Canonical/unique smiles

Hi all,

I am running molconvert smiles:u to generate unique/canonical smiles and observed that 2 of the structures in my input file which are identical are represented with 2 different smiles strings, the difference is highlighted in red

C[C@@H]1[C@@H](O)[C@@H](OC(=O)C)[C@H](OC(=O)c2ccccc2)[C@@]2(C)[C@H](C[C@@H]3C[C@]12OC3(C)C)OC(=O)\C=C\c1ccccc1

C[C@@H]1[C@@H](O)[C@@H](OC(C)=O)[C@H](OC(=O)c2ccccc2)[C@@]2(C)[C@H](C[C@@H]3C[C@]12OC3(C)C)OC(=O)\C=C\c1ccccc1

I am using JChem 5.8.0, with Java 1.6.0_29 on Mac OX

Oleg.

Dear Oleg,

Could you send us your original input file which contains the identical structures please?

Thanks,

Erika

Hi Erika,

I attached original SDF file, I then converted to unique/canonical smiles using:

molconvert smiles:u c1.sdf -o c1.smi -T MOLREGNO

The duplicate structures have MOLREGNO 10000486 and 392308, chemical depiction in Marvin shows these as identical where is the smiles strings are not.

Oleg.

Dear Oleg,

Thank you for the report. This is definitely a bug we will fix it ASAP.

Andras