Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IAtomContainer.addAtom()

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    // decide on which side to draw the ring??
    IAtomContainer connectedAtoms = bond.getBuilder().newInstance(IAtomContainer.class);
    for (IAtom atom : sourceContainer.getConnectedAtomsList(firstAtom)) {
      if (atom != secondAtom)
        connectedAtoms.addAtom(atom);
    }
    for (IAtom atom : sourceContainer.getConnectedAtomsList(secondAtom)) {
      if (atom != firstAtom)
        connectedAtoms.addAtom(atom);
    }
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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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      if (atom != secondAtom)
        connectedAtoms.addAtom(atom);
    }
    for (IAtom atom : sourceContainer.getConnectedAtomsList(secondAtom)) {
      if (atom != firstAtom)
        connectedAtoms.addAtom(atom);
    }
    Point2d conAtomsCenter = GeometryTools.get2DCenter(connectedAtoms);
    double distance1 = newPoint1.distance(conAtomsCenter);
    double distance2 = newPoint2.distance(conAtomsCenter);
    Vector2d ringCenterVector = new Vector2d(sharedAtomsCenter);
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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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