Package org.openscience.cdk

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

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        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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        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));
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        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));
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        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));
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        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));
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        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);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
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        a1D.setImplicitHydrogenCount(1);
        a3D.setImplicitHydrogenCount(2);
        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
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        a3D.setImplicitHydrogenCount(2);
        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
        acD.addBond(new Bond(a1D, a2D, CDKConstants.BONDORDER_SINGLE));
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        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
        acD.addBond(new Bond(a1D, a2D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a3D, CDKConstants.BONDORDER_SINGLE));
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        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
        acD.addBond(new Bond(a1D, a2D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a3D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a4D, CDKConstants.BONDORDER_SINGLE));
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