Exemplo n.º 1
0
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
Exemplo n.º 2
0
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