Package org.openscience.cdk

Examples of org.openscience.cdk.AtomContainer.addAtom()

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        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(1);
        a2.setImplicitHydrogenCount(1);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_TRIPLE));
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/C2H2/c1-2/h1-2H");
    }
   
    /**
 
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        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));
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        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));
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        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));
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        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));
       
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        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);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
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        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);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
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        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);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
        acZ.addBond(new Bond(a2Z, a4Z, CDKConstants.BONDORDER_SINGLE));
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        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
        acZ.addBond(new Bond(a2Z, a4Z, CDKConstants.BONDORDER_SINGLE));
       
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        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);
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