NetworkX InterfaceΒΆ

[1]:

import networkx as nx

import rdkit2ase

[2]:

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"
)

[3]:

graph = rdkit2ase.ase2networkx(box)
print(f"Graph with {len(graph)} atoms and {len(graph.edges())} bonds.")

Graph with 60 atoms and 50 bonds.

[4]:

molecules = len(list(nx.connected_components(graph)))
print(f"Found {molecules} molecules")

Found 10 molecules

[5]:

rdkit2ase.networkx2rdkit(graph)

[5]:
_images/networkx_tools_5_0.png

Some information, like pbc and box size are silently lost.

[6]:

rdkit2ase.networkx2ase(graph)

[6]:

Atoms(symbols='OH2OH2OH2OH2OH2C2OH6C2OH6C2OH6C2OH6C2OH6', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366], initial_charges=...)