Using the Scrub API

The python API revolves around the Scrub object which instantiates a function that is used to scrub molecules. The Scrub class takes more or less the same as the CLI Options. See the signature of molscrub.core.Scrub class in the API Docs

To use the class:

from rdkit import Chem
from molscrub import Scrub

scrub = Scrub(
    ph_low=7.4,
    ph_high=7.4,
    # ... other options...
)

mol = Chem.MolFromSmiles("Clc1c(OCCC3)c3ccc1C(=O)Nc2nc[nH]c2")

scrubbed_mols = scrub(mol)

The instatiated scrub function takes an RDKit mol as input and produces an list of RDKit mols as output (with embedded 3D coords). Then you can handle these or perform any operations that you would on RDKit mols.