def add_conformer(rdkit_mol: Chem.Mol,
conformer_coordinates: np.ndarray) -> Chem.Mol:
"""
Add a new conformation to the rdkit molecule
:param conformer_coordinates: A numpy array of the coordinates to be added
:param rdkit_mol: The rdkit molecule instance
:return: The rdkit molecule with the conformer added
"""
conformer = Chem.Conformer()
for i, coord in enumerate(conformer_coordinates):
atom_position = Point3D(*coord)
conformer.SetAtomPosition(i, atom_position)
rdkit_mol.AddConformer(conformer, assignId=True)
return rdkit_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 add_conformers_to_rdmol(mol: Chem.Mol,
conformer_coordinates: np.ndarray) -> None:
"""Add conformers to RDKit Mol object.
:param mol: rdkit mol object
:type mol: rdkit.Chem.Mol
:param conformer_coordinates: list of conformers 3D coordinate arrays
:type conformer_coordinates: np.ndarray
"""
conformer_coordinates = np.array(conformer_coordinates)
if len(conformer_coordinates.shape) == 2:
conformer_coordinates.reshape(-1, conformer_coordinates.shape[0], 3)
for coordinates in conformer_coordinates:
conformer = Chem.Conformer()
for i, coord in enumerate(coordinates):
point = Geometry.Point3D(*coord)
conformer.SetAtomPosition(i, point)
mol.AddConformer(conformer, assignId=True)
