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

Documentation

• ASE Interface
• RDKit Interface
• Packmol Interface
• NetworkX Interface
• Advanced Atom Selection with SMARTS and Mapped SMILES
  • Basic Atom Selection with SMARTS
  • Hydrogen Handling Options
• Mapped SMILES Support and Atom Ordering
• Visualization of Selected Atoms
  • Advanced Example: Selecting Functional Groups
• API Reference
  • ase2networkx()
  • ase2rdkit()
  • compress()
  • get_centers_of_mass()
  • get_substructures()
  • iter_fragments()
  • match_substructure()
  • networkx2ase()
  • networkx2rdkit()
  • pack()
  • rdkit2ase()
  • rdkit2networkx()
  • select_atoms_flat_unique()
  • select_atoms_grouped()
  • smiles2atoms()
  • smiles2conformers()
  • unwrap_structures()
  • visualize_selected_molecules()