https://github.com/zincware/rdkit2ase

Create atomistic structures with ASE, rdkit and packmol
https://github.com/zincware/rdkit2ase

ase packmol rdkit

Last synced: 11 months ago
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Create atomistic structures with ASE, rdkit and packmol

• Host: GitHub
• URL: https://github.com/zincware/rdkit2ase
• Owner: zincware
• License: apache-2.0
• Created: 2023-08-16T08:46:33.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2025-07-21T08:40:49.000Z (11 months ago)
• Last Synced: 2025-07-21T10:12:18.450Z (11 months ago)
• Topics: ase, packmol, rdkit
• Language: Python
• Homepage: https://zincware.github.io/rdkit2ase/
• Size: 1.44 MB
• Stars: 12
• Watchers: 1
• Forks: 1
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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# rdkit2ase - Interface between the rdkit and ASE package.

Installation via `pip install rdkit2ase`.

```py

from rdkit2ase import rdkit2ase, ase2rdkit

atoms: ase.Atoms = rdkit2ase(mol)

mol = ase2rdkit(atoms)

```

```py

from rdkit2ase import smiles2atoms

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

print(atoms)

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

```

## Packmol Interface

If you have [packmol](https://github.com/m3g/packmol) (at least `v20.15.0`) you

can use the rdkit2ase interface.

```py

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.