def mol_supplier(lines, no_halt, assign_descriptors):
"""Yields molecules generated from CTAB text
Args:
lines (iterable): CTAB text lines
no_halt (boolean):
True: shows warning messages for invalid format and go on.
False: throws an exception for it and stop parsing.
assign_descriptors (boolean):
if True, default descriptors are automatically assigned.
"""
def sdf_block(lns):
mol = []
opt = []
is_mol = True
for line in lns:
if line.startswith("$$$$"):
yield mol[:], opt[:]
is_mol = True
mol.clear()
opt.clear()
elif line.startswith("M END"):
is_mol = False
elif is_mol:
mol.append(line.rstrip())
else:
opt.append(line.rstrip())
if mol:
yield mol, opt
for i, (mol, opt) in enumerate(sdf_block(lines)):
try:
c = molecule(mol)
if assign_descriptors:
molutil.assign_descriptors(c)
except ValueError as err:
if no_halt:
print("Unsupported symbol: {} (#{} in v2000reader)".format(
err, i + 1))
c = molutil.null_molecule(assign_descriptors)
else:
raise ValueError("Unsupported symbol: {}".format(err))
except:
if no_halt:
print("Unexpected error (#{} in v2000reader)".format(i + 1))
c = molutil.null_molecule(assign_descriptors)
c.data = optional_data(opt)
yield c
continue
else:
print(traceback.format_exc())
raise Exception("Unsupported Error")
c.data = optional_data(opt)
yield c
def from_indigo(idgmol, assign_descriptor=True):
"""Convert RDMol to molecule"""
mol = Compound()
for atom in idgmol.iterateAtoms():
key = atom.index()
a = Atom(atom.symbol())
a.coords = list(atom.xyz())
mol.add_atom(key, a)
for bond in idgmol.iterateBonds():
u = bond.source()
v = bond.destination()
b = Bond()
b.order = int(bond.bondOrder())
mol.add_bond(u.index(), v.index(), b)
if assign_descriptor:
molutil.assign_descriptors(mol)
return mol
def smiles_to_compound(smiles, assign_descriptors=True):
"""Convert SMILES text to compound object
Raises:
ValueError: SMILES with unsupported format
"""
it = iter(smiles)
mol = molecule()
try:
for token in it:
mol(token)
result, _ = mol(None)
except KeyError as err:
raise ValueError("Unsupported Symbol: {}".format(err))
result.graph.remove_node(0)
logger.debug(result)
if assign_descriptors:
molutil.assign_descriptors(result)
return result
def from_rdmol(rdmol, assign_descriptor=True):
"""Convert RDMol to molecule"""
mol = Compound()
conf = rdmol.GetConformer()
Chem.Kekulize(rdmol)
for atom in rdmol.GetAtoms():
key = atom.GetIdx()
a = Atom(atom.GetSymbol())
a.coords = conf.GetAtomPosition(key)
mol.add_atom(key, a)
for bond in rdmol.GetBonds():
u = bond.GetBeginAtomIdx()
v = bond.GetEndAtomIdx()
b = Bond()
b.order = int(bond.GetBondTypeAsDouble())
mol.add_bond(u, v, b)
if assign_descriptor:
molutil.assign_descriptors(mol)
return mol