rdkit2ase

Name	rdkit2ase JSON
Version	0.1.3 JSON
	download
home_page	None
Summary	interface between rdkit and ASE
upload_time	2024-08-16 10:50:09
maintainer	None
docs_url	None
author	zincwarecode
requires_python	<4.0,>=3.10
license	Apache-2.0
keywords
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

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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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