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
def to_fmt_obj(self, fmtobj, *args, **kwargs):
self.rdkit_mol.RemoveAllConformers()
for ii in range(self.get_nframes()):
conf = Conformer()
for idx in range(self.get_natoms()):
conf.SetAtomPosition(idx, self.data["coords"][ii][idx])
self.rdkit_mol.AddConformer(conf, assignId=True)
return fmtobj.to_bond_order_system(self.data, self.rdkit_mol, *args,
**kwargs)
def get_mol(self, ids=None):
pmol = Chem.RWMol()
all_coords = self.get_feature_coords(ids=ids)
for item in all_coords:
a = Chem.Atom(self.__feat_dict_mol[item[0]])
pmol.AddAtom(a)
c = Conformer(len(all_coords))
for i, coords in enumerate(all_coords):
c.SetAtomPosition(i, Point3D(*coords[1]))
pmol.AddConformer(c, True)
return pmol
def xyz_to_rdmol(nxyz, smiles):
mol = get_mol(smiles)
mol = AddHs(mol)
num_atoms = len(nxyz)
conformer = Conformer(num_atoms)
for i, quad in enumerate(nxyz):
conformer.SetAtomPosition(i, quad[1:])
mol.AddConformer(conformer)
return mol
def conf2xyz(conf: Chem.Conformer,
outputname,
atom_list: list,
comment_line=''):
natoms = conf.GetNumAtoms()
s = "{}\n{}\n".format(natoms, comment_line)
for i in range(natoms):
position = conf.GetAtomPosition(i)
symbol = atom_list[i]
s += "{}\t{:.6} {:.6} {:.6}\n".format(symbol, position.x,
position.y, position.z)
with open(outputname, 'w') as f:
f.write(s)
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 convert_molecule(molecule):
from rdkit.Chem import Mol, EditableMol, Atom, Conformer
mol = Mol()
emol = EditableMol(mol)
conformer = Conformer()
atom_map = {}
for atom in molecule.atoms:
a = Atom(atom.element.number)
atom_map[atom] = i = emol.AddAtom(a)
conformer.SetAtomPosition(i, atom.coord().data())
for bond in molecule.bonds:
a1, a2 = bond.atoms
emol.AddBond(atom_map[a1], atom_map[a2])
mol = emol.GetMol()
mol.AddConformer(conformer)
return mol, atom_map
def get_mol(self, ids=None):
"""
Returns RDKit Mol object of a pharmacophore where features are replaced with atoms
:param ids: iterable with feature ids to be used
:type ids: iterable (int)
:return: RDKit RWMol
"""
pmol = Chem.RWMol()
all_coords = self.get_feature_coords(ids=ids)
for item in all_coords:
a = Chem.Atom(self.__feat_dict_mol[item[0]])
pmol.AddAtom(a)
c = Conformer(len(all_coords))
for i, coords in enumerate(all_coords):
c.SetAtomPosition(i, Point3D(*coords[1]))
pmol.AddConformer(c, True)
return pmol
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 check_conformer(
mol: Mol,
conformer: Conformer,
) -> bool:
# throw warnings if
# - the conformer is actually 2D (useless Z coordinate in graph)
# - some atoms have all-zero coordinates, which implies bad conformer
_positions: np.array = conformer.GetPositions()
if not _positions[:, 2].any():
_warning_msg = f'Conformer has no Z coordinates. Continuing ...'
_LOGGER.warning(_warning_msg)
if not np.array([_p.any() for _p in _positions]).all():
_warning_msg = f'Conformer has atom(s) with invalid coordinates ' \
f'(0.0, 0.0, 0.0). Continuing ...'
_LOGGER.warning(_warning_msg)
# make sure that the molecule and conformer are of the same size
return len(mol.GetAtoms()) == len(mol.GetConformer().GetPositions())
def atom_coords(atom: Chem.Atom, conf: Chem.Conformer) -> List[float]:
"""Returns the x, y, and z coordinates of an atom in a molecule conformer.
"""
p = conf.GetAtomPosition(atom.GetIdx())
fts = [p.x, p.y, p.z]
return fts