molify 0.0.1a0

Interface between rdkit and ASE

rdkit2ase - Interface between the rdkit and ASE package.

Installation via pip install rdkit2ase. For more information please visit the documentation.

A common use case is to create 3D structures from SMILES strings. This can be achieved using the rdkit2ase.rdkit2ase function.

import ase
from rdkit import Chem
from rdkit2ase import rdkit2ase, ase2rdkit

mol = Chem.MolFromSmiles("O")
atoms: ase.Atoms = rdkit2ase(mol)
mol = ase2rdkit(atoms)

Because this is such a common use case, there is a convenience function rdkit2ase.smiles2atoms that combines the two steps.

import ase
from rdkit2ase import smiles2atoms

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

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

Packmol Interface

Given the molecular units, you can build periodic boxes with a given density using the rdkit2ase.pack function.

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

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])

Many additional features are described in the documentation.