#943 SMILES perceptions of aromatic heterocycle converts to saturated

[Jeff Janes]

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.

[James Jeffryes]

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