rdkit2ase


Namerdkit2ase JSON
Version 0.1.11 PyPI version JSON
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home_pageNone
SummaryInterface between rdkit and ASE
upload_time2025-07-16 18:25:52
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docs_urlNone
authorNone
requires_python>=3.10
licenseNone
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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.

            

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