Examples of org.openscience.cdk.Atom

     */
    @Test public void testGetInchiEandZ12Dichloroethene2D() throws Exception {


        // (E)-1,2-dichloroethene
        IAtomContainer acE = new AtomContainer();
        IAtom a1E = new Atom("C", new Point2d(2.866, -0.250));
        IAtom a2E = new Atom("C", new Point2d(3.732, 0.250));
        IAtom a3E = new Atom("Cl", new Point2d(2.000, 2.500));
        IAtom a4E = new Atom("Cl", new Point2d(4.598, -0.250));
        a1E.setImplicitHydrogenCount(1);
        a2E.setImplicitHydrogenCount(1);
        acE.addAtom(a1E);
        acE.addAtom(a2E);
        acE.addAtom(a3E);
        acE.addAtom(a4E);


        acE.addBond(new Bond(a1E, a2E, CDKConstants.BONDORDER_DOUBLE));
        acE.addBond(new Bond(a1E, a3E, CDKConstants.BONDORDER_SINGLE));
        acE.addBond(new Bond(a2E, a4E, CDKConstants.BONDORDER_SINGLE));
        
        Assert.assertEquals(gen.generateInchi(acE).getInChI(), "InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+");
        
        // (Z)-1,2-dichloroethene
        IAtomContainer acZ = new AtomContainer();
        IAtom a1Z = new Atom("C", new Point2d(2.866, -0.440));
        IAtom a2Z = new Atom("C", new Point2d(3.732, 0.060));
        IAtom a3Z = new Atom("Cl", new Point2d(2.000, 0.060));
        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);

    @Test
    public void testGetInchiFromLandDAlanine3D() throws Exception {
        
        // L-Alanine
        IAtomContainer acL = new AtomContainer();
        IAtom a1L = new Atom("C", new Point3d(-0.358, 0.819, 20.655));
        IAtom a2L = new Atom("C", new Point3d(-1.598, -0.032, 20.905));
        IAtom a3L = new Atom("N", new Point3d(-0.275, 2.014, 21.574));
        IAtom a4L = new Atom("C", new Point3d(0.952, 0.043, 20.838));
        IAtom a5L = new Atom("O", new Point3d(-2.678, 0.479, 21.093));
        IAtom a6L = new Atom("O", new Point3d(-1.596, -1.239, 20.958));
        a1L.setImplicitHydrogenCount(1);
        a3L.setImplicitHydrogenCount(2);
        a4L.setImplicitHydrogenCount(3);
        a5L.setImplicitHydrogenCount(1);
        acL.addAtom(a1L);
        acL.addAtom(a2L);
        acL.addAtom(a3L);
        acL.addAtom(a4L);
        acL.addAtom(a5L);
        acL.addAtom(a6L);
        
        acL.addBond(new Bond(a1L, a2L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a3L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a4L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a5L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a6L, CDKConstants.BONDORDER_DOUBLE));
        
        Assert.assertEquals(gen.generateInchi(acL).getInChI(), "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1");
        
        
        // D-Alanine
        IAtomContainer acD = new AtomContainer();
        IAtom a1D = new Atom("C", new Point3d(0.358, 0.819, 20.655));
        IAtom a2D = new Atom("C", new Point3d(1.598, -0.032, 20.905));
        IAtom a3D = new Atom("N", new Point3d(0.275, 2.014, 21.574));
        IAtom a4D = new Atom("C", new Point3d(-0.952, 0.043, 20.838));
        IAtom a5D = new Atom("O", new Point3d(2.678, 0.479, 21.093));
        IAtom a6D = new Atom("O", new Point3d(1.596, -1.239, 20.958));
        a1D.setImplicitHydrogenCount(1);
        a3D.setImplicitHydrogenCount(2);
        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);

Examples of org.openscience.cdk.Atom

Related Classes of org.openscience.cdk.Atom