def make_mol(struct, verbose=False):
mol = openbabel.OBMol()
mol.BeginModify()
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)
connect_the_dots(mol, atoms, struct)
fixup(atoms, mol, struct)
mol.PerceiveBondOrders()
fixup(atoms, mol, struct)
for (i, a) in enumerate(atoms):
openbabel.OBAtomAssignTypicalImplicitHydrogens(a)
fixup(atoms, mol, struct)
mol.EndModify()
mol.AddHydrogens()
fixup(atoms, mol, struct)
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 not a.IsHbondAcceptorSimple(
):
#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())
mol.DeleteHydrogens()
return mol, mismatches
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
def fill_rem_valences(self, ob_mol, atoms, struct):
'''
Fill empty valences with hydrogens up to the
amount expected by the atom type, or a typical
amount according to openbabel, and then fill
remaining empty valences with higher bond orders.
'''
max_vals = get_max_valences(atoms)
for ob_atom, atom_type in zip(atoms, struct.atom_types):
if struct.typer.explicit_h:
# all Hs should already be present
continue
max_val = max_vals.get(ob_atom.GetIdx(), 1)
if Atom.h_count in struct.typer:
# this should have already been set
# by set_min_h_counts, but whatever
h_count = Atom.h_count(ob_atom)
if h_count < atom_type.h_count:
n = ob_atom.GetImplicitHCount()
ob_atom.SetImplicitHCount(n + atom_type.h_count - h_count)
elif ob_atom.GetExplicitValence() < max_val:
# this uses explicit valence and formal charge,
# and only ever INCREASES hydrogens, since it
# never sets implicit H to a negative value
# but it does overwrite the existing value, so
# we need to save it beforehand and then add
n = ob_atom.GetImplicitHCount()
ob.OBAtomAssignTypicalImplicitHydrogens(ob_atom)
n += ob_atom.GetImplicitHCount()
ob_atom.SetImplicitHCount(n)
# these have possibly changed
max_vals = get_max_valences(atoms)
# now increment bond orders to fill remaining valences
atom_info = sort_atoms_by_valence(atoms, max_vals)
for max_val, rem_val, atom in reversed(atom_info):
if atom.GetExplicitValence() >= max_val:
continue
# else, the atom could have an empty valence
# so check whether we can augment a bond,
# prioritizing bonds that are too short
bond_info = sort_bonds_by_stretch(ob.OBAtomBondIter(atom))
for bond_stretch, bond_len, bond in reversed(bond_info):
if bond.GetBondOrder() >= 3:
continue # don't go above triple
# do the atoms involved in this bond have empty valences?
# since we are modifying the valences in the loop, this
# could have changed since calling sort_atoms_by_valence
a1, a2 = bond.GetBeginAtom(), bond.GetEndAtom()
min_val_diff = min( # by how much are the valences under?
max_vals.get(a1.GetIdx(), 1) - a1.GetExplicitValence(),
max_vals.get(a2.GetIdx(), 1) - a2.GetExplicitValence())
if min_val_diff > 0: # increase bond order
bond_order = bond.GetBondOrder() # don't go above triple
bond.SetBondOrder(min(bond_order + min_val_diff, 3))
# if the current atom now has its preferred valence,
# break and let other atoms choose next bonds to augment
if atom.GetExplicitValence() == max_vals[atom.GetIdx()]:
break