Parity information

    See also for scientific details

    Working example to get the parity and chirality of the atoms

    import java.io.IOException; 

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

public class ParityExample { 

    /**
     * Example to get the parity and chirality of the atoms.
     * @param args   command line arguments
     * @throws java.io.IOException
     *
     * @version 5.1 04/24/2008
     * @since Marvin 5.1
     * @author Andras Volford
     */
    public static void main(String[] args) throws IOException {
         if (args.length < 1) {
             System.err.println("Usage: java ParityExample 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(); 

        // counter for molecules 
        int n = 0; 

        while (molimp.read(m)) {  // read molecules from the file 
            ++n;                  // increment counter 
            System.out.println("mol " + n); 

            // print parity information followed by the chirality 
            for (int i = 0; i < m.getAtomCount(); i++) {
                 int c = m.getChirality(i);
                 System.out.println( 
                    i + " Parity " + m.getParity(i) +
                     " Chirality " +
                     ((c == StereoConstants.CHIRALITY_R) ? "R" :
                          (c == StereoConstants.CHIRALITY_S) ? "S" :
                              ("" + c)) + " " + c);
             } 
        } 
    } 
}