query regarding structure standardizer and structure checker

Hello

We are using structure checker and structure standardizer API along with JChemBase to handle structures and structure search.

I wanted to have a clarification about the role played by structure standardizer and structure checker.

I have attached the two .mol (A.mol and B.mol) files. Both the mol files have the same structure but the orientation is different. When these structure are passed through the API's, will they be treated as different structures or the same structure?

Thanks

Ashish Dugar

Hi Ashish,

The two attached structures will be treated as equivalent molecules by JChem search regardless of the orientation. You need not apply structure checker or standardizer to achieve the equality of these structures.

Best regards,

Peter

Hello Peter

I understand the point you are trying to make here. However, in the case that I have presented in this topic, what actually happens in, the SMILE string for both these structures are different.
To identify, whether the molecular are similar or not, we are carrying out a SMILE string comparison. This comparison will always result  in treating both these structures as different, whereas, they are the same.

I hope you are getting the point I am trying to make here.

Thanks
Ashish 

Hi Ashish,

If you would like to use SMILES string comparison to compare molecular structures, then you should use unique/canonical SMILES representation, i.e. use "smiles:u" as export format. For more information, see:
http://www.chemaxon.com/marvin/help/formats/smiles-doc.html

Anyway, a more sophisticated way of comapring two structures is by means of duplicate search:
http://www.chemaxon.com/jchem/doc/user/query_searchtypes.html#otherSearchTypes

Peter

Thanks Peter

 

Will re-configure the search and let you know the outcome.

Thanks

Ashish