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);
                 } 
            } 
        } 
    }