RingTests.java

package tests;

import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.geometry.cip.CIPTool;
import org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.stereo.TetrahedralChirality;

public class RingTests {

    public IAtomContainer makeChiralRing(int ringSize, int oxygenOffset) {
        IAtomContainer ring = new AtomContainer();
        for (int i = 0; i < ringSize; i++) {
            ring.addAtom(new Atom("C"));
        }
        for (int j = 0; j < ringSize - 1; j++) {
            ring.addBond(j, j + 1, IBond.Order.SINGLE);
        }
        ring.addBond(ringSize - 1, 0, IBond.Order.SINGLE);
        
        ring.addAtom(new Atom("Cl"));
        ring.addAtom(new Atom("F"));
        ring.addBond(0, ringSize, IBond.Order.SINGLE);
        ring.addBond(0, ringSize + 1, IBond.Order.SINGLE);
        ring.addAtom(new Atom("O"));
        ring.addBond(oxygenOffset, ringSize + 2, IBond.Order.SINGLE);
        IAtom[] atoms = new IAtom[] {
                ring.getAtom(ringSize), 
                ring.getAtom(ringSize + 1), 
                ring.getAtom(ringSize - 1), 
                ring.getAtom(1) 
        };
        ring.addStereoElement(
                new TetrahedralChirality(ring.getAtom(0), atoms, Stereo.ANTI_CLOCKWISE)
        );
        return ring;
    }
    
    public void printOut(IAtomContainer atomContainer) {
        for (IBond bond : atomContainer.bonds()) {
            int ai = atomContainer.getAtomNumber(bond.getAtom(0));
            int bi = atomContainer.getAtomNumber(bond.getAtom(1));
            System.out.println(ai + " " + bi);
        }
        SmilesGenerator generator = new SmilesGenerator();
        String smiles = generator.createSMILES(atomContainer);
        System.out.println(smiles);
    }
    
    public TetrahedralChirality getChiralityElement(IAtomContainer container) {
        for (IStereoElement element : container.stereoElements()) {
            return (TetrahedralChirality) element;
        }
        return null;
    }
    
    public void analyseChirality(IAtomContainer container) {
        TetrahedralChirality stereoCenter = getChiralityElement(container);
        CIP_CHIRALITY chirality = CIPTool.getCIPChirality(container, stereoCenter);
        System.out.println(chirality);
    }
    
    @Test
    public void threeRing() {
        IAtomContainer threeRing = makeChiralRing(3, 1);
        printOut(threeRing);
        analyseChirality(threeRing);
    }
    
    @Test
    public void fourRing() {
        IAtomContainer fourRing = makeChiralRing(4, 1);
        printOut(fourRing);
        analyseChirality(fourRing);
    }
    
    @Test
    public void fiveRing() {
        IAtomContainer fiveRing = makeChiralRing(5, 1);
        printOut(fiveRing);
        analyseChirality(fiveRing);
    }
    
    @Test
    public void sixRing() {
        IAtomContainer sixRing = makeChiralRing(6, 1);
        printOut(sixRing);
        analyseChirality(sixRing);
    }
    
    @Test
    public void sevenRing() {
        IAtomContainer sevenRing = makeChiralRing(7, 1);
        printOut(sevenRing);
        analyseChirality(sevenRing);
    }
    
    @Test
    public void fourRingOffset2() {
        IAtomContainer fourTwoRing = makeChiralRing(4, 2);
        printOut(fourTwoRing);
        analyseChirality(fourTwoRing);
    }
    
    @Test
    public void fiveRingOffset2() {
        IAtomContainer fiveTwoRing = makeChiralRing(5, 2);
        printOut(fiveTwoRing);
        analyseChirality(fiveTwoRing);
    }
    
    @Test
    public void sixRingOffset2() {
        IAtomContainer sixTwoRing = makeChiralRing(6, 2);
        printOut(sixTwoRing);
        analyseChirality(sixTwoRing);
    }
    
    @Test
    public void sevenRingOffset3() {
        IAtomContainer sevenThreeRing = makeChiralRing(7, 3);
        printOut(sevenThreeRing);
        analyseChirality(sevenThreeRing);
    }


}