def GetNumRings(mol):
count = 0
for ring in openbabel.OBMolRingIter(mol):
count += 1
return count
def test_ring_center_and_normal(self):
mol = parse_smiles("c1ccccc1")
R = 1.5
for i in range(6):
atom = mol.GetAtom(i + 1)
atom.SetVector(R * math.cos(2 * math.pi * i / 6),
R * math.sin(2 * math.pi * i / 6), 0.0)
for ring in ob.OBMolRingIter(mol):
break
center = ob.vector3()
norm1 = ob.vector3()
norm2 = ob.vector3()
ring.findCenterAndNormal(center, norm1, norm2)
self.assertZero(center.GetX())
self.assertZero(center.GetY())
self.assertZero(center.GetZ())
self.assertZero(norm1.GetX())
self.assertZero(norm1.GetY())
self.assertClose(norm1.GetZ(), 1.0)
self.assertZero(norm2.GetX())
self.assertZero(norm2.GetY())
self.assertClose(norm2.GetZ(), -1.0)
def make_obmol(struct, verbose=False):
'''Create an OBMol from AtomStruct that attempts to maintain
correct atom typing'''
mol = ob.OBMol()
mol.BeginModify()
visited_mols = []
atoms = []
for xyz, t in zip(struct.xyz, struct.c):
x, y, z = map(float, xyz)
ch = struct.channels[t]
atom = mol.NewAtom()
atom.SetAtomicNum(ch.atomic_num)
atom.SetVector(x, y, z)
atoms.append(atom)
fixup(atoms, mol, struct)
visited_mols.append(ob.OBMol(mol))
connect_the_dots(mol, atoms, struct)
fixup(atoms, mol, struct)
visited_mols.append(ob.OBMol(mol))
mol.EndModify()
mol.AddPolarHydrogens() #make implicits explicit
visited_mols.append(ob.OBMol(mol))
mol.PerceiveBondOrders()
fixup(atoms, mol, struct)
visited_mols.append(ob.OBMol(mol))
for (i, a) in enumerate(atoms):
ob.OBAtomAssignTypicalImplicitHydrogens(a)
fixup(atoms, mol, struct)
visited_mols.append(ob.OBMol(mol))
mol.AddHydrogens()
fixup(atoms, mol, struct)
visited_mols.append(ob.OBMol(mol))
#make rings all aromatic if majority of carbons are aromatic
for ring in ob.OBMolRingIter(mol):
if 5 <= ring.Size() <= 6:
carbon_cnt = 0
aromatic_ccnt = 0
for ai in ring._path:
a = mol.GetAtom(ai)
if a.GetAtomicNum() == 6:
carbon_cnt += 1
if a.IsAromatic():
aromatic_ccnt += 1
if aromatic_ccnt / carbon_cnt >= .5 and aromatic_ccnt != ring.Size(
):
#set all ring atoms to be aromatic
for ai in ring._path:
a = mol.GetAtom(ai)
a.SetAromatic(True)
#bonds must be marked aromatic for smiles to match
for bond in ob.OBMolBondIter(mol):
a1 = bond.GetBeginAtom()
a2 = bond.GetEndAtom()
if a1.IsAromatic() and a2.IsAromatic():
bond.SetAromatic(True)
visited_mols.append(ob.OBMol(mol))
mismatches = 0
for (a, t) in zip(atoms, struct.c):
ch = struct.channels[t]
if 'Donor' in ch.name and not a.IsHbondDonor():
mismatches += 1
if verbose:
print("Not Donor", ch.name, a.GetX(), a.GetY(), a.GetZ())
if ch.name != 'NitrogenXSDonorAcceptor' and 'Acceptor' in ch.name and a.GetExplicitDegree(
) != a.GetTotalDegree():
#there are issues with nitrogens and openbabel protonation..
mismatches += 1
if verbose:
print("Not Acceptor", ch.name, a.GetX(), a.GetY(), a.GetZ())
if 'Aromatic' in ch.name and not a.IsAromatic():
mismatches += 1
if verbose:
print("Not Aromatic", ch.name, a.GetX(), a.GetY(), a.GetZ())
return pybel.Molecule(mol), mismatches, visited_mols