Re: [Rdkit-discuss] Delete atoms can leave dangling aromaticity

[Tim D. <tdu...@gm...>]

Thanks Paolo, that does the trick.
Tim

On Mon, Feb 14, 2022 at 11:23 AM Paolo Tosco <pao...@gm...>
wrote:

> Hi Tim,
>
> after you are done removing the atoms you can do loop through remaining
> ring atoms and bonds and clear aromatic flags, e.g.
>
> from rdkit import Chem
>
> rwmol = Chem.RWMol(Chem.MolFromSmiles("c1ccccc1"))
> rwmol.RemoveAtom(0)
>
> for a in rwmol.GetAtoms():
>     if (not a.IsInRing()) and a.GetIsAromatic():
>         a.SetIsAromatic(False)
> for b in rwmol.GetBonds():
>     if (not b.IsInRing()) and b.GetIsAromatic():
>         b.SetIsAromatic(False)
>
> Chem.SanitizeMol(rwmol)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> rwmol
> [image: image.png]
>
> However, this will still leave you with not particularly useful AROMATIC
> bond types.
> Probably a better option is to kekulize the molecule and clear aromatic
> flags before starting to remove atoms, then sanitize:
>
> rwmol = Chem.RWMol(Chem.MolFromSmiles("c1ccccc1"))
> Chem.Kekulize(rwmol, clearAromaticFlags=True)
> rwmol.RemoveAtom(0)
>
> Chem.SanitizeMol(rwmol)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> rwmol
> [image: image.png]
>
> Cheers,
> p.
>
> On Mon, Feb 14, 2022 at 11:55 AM Tim Dudgeon <tdu...@gm...>
> wrote:
>
>> I'm using mol.RemoveAtom(atom) to remove atoms from a molecule, and then
>> calling Chem.SanitizeMol(mol) at the end to clean up the molecule. Mostly
>> this works fine.
>> But when I delete atoms in an aromatic ring but leave a single ring atom
>> remaining in the molecule then the sanitize function fails:
>>
>> rdkit.Chem.rdchem.AtomKekulizeException: non-ring atom 0 marked aromatic
>>
>> I'm using SanitizeMol() with default options
>> so SanitizeFlags.SANITIZE_ALL should be in place.
>> What do I need to do to have sanitize to fix the atom type in the general
>> case?
>>
>> Tim
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>