Re: [Rdkit-discuss] Clearing isotope info

[Andrew D. <da...@da...>]

On Dec 12, 2019, at 17:39, Rafal Roszak <rmr...@gm...> wrote:
> I also had situation when I need to generate smiles with either
> isotopes or stereochemistry but not both. Maybe it is worth to add two
> options to ChemMolToSmiles function:
> 
> dontIncludeStereochemistry=True/False
> dontIncludeIsotopes=True/False
> 
> Right now it is not straightforward to generate smiles w/o isotopes
> (but with stereochemistry) - one need to remove isotope, export to
> smiles and restore isotopes.

Bear in mind a few complications. I believe the following correctly implements what you describe:

from rdkit import Chem

def MolWithoutIsotopesToSmiles(mol):
  atom_data = [(atom, atom.GetIsotope()) for atom in mol.GetAtoms()]
  for atom, isotope in atom_data:
      if isotope:
          atom.SetIsotope(0)
  smiles = Chem.MolToSmiles(mol)
  for atom, isotope in atom_data:
      if isotope:
          atom.SetIsotope(isotope)
  return smiles


>>> mol = Chem.MolFromSmiles("[19F][13C@H]([16OH])[35Cl]")
>>> MolWithoutIsotopesToSmiles(mol)
'O[C@@H](F)Cl'

Testing reveals two problems with my implementation:

1) isotopic hydrogens 

Consider the same structure with tritium instead of fluorine:

>>> mol = Chem.MolFromSmiles("[3H][13C@H]([16OH])[35Cl]")
>>> MolWithoutIsotopesToSmiles(mol)
'[H][C@H](O)Cl'

That output should be 'OCCl'.

2) stereochemistry assignment needs to be recalculated after the isotopes have been removed:

>>> mol = Chem.MolFromSmiles("C[C@H]([13CH3])CI")
>>> MolWithoutIsotopesToSmiles(mol)
'C[C@@H](C)CI'
>>> Chem.CanonSmiles("C[C@H]([CH3])CI")
'CC(C)CI'

2b) This includes directional bonds

>>> mol = Chem.MolFromSmiles("C/C(=C/CO)/[11CH3]")
>>> MolWithoutIsotopesToSmiles(mol)
'C/C(C)=C/CO'
>>> Chem.CanonSmiles("C/C(=C/CO)/[CH3]")
'CC(C)=CCO'



				Andrew
				da...@da...