdMD.GetConnectivityInvariants(mol, False)
self.assertEqual(len(vs2), mol.GetNumAtoms())
self.assertNotEqual(vs1, vs2)
fp1 = rdMD.GetMorganFingerprint(mol, 2, invariants=vs2)
self.assertNotEqual(fp1, fp2)
mol = Chem.MolFromSmiles('Cc1ccccc1')
vs1 = rdMD.GetFeatureInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
self.assertEqual(vs1[0], 0)
self.assertNotEqual(vs1[1], 0)
self.assertEqual(vs1[1], vs1[2])
self.assertEqual(vs1[1], vs1[3])
self.assertEqual(vs1[1], vs1[4])
mol = Chem.MolFromSmiles('FCCCl')
vs1 = rdMD.GetFeatureInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
self.assertEqual(vs1[1], 0)
self.assertEqual(vs1[2], 0)
self.assertNotEqual(vs1[0], 0)
self.assertEqual(vs1[0], vs1[3])
fp1 = rdMD.GetMorganFingerprint(mol, 0, invariants=vs1)
fp2 = rdMD.GetMorganFingerprint(mol, 0, useFeatures=True)
self.assertEqual(fp1, fp2)
