Re: [Rdkit-discuss] SMILES validation question

Hi Pat, On Sat, Jan 12, 2019 at 2:41 AM Patrick Walters 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)c1c1N") > > In [3]: mol > Out[3]: > > However, if

Re: [Rdkit-discuss] SMILES validation question

This one is tricky and I bumped into something similar not too long ago. What happened is that by default: [2] mol = Chem.MolFromSmiles("O=C(CC1SCCC1)c1c1N") automatically has sanitize set to True. One of the steps is aromaticity sanitization. Since I don't think the mol satisfies 4n+2, sanit

[Rdkit-discuss] SMILES validation question

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)c1c1N") In [3]: mol Out[3]: However, if I convert the molecule to SMILES then covert it back to a molecule, it is no longer