rdkit.Chem.SaltRemover module

class rdkit.Chem.SaltRemover.SaltRemover(defnFilename=None, defnData=None)

Bases: object

StripMol(mol, dontRemoveEverything=False)

>>> remover = SaltRemover(defnData="[Cl,Br]")
>>> len(remover.salts)
1

>>> mol = Chem.MolFromSmiles('CN(C)C.Cl')
>>> res = remover.StripMol(mol)
>>> res is not None
True
>>> res.GetNumAtoms()
4

Notice that all salts are removed: >>> mol = Chem.MolFromSmiles(‘CN(C)C.Cl.Cl.Br’) >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4

Matching (e.g. “salt-like”) atoms in the molecule are unchanged: >>> mol = Chem.MolFromSmiles(‘CN(Br)Cl’) >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4

>>> mol = Chem.MolFromSmiles('CN(Br)Cl.Cl')
>>> res = remover.StripMol(mol)
>>> res.GetNumAtoms()
4

Charged salts are handled reasonably: >>> mol = Chem.MolFromSmiles(‘C[NH+](C)(C).[Cl-]’) >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 4

Watch out for this case (everything removed): >>> remover = SaltRemover() >>> len(remover.salts)>1 True >>> mol = Chem.MolFromSmiles(‘CC(=O)O.[Na]’) >>> res = remover.StripMol(mol) >>> res.GetNumAtoms() 0

dontRemoveEverything helps with this by leaving the last salt: >>> res = remover.StripMol(mol,dontRemoveEverything=True) >>> res.GetNumAtoms() 4

but in cases where the last salts are the same, it can’t choose between them, so it returns all of them: >>> mol = Chem.MolFromSmiles(‘Cl.Cl’) >>> res = remover.StripMol(mol,dontRemoveEverything=True) >>> res.GetNumAtoms() 2

defnFilename = '/scratch/RDKit_git/Data/Salts.txt'