molify - Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX

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)

Command Line Interface

Commands mirror the molify functions and write to standard output. --format takes any ASE format name or extension, defaulting to extxyz.

molify smiles2atoms CCO > etoh.xyz

Packmol Interface

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

The molify package ships with an installation of packmol. If you like packmol, give it a star on GitHub!

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.

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