rdkit2ase 0.1.13

Interface between rdkit and ASE

rdkit2ase - Interface between the rdkit and ASE package.

Installation via pip install rdkit2ase.

from rdkit2ase import rdkit2ase, ase2rdkit

atoms: ase.Atoms = rdkit2ase(mol)
mol = ase2rdkit(atoms)

from rdkit2ase import smiles2atoms

atoms: ase.Atoms = smiles2atoms("O")

print(atoms)
>>> Atoms(symbols='OH2', pbc=False)

Packmol Interface

If you have packmol (at least v20.15.0) you can use the rdkit2ase interface.

from rdkit2ase import pack, smiles2conformers

water = smiles2conformers("O", 2)
ethanol = smiles2conformers("CCO", 5)
density = 1000  # kg/m^3
box = pack([water, ethanol], [7, 5], density)
print(box)
>>> Atoms(symbols='C10H44O12', pbc=True, cell=[8.4, 8.4, 8.4])

Limitations

• rdkit2ase.ase2rdkit won't be able to detect higher order bonds.