Molecular Handling

Hi, I've been looking hard for documentation on how to handle molecules on an atomic basis, but the best I could find was http://www.chemaxon.com/jchem/doc/guide/utils/index.html#molhand which says its unlikely that devlopers will need to access the molecule directly, so I apologise if the answer is trivial.

I was wondering how to manually add and remove atoms and bonds. I have experimented but not had much success:

mol = MolHandler('NCCCC').getMolecule()

#Creates Oxygen 'MolAtom'
oxygenAtom = MolAtom(8)

#creates bond between the atoms
bond = MolBond(oxygenAtom, mol.getAtom(3))

however when the molecule is printed toFormat smiles,  the oxygen is not present (nor is the atom or bond made present on the molecules bond/atom array).

I have also tried the mol.AddNode0(CNode) method, considering CNodes are abstract I tried:

mol.AddNode0(oxygenAtom)

however this returns the error:
"AttributeError: 'chemaxon.struc.Molecule' object has no attribute 'addNode0'"

So all in all I'm quite confused,

Thanks for any help,
-Ben

I move this topic to the appropriate forum.

Robert

 

(Sorry, I put it under Base because thats where the relevant documentation (http://www.chemaxon.com/jchem/doc/guide/utils/index.html#molhand) I could find was listed.)

Dear Ben,

Use Molecule.add() to add new atoms and bonds. Before adding a bond all of its atoms should be added to the molecule.

Example:

import chemaxon.formats.MolFormatException;
import chemaxon.formats.MolImporter;
import chemaxon.struc.MolAtom;
import chemaxon.struc.MolBond;
import chemaxon.struc.Molecule;

public class Example {
    public static void main( String [] args ) throws MolFormatException {
        Molecule mol = MolImporter.importMol("NCCCC");
        System.out.println("Molecule before: "+mol.toFormat("smiles"));
        MolAtom newAtom = new MolAtom(8);
        // Add new atom first
        mol.add( newAtom );
        System.out.println("Molecule after1: "+mol.toFormat("smiles"));
        MolBond newBond = new MolBond(newAtom, mol.getAtom(3) );
        // Add new bond
        mol.add( newBond );
        System.out.println("Molecule after2: "+mol.toFormat("smiles"));
    }
}

Output:

Molecule before: CCCCN
Molecule after1: O.CCCCN
Molecule after2: CC(O)CCN

If you have any further questions, please do not hesitate to ask them

Regards,

Gabor

Excellent, Thanks!