Problem with Uniquing SMILES structures

I have an issue that is related to the topic at http://www.chemaxon.com/forum/ftopic732.html&highlight=unique





We have a client that is trying to find a unique SMILES string for two different SMILES strings of the same structure:





NC1=CC=C(O)C2=CC=CC=C12


NC1=CC=C(O)C2=C1C=CC=C2





However, using the Molecule.toFormat("smiles:u") method I have not been able to find a uniqued SMILES string. Also tried converting to SD and then back to unique SMILES but still its not working.





Im attaching a small Java test program to demonstrate this. I have tested this with jchem.jar from 3.1.1.





Let me know if im not using the API properly, or if this is a bug.





Thanks





Kanishka

Hi,





I have checked also. This is a bug.


Thank you for the report.


Andras

Hi!





I have checked the problem thoughtfully. I realised that this two molecule looks to be identical but they are not. The difference between them is the arrangement of the double bonds.


Please take a closer look:


- in SMILES NC1=CC=C(O)C2=CC=CC=C12 the common bond of the two ring is a single bond.


- in SMILES NC1=CC=C(O)C2=C1C=CC=C2 the common bond of the two ring is a double bond.





So we cannot export them to the same uniqe SMILES string as they are different.


However, if you aromatize them both will result the same uniqe SMILES: Nc1ccc(O)c2ccccc12





All the best


Andras