SMILES perceptions of aromatic heterocycle converts to saturated

[openbabel-bot]

Open babel correctly reads the sdf containing the kekule-drawing of attached molecule, and produces the aromatic SMILES. But when fed that SMILES, it converts it to a saturated form.

obabel -isdf sulfurish.sdf -ocan
CCn1c(=S)sc2c1nc1c3ccccc3c(=O)[nH]n1c2=O

obabel -isdf sulfurish.sdf -ocan|obabel -ican - -ocan
CCN1C(=S)SC2C1NC1N(C2=O)NC(=O)C2C1CCCC2

This is both 2.3.2 and current git master.

Reported by: jeff-janes

Original Ticket: openbabel/bugs/943

[openbabel-bot]

I've also encountered this bug with the thiazole ring in Thiamine: n1c(c(cnc1C)Cn2c(c(sc2)CCO)C)N
I noticed that the program raised a stereochemistry warning (in spite of the fact that thiamine has no chiral centers)

However when the SMILES is properly charged, the SDF retains the aromaticity
n1c(c(cnc1C)C[n+]2c(c(sc2)CCO)C)N

There seems to be some issue with the combination of heteroaromaticity and charge assignment

Original comment by: jjeffryes

[baoilleach]

Fixed by #1576. (FYI @jeffjanes and @JamesJeffryes)

The first doesn't lose aromaticity.

>obabel -:"CCn1c(=S)sc2c1nc1c3ccccc3c(=O)[nH]n1c2=O" -ocan
CCn1c(=S)sc2c1nc1c3ccccc3c(=O)[nH]n1c2=O

The second cannot be kekulized (and that's what the error message says):

> obabel -:"n1c(c(cnc1C)Cn2c(c(sc2)CCO)C)N" -ocan
==============================
*** Open Babel Warning  in OpenBabel::OBSmilesParser::ParseSmiles
  Failed to kekulize aromatic SMILES

OCCC1=C(C)N([CH]S1)Cc1cnc(nc1N)C