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Converting implicit Hydrogens to explicit

The following methods are available in chemaxon.calculations.Hydrogenizeclass to convert implicit hydrogen atoms to explicit ones:

  • Hydrogenize.convertImplicitHToExplicit(MoleculeGraph molecule, MolAtom[] atoms, int f)
  • Hydrogenize.convertImplicitHToExplicit(MoleculeGraph molecule)

In the first method the coordinate refinement to avoid atom collisions can be skipped using the OMIT_POSTCLEAN option.

You can convert implicit Hydrogens to explicit ones without additional cleaning:

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//import a simple chain
Molecule mol = MolImporter.importMol("methylhexene.mol");
Hydrogenize.convertImplicitHToExplicit(mol, null, MoleculeGraph.OMIT_POSTCLEAN);
images/download/thumbnails/1806276/image071.png images/download/thumbnails/1806276/image072.png images/download/thumbnails/1806276/image073.png
original methylhexene molecule with OMIT_POSTCLEAN option without OMIT_POSTCLEAN option

Working example to add explicit H to chiral centers only

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import java.io.IOException; 

import chemaxon.struc.Molecule; 
import chemaxon.struc.MolAtom; 
import chemaxon.formats.MolImporter; 
import chemaxon.struc.StereoConstants; 

public class ExplicitHToChiralCenter { 
    /** 
     * Example to add Explicit H to Chiral centers only. 
     * @param args   command line arguments 
     * @throws java.io.IOException  
     *  
     * @version 5.1 04/24/2008 
     * @since Marvin 5.1 
     * @author Andras Volford 
     */ 

    // ODD and EVEN parity values 
    static int ODD = StereoConstants.PARITY_ODD;     
    static int EVEN = StereoConstants.PARITY_EVEN; 

    public static void main(String[] args) throws IOException { 
        if (args.length < 1) {
             System.err.println("Usage: java ExplicitHToChiralCenter 
               filename"); 
            System.exit(0); 
        } 

        // create importer for the file argument 
        String s = (String) args[0]; 
        MolImporter molimp = new MolImporter(s); 

        // store the imported molecules in m 
        Molecule m = new Molecule(); 

        while (molimp.read(m)) {  // read molecules from the file 
            int ac = m.getAtomCount(); 

           // Atoms with odd or even parity 
            MolAtom[] t = new MolAtom[ac];
             int n = 0;
             for (int i = 0; i < ac; i++){
                 int p = m.getParity(i);
                 boolean add = p == ODD || p == EVEN; 

                // if the atom has ODD or EVEN parity 
                if (add) {
                     t[n++] = m.getAtom(i); 
                } 
            } 

            // reduce atom array 
            MolAtom[] a = new MolAtom[n];
            System.arraycopy(t, 0, a, 0, n); 

            // add explicit H 
            Hydrogenize.convertImplicitHToExplicit(m, a, 0);

            if (m.getDim() != 2)
                 m.clean(2, null);              

            // write the result 
            System.out.print(m.toFormat("sdf"));
          } 
    } 
}