Conversion of Molecules with HN to SMILES

Regularly, BindingDB populates new molecules to the database.  BindingDB uses JChem APIs for this process.  A enclosed molfile from US Patents Office is converted to a wrong SMILES.

BindingDB_111821.mol    OC(=O)CCC(=O)N1CCc2cc(ccc12)S(=O)(=O)N1CCN(CC1)c1cccc(Cl)c1
BindingDB_111837.mol    OC(=O)CCC(=O)N1CCc2cc(ccc12)S(=O)(=O)N1CCN(CC1)c1cccc(Cl)c1
BindingDB_111837M.mol OC(=O)CNC(=O)N1CCc2cc(ccc12)S(=O)(=O)N1CCN(CC1)c1cccc(Cl)c1

  BindingDB_111821.mol and BindingDB_111837.mol  are converted to the same SMILES.

BindingDB_111837.mol has a section in its MOL file:

A   28
HN

BindingDB_111837.mol is imported to a Marvin applet, whose N (28) is replaced with C, and back to N, and exported to BindingDB_111837M.mo.

Is there a way in JChem programmatically reorganizing the HN part like BindingDB_111837M.mol to retain the molecule?

Thank you in advance for your help.

Hi,

The "A 28 NH" part is an atom alias. What do you want to do exactly? Do you want to get a smiles with this NH part except the C?

Janos

Hi Janos,

  Yes, I would like to get the correct SMILES with NH not C.  It is very important to us.

Hi,

It is possible from API, with the following method:

-after import, iterate over the atoms

-check if the atom is an alias atom

-process the atom alias string  and convert it to an atomic number

-change the atomic numbert from alias atom to the new one

-export to smiles

Can you write the code, or do you want a code example?

Janos

Hi Janos,

  Thank you for the kind reply.

  Please give the example codes to do that at your convenience.

Hi,

Try this:

        MolImporter molImporter = new MolImporter(filename);
        Molecule molecule = molImporter.read();
        for(MolAtom molAtom : molecule.getAtomArray()) {
            String alias = molAtom.getAliasstr();
            if(alias != null) {
                alias = alias.replace("H", "");
                molAtom.setAtno(PeriodicSystem.findAtomicNumber(alias));
            }
        }

        System.out.println(MolExporter.exportToFormat(molecule, "smiles"));

 

Janos