Expanding Abbreviated Amino Acids

Hi,

Attached sdf file has amino acids in abbreviated format. Furthermore it does not have smiles in it. How do I add smiles strings, expand abbreviated groups, and write it back to a new sdf file?? Following is the code I tried..it doesn't seem to expand abbreviations..Is it because it doesn't have smiles??

public void marvinWrite()
    {
        try
        {
        FileInputStream fileInputStream = new FileInputStream("abbr.sdf");
    FileOutputStream os = new FileOutputStream("out.sdf");
    MolImporter molImporter = new MolImporter(fileInputStream);
    MolExporter molExporter = new MolExporter(os, "sdf");
    Molecule molecule;
    while ((molecule = molImporter.read()) != null) {
            molecule.ungroupSgroups();
        molExporter.write(molecule);
    }
    molImporter.close();
    molExporter.close();  
        }
        catch (Exception e)
        {
            e.printStackTrace();
        }
    }

Hi Lochana,

The file you attached contains only atoms with the labels of aminoacids on them, not actual groups.

I attached the same file that contains abbreviated groups correctly.

If you created the file using Marvin, you can find how to draw abbreviated groups here. 

 

Your code will result the same as you run " molconvert  sdf -o outputfile.sdf inputfile.sdf{Usg} " in console or command line.

Best regards,

Peter

 

gezapeti wrote:

Hi Lochana, The file you attached contains only atoms with the labels of aminoacids on them, not actual groups. I attached the same file that contains abbreviated groups correctly. If you created the file using Marvin, you can find how to draw abbreviated groups here.    Your code will result the same as you run " molconvert  sdf -o outputfile.sdf inputfile.sdf{Usg} " in console or command line. Best regards, Peter

Thanks Peter..