def draw_molecule(mol: Molecule) -> PIL.Image.Image:
"""
Draw a single molecule `mol` (make it `PIL.Image.Image`)
:param mol: molecule to draw
:return: corresponding image to `mol`
"""
img = Draw.MolToImage(mol.to_rdkit())
return img
def get_graph_data_for_distance_computation(mol):
""" Returns graph representation for a molecule. """
if isinstance(mol, str):
from mols.molecule import Molecule
mol = Molecule(mol)
rdk_mol = mol.to_rdkit()
rdk_mol = Chem.AddHs(rdk_mol)
adj_matrix = Chem.rdmolops.GetAdjacencyMatrix(rdk_mol)
bonds = [(b.GetBeginAtomIdx(), b.GetEndAtomIdx())
for b in rdk_mol.GetBonds()]
bond_types = [
rdk_mol.GetBondBetweenAtoms(b[0], b[1]).GetBondType() for b in bonds
]
atom_idxs = list(range(len(rdk_mol.GetAtoms())))
atomic_numbers = [
rdk_mol.GetAtomWithIdx(idx).GetAtomicNum() for idx in atom_idxs
]
atomic_symbols = [
rdk_mol.GetAtomWithIdx(idx).GetSymbol() for idx in atom_idxs
]
atomic_masses = [
rdk_mol.GetAtomWithIdx(idx).GetMass() for idx in atom_idxs
]
num_atoms = len(atom_idxs)
bonds_of_each_atom = [
get_neighbors_and_bond_types(idx, bonds, atomic_symbols, bond_types)
for idx in range(num_atoms)
]
bond_type_counts_of_each_atom = [
get_bond_type_counts(bt) for bt in bonds_of_each_atom
]
# Return
graph_data = Namespace(
rdk_mol=rdk_mol,
adj_matrix=adj_matrix,
bonds=bonds,
bond_types=bond_types,
atom_idxs=atom_idxs,
atomic_numbers=atomic_numbers,
atomic_symbols=atomic_symbols,
atomic_masses=atomic_masses,
num_atoms=num_atoms,
bonds_of_each_atom=bonds_of_each_atom,
bond_type_counts_of_each_atom=bond_type_counts_of_each_atom,
)
return graph_data
