Packmol Interface¶

If you have packmol installed, you can use it via pack create periodic boxed from ase.Atoms objects.

[1]:

from ase.build import separate

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]:

print(box)
separate(box)

Atoms(symbols='OH2OH2OH2OH2OH2C2OH6C2OH6C2OH6C2OH6C2OH6', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366], atomtypes=..., bfactor=..., occupancy=..., residuenames=..., residuenumbers=...)

[3]:

[Atoms(symbols='OH2', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='OH2', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='OH2', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='OH2', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='OH2', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='C2H3OH3', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='C2H3OH3', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='C2H3OH3', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='C2H3OH3', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366]),
 Atoms(symbols='C2H3OH3', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366])]

You can utilize all other features here as well.

[4]:

waters = rdkit2ase.match_substructure(
    box,
    smiles="O",
)
etohs = rdkit2ase.match_substructure(
    box,
    smiles="CCO",
)
print(f"Found {len(waters)} water molecules and {len(etohs)} ethanol molecules.")

Found 5 water molecules and 5 ethanol molecules.