Unwanted abbreviation recognization in marvinview

Dear MarvinView Developer,





If I put "CAT" in as a SMILES string to MolImporter.importMol() function, it changes it to the SMILES for the polypeptide: cysteine-alanine-threonine .





That's,


input : CAT


output: [H]NC(CS)C(=O)NC(C)C(=O)NC(C(C)O)C(O)=O





Actually I don't want this feature and I want to turn it off (If the users still input a String likes "CAT", then I want to throw an unexpected SMILES string error). I searched the chemaxon forum and marvin view documents, but I can't find answers. Can you let me know how to do this? Thanks for your suggestions!





The related code is,

Code:

Molecule substrateMol = null;         try {             substrateMol = MolImporter.importMol(substrate);         } catch(MolFormatException exc) {             System.out.println(exc.getMessage());             return;         }      System.out.println("Molecule String=" + substrateMol.toFormat("smiles"));

Regards,


- Jeff

Dear Jeff,


File recognition problems can be avoided by constructing a MolImporter object with the file format specified as import option.


If you prefer using a static importMol method, then you will be able to specify the format only in Marvin 5.0 (will be released in a few days hopefully). I created some new importMol methods with additional option and encoding arguments.

cspeter wrote:

Dear Jeff, File recognition problems can be avoided by constructing a MolImporter object with the file format specified as import option. If you prefer using a static importMol method, then you will be able to specify the format only in Marvin 5.0 (will be released in a few days hopefully). I created some new importMol methods with additional option and encoding arguments.

Thanks! I will try Marvin 5.0.





Jeff