Hi Pat,
On Sat, Jan 12, 2019 at 2:41 AM Patrick Walters <wpwalt...@gmail.com> wrote:
> Hi all,
>
> I ran into a case that I found confusing. If convert this SMILES to an
> RDKit molecule, I get a valid molecule.
>
> In [2]: mol = Chem.MolFromSmiles("O=C(CC1SCCC1)c1coooo1N")
>
> In [3]: mol
> Out[3]: <rdkit.Chem.rdchem.Mol at 0x10caefbc0>
>
> However, if I convert the molecule to SMILES then covert it back to a
> molecule, it is no longer valid.
>
I believe the initial sanitization should fail here. That degree-three
neutral O should result in an error.
Here's the bug: https://github.com/rdkit/rdkit/issues/2218
These things almost always end up being more complicated than I'd like to
fix, but it shouldn't be too bad.
-greg
> In [4]: smi = Chem.MolToSmiles(mol)
>
> In [5]: new_mol = Chem.MolFromSmiles(smi)
> [20:35:06] Explicit valence for atom # 1 O, 3, is greater than permitted
> RDKit ERROR: [20:35:06] Explicit valence for atom # 1 O, 3, is greater
> than permitted
>
> In [6]: new_mol
>
> In [7]: new_mol is None
> Out[7]: True
>
> I'd like to be able to catch invalid molecules like this in one step
> rather than two. What am I
> doing wrong?
>
> Thanks,
>
> Pat
>
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