molify 0.0.1a1

Interface between rdkit and ASE

molify - Interface between the rdkit and ASE package.

Installation via pip install molify. 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 molify.rdkit2ase function.

import ase
from rdkit import Chem
from molify 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 molify.smiles2atoms that combines the two steps.

import ase
from molify 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 molify.pack function.

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

from molify 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.