ASE Interface

import rdkit2ase

The main functionality of rdkit2ase is to generate new structures from SMILES. For this purpose, you can utilize smiles2atoms and smiles2conformers

water = rdkit2ase.smiles2atoms("O")
water

Atoms(symbols='OH2', pbc=False)

aspirin = rdkit2ase.smiles2conformers("CC(=O)OC1=CC=CC=C1C(=O)O", numConfs=3)
aspirin

[Atoms(symbols='C2O2C7O2H8', pbc=False),
 Atoms(symbols='C2O2C7O2H8', pbc=False),
 Atoms(symbols='C2O2C7O2H8', pbc=False)]

Within rdkit2ase you can translate structures between ASE and rdkit.

mol = rdkit2ase.ase2rdkit(aspirin[0])
print(mol)
mol

<rdkit.Chem.rdchem.Mol object at 0x11b40b290>

If a structure has been generated using rdkit2ase it includes smiles and connectivity in it’s atoms.info key. This information is utilized to quickly transform ase.Atoms to rdkit structures.

aspirin[0].info

{'smiles': 'CC(=O)OC1=CC=CC=C1C(=O)O',
 'connectivity': [(0, 1, 1.0),
  (1, 2, 2.0),
  (1, 3, 1.0),
  (3, 4, 1.0),
  (4, 5, 1.5),
  (5, 6, 1.5),
  (6, 7, 1.5),
  (7, 8, 1.5),
  (8, 9, 1.5),
  (9, 10, 1.0),
  (10, 11, 2.0),
  (10, 12, 1.0),
  (9, 4, 1.5),
  (0, 13, 1.0),
  (0, 14, 1.0),
  (0, 15, 1.0),
  (5, 16, 1.0),
  (6, 17, 1.0),
  (7, 18, 1.0),
  (8, 19, 1.0),
  (12, 20, 1.0)]}

Without this information, rdkit2ase will try to guess the bond information. You can aid this process, by including SMILES into the suggestions= keyword.

aspirin_0 = aspirin[0]
del aspirin_0.info["smiles"]
del aspirin_0.info["connectivity"]
rdkit2ase.ase2rdkit(aspirin_0, suggestions=[])

rdkit2ase.ase2rdkit(aspirin_0, suggestions=["CC(=O)OC1=CC=CC=C1C(=O)O"])

You can use match_substructure to select parts of the structure based on SMILES, SMARTS, molecules or even ase.Atoms.

from rdkit.Chem import Draw

mol = rdkit2ase.ase2rdkit(aspirin_0, suggestions=["CC(=O)OC1=CC=CC=C1C(=O)O"])
Draw.MolToImage(
    mol,
    highlightAtoms={
        i
        for group in rdkit2ase.match_substructure(
            aspirin[0], smarts="C(=O)O", suggestions=[]
        )
        for i in group
    },
)