rdkit.Chem.SaltRemover module¶
- class rdkit.Chem.SaltRemover.InputFormat¶
Bases:
object
- MOL = 'mol'¶
- SMARTS = 'smarts'¶
- SMILES = 'smiles'¶
- class rdkit.Chem.SaltRemover.SaltRemover(defnFilename=None, defnData=None, defnFormat='smarts', useChirality=False)¶
Bases:
object
- StripMol(mol, dontRemoveEverything=False, sanitize=True)¶
>>> 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
- StripMolWithDeleted(mol, dontRemoveEverything=False)¶
Strips given molecule and returns it, with the fragments which have been deleted.
>>> remover = SaltRemover(defnData="[Cl,Br]") >>> len(remover.salts) 1
>>> mol = Chem.MolFromSmiles('CN(C)C.Cl.Br') >>> res, deleted = remover.StripMolWithDeleted(mol) >>> Chem.MolToSmiles(res) 'CN(C)C' >>> [Chem.MolToSmarts(m) for m in deleted] ['[Cl,Br]']
>>> mol = Chem.MolFromSmiles('CN(C)C.Cl') >>> res, deleted = remover.StripMolWithDeleted(mol) >>> res.GetNumAtoms() 4 >>> len(deleted) 1 >>> deleted[0].GetNumAtoms() 1 >>> Chem.MolToSmarts(deleted[0]) '[Cl,Br]'
Multiple occurrences of ‘Cl’ and without tuple destructuring
>>> mol = Chem.MolFromSmiles('CN(C)C.Cl.Cl') >>> tup = remover.StripMolWithDeleted(mol)
>>> tup.mol.GetNumAtoms() 4 >>> len(tup.deleted) 1 >>> tup.deleted[0].GetNumAtoms() 1 >>> Chem.MolToSmarts(deleted[0]) '[Cl,Br]'
- defnFilename = '/scratch/RDKit_git/Data/Salts.txt'¶