A small function to fix the pH protonation/deprotonation of RDKit Chem objects —fixes the charge of simple, i.e. biological cases. So amino acid is fine, but complex artificial drug won't be.

set_to_neutral_pH

from rdkit import mol

def set_to_neutral_pH(mol: Chem):
    """
    Not great, but does the job.
    
    * Protonates amines, but not aromatic bound amines.
    * Deprotonates carboxylic acid, phosphoric acid and sulfuric acid, without ruining esters.
    """
    protons_added = 0
    protons_removed = 0
    for indices in mol.GetSubstructMatches(Chem.MolFromSmarts('[N;D1]')):
        atom = mol.GetAtomWithIdx(indices[0])
        if atom.GetNeighbors()[0].GetIsAromatic():
            continue # aniline
        atom.SetFormalCharge(1)
        protons_added += 1
    for indices in mol.GetSubstructMatches(Chem.MolFromSmarts('C(=O)[O;D1]')):
        atom = mol.GetAtomWithIdx(indices[2])
        # benzoic acid pKa is low.
        atom.SetFormalCharge(-1)
        protons_removed += 1
    for indices in mol.GetSubstructMatches(Chem.MolFromSmarts('P(=O)[Oh1]')):
        atom = mol.GetAtomWithIdx(indices[2])
        # benzoic acid pKa is low.
        atom.SetFormalCharge(-1)
        protons_removed += 1
    for indices in mol.GetSubstructMatches(Chem.MolFromSmarts('S(=O)(=O)[Oh1]')):
        atom = mol.GetAtomWithIdx(indices[3])
        # benzoic acid pKa is low.
        atom.SetFormalCharge(-1)
        protons_removed += 1
    return (protons_added, protons_removed)