def to_rdkit_molecule(data):
"""
MoleculeContainer to RDKit molecule object converter
"""
mol = RWMol()
mapping = {}
for n, a in data.atoms():
ra = Atom(a.atomic_number)
ra.SetAtomMapNum(n)
if a.charge:
ra.SetFormalCharge(a.charge)
if a.isotope:
ra.SetIsotope(a.isotope)
if a.is_radical:
ra.SetNumRadicalElectrons(1)
mapping[n] = mol.AddAtom(ra)
for n, m, b in data.bonds():
mol.AddBond(mapping[n], mapping[m], _bond_map[b.order])
conf = Conformer()
for n, a in data.atoms():
conf.SetAtomPosition(mapping[n], (a.x, a.y, 0))
conf.Set3D(False)
mol.AddConformer(conf)
for c in data._conformers:
conf = Conformer()
for n, xyz in c.items():
conf.SetAtomPosition(mapping[n], xyz)
mol.AddConformer(conf)
SanitizeMol(mol)
return mol
def to_rdkit_molecule(data: MoleculeContainer):
"""
MoleculeContainer to RDKit molecule object converter
"""
mol = RWMol()
mapping = {}
bonds = data._bonds
for n, a in data.atoms():
ra = Atom(a.atomic_number)
ra.SetAtomMapNum(n)
if a.charge:
ra.SetFormalCharge(a.charge)
if a.isotope:
ra.SetIsotope(a.isotope)
if a.is_radical:
ra.SetNumRadicalElectrons(1)
mapping[n] = mol.AddAtom(ra)
for n, m, b in data.bonds():
mol.AddBond(mapping[n], mapping[m], _bond_map[b.order])
for n in data._atoms_stereo:
ra = mol.GetAtomWithIdx(mapping[n])
env = bonds[n]
s = data._translate_tetrahedron_sign(n, [x for x in mapping if x in env])
ra.SetChiralTag(_chiral_ccw if s else _chiral_cw)
for nm, s in data._cis_trans_stereo.items():
n, m = nm
if m in bonds[n]: # cumulenes unsupported
nn, nm, *_ = data._stereo_cis_trans[nm]
b = mol.GetBondBetweenAtoms(mapping[n], mapping[m])
b.SetStereoAtoms(mapping[nn], mapping[nm])
b.SetStereo(_cis if s else _trans)
conf = Conformer()
for n, a in data.atoms():
conf.SetAtomPosition(mapping[n], (a.x, a.y, 0))
conf.Set3D(False)
mol.AddConformer(conf, assignId=True)
for c in data._conformers:
conf = Conformer()
for n, xyz in c.items():
conf.SetAtomPosition(mapping[n], xyz)
mol.AddConformer(conf, assignId=True)
SanitizeMol(mol)
AssignStereochemistry(mol, flagPossibleStereoCenters=True, force=True)
return mol
def to_rdkit_molecule(data):
"""
MoleculeContainer to RDKit molecule object converter
"""
mol = RWMol()
conf = Conformer()
mapping = {}
is_3d = False
for n, a in data.atoms():
ra = Atom(a.number)
ra.SetAtomMapNum(n)
if a.charge:
ra.SetFormalCharge(a.charge)
if a.isotope != a.common_isotope:
ra.SetIsotope(a.isotope)
if a.radical:
ra.SetNumRadicalElectrons(a.radical)
mapping[n] = m = mol.AddAtom(ra)
conf.SetAtomPosition(m, (a.x, a.y, a.z))
if a.z:
is_3d = True
if not is_3d:
conf.Set3D(False)
for n, m, b in data.bonds():
mol.AddBond(mapping[n], mapping[m], _bond_map[b.order])
mol.AddConformer(conf)
SanitizeMol(mol)
return mol