Unexpected null cd_smiles during structure creation

I have a structure, O=c1cccc[nH]1, that is valid and being created, but cd_smiles is NULL. If I run the structure through the Standardizer separately and re-create, I get a structure that is both valid and has a non-null cd_smiles. Our code currently expects there to be a cd_smiles, so this is a problem.

JChem version: 6.1.4

Standardizer Configuration: "removeatomvalues..removeattacheddata..unmap..dearomatize..aromatize:b..removeexplicitH..absolutestereo:set..[O-:2][N+:1]=O>>[O:2]=[N:1]=O..neutralize"

Thanks,

Xiao

Hi Xiao,

We could reproduce the NULL value of the cd-smiles field in case of structure O=c1cccc[nH]1 when the listed standardizer actions were applied. The successful output in smiles format was also reproduced using the same actions (only  'dearomatize' was relevant) in the standalone Standardizer tool. We will further investigate what is the cause of the different behavior.

Nevertheless, cd_smiles field is originally implemented for internal use only, mainly for improving search performance. It is known that there are cases when this field is NULL. What is your workflow? Couldn't you avoid the use of this field?

Best regards,

Krisztina

Thanks for the reply Krisztina.

We have decided to use the standardizer as part of the work flow to handle this particular problem.

Xiao