Does MolConverter creates canonical SMILES?

Hello all,

 

I am using JChem in .NET to convert mol files into SMILES forms, by using the code below:

 

               MolConverter.Builder mcbuilder = new MolConverter.Builder();

                mcbuilder.addInput("C00004.mol", "mol");

                mcbuilder.setOutput("C00004.smi", "smiles");

                mcbuilder.setOutputFlags(MolExporter.TEXT);

                MolConverter mc = mcbuilder.build();

                while (mc.convert()) ;

                mc.close();

 

I wonder is the created SMILES is canonical or not? If not, is there a way to convert it by using MolConverter?

 

Best regards,

Dolunay

Hi,

I have moved your question to the appropriate topic, my colleagues  will answer soon.

Best regards,

Szilard

Yes, the generated SMILES is canonical, but you may rather want unique SMILES.

Please see our documentation about SMILES (specially the part which deals with the unique vs canonical part).

 

Yes, thank you! In some of the articles canonical SMILES is referred as unique, but apparently it also is divided into two categories .

Then, what  I require is unique SMILES, in which the documentation advices to use "u" option. I am a little confused about how to use it via developing interface. Could you give me advice about it?

 

Thanks in advance,

Dolunay

You could use

                mcbuilder.setOutput("C00004.smi", "smiles:u");

to export unique SMILES or create a MolExporter with the "smiles:u" option.

BRs,

Peter

Thank you very much!

 

Best Regards,

Dolunay

Hello again,

I have again a question in mind, I appreciate it a lot if you enlighten me. In documentation for SMILES, it is stated that,

With option u it is possible to include chirality into graph invariants.

So we are informed that chirality is also consired if we use :u, however can we say that we create also isomeric SMILES?

Best Regards,

Dolunay

 

 

Hi,

 

The isotope information is considered in our unique smiles generation.

The unique SMILES generation (option u) currently uses an approximation to make the SMILES string as absolute (unique for isomeric structures) as possible.

BRs,

Peter