Does MolConverter creates canonical SMILES?

User 3d07a7b484

31-03-2014 10:37:25

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

ChemAxon 9c0afc9aaf

01-04-2014 04:56:17

Hi,


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


Best regards,


Szilard

ChemAxon 25dcd765a3

01-04-2014 06:43:35

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).


 

User 3d07a7b484

01-04-2014 10:28:20

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

ChemAxon d26931946c

01-04-2014 11:54:40

You could use



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




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


BRs,


Peter

User 3d07a7b484

01-04-2014 13:08:27

Thank you very much!


 


Best Regards,


Dolunay

User 3d07a7b484

13-08-2014 20:55:59

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


 



 




ChemAxon d26931946c

14-08-2014 12:38:24

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