Standardize Smile generated by JChem Manage and Sketch

I wonder what kind of smiles and the JChem Manager inserts the selected database, For Smiles generated by Mavin Sketch and different generated by JChem Manager. I wonder how I can standardize the two both JChem Manager and Marvin Sketch

Hi Patrick,

Marvin Sketch generates smiles without standardization.

In JChem Manager, there is a default standardization (aromatization and removing explicit hydrogens), additionally there is the possibility of setting customized standardization during table creation, or later by changing table settings.

See: https://www.chemaxon.com/jchem/doc/admin/#create

https://www.chemaxon.com/jchem/doc/admin/#table_settings

https://www.chemaxon.com/jchem/doc/user/query_standard.html#standardizationDB

However, you can freely standardize structures using our Standardizer application:

https://www.chemaxon.com/jchem/doc/user/Standardizer.html

Best regards,

Krisztina

 

Hi,

A couple of remarks:

- The SMILES in the cd_smiles column of the JChemBase table is generally for internal use only. It can also be NULL in certain cases.

- Even if the structure is standardized to the same form, the generated SMILES can be different. Generating unique SMILES (":u" option) is needed if one wants to compare strings.

- In general for detecting duplicates the fast and efficient DUPLICATE database search type is recommended.

Best regards,

Szilard