rdkit2ase Documentation¶
rdkit2ase provides a bridge between RDKit and ASE. It further integrates features from Packmol and NetworkX.
import rdkit2ase
water = rdkit2ase.smiles2conformers("O", numConfs=10)
etoh = rdkit2ase.smiles2conformers("CCO", numConfs=10)
box = rdkit2ase.pack(
data=[water, etoh], counts=[5, 5], density=800, packmol="packmol.jl"
)
mol = rdkit2ase.ase2rdkit(water[0])
graph = rdkit2ase.ase2networkx(box)
More examples are provided below.
Installation¶
You can install rdkit2ase from PyPI:
(.venv) $ pip install rdkit2ase
From Source¶
To install and develop rdkit2ase from source, we recommend using uv.
More information and installation instructions can be found in the UV documentation.
(.venv) $ git clone https://github.com/zincware/rdkit2ase
(.venv) $ cd rdkit2ase
(.venv) $ uv sync
(.venv) $ source .venv/bin/activate