On Fri, Nov 21, 2008 at 4:47 PM, Adel Golovin <[EMAIL PROTECTED]> wrote:
> Even when I explicitly set all coordinates to 0:
>
> javax.vecmath.Point3d point3d = new javax.vecmath.Point3d();
> Iterator<org.openscience.cdk.interfaces.IAtom> itatoms = mol.atoms();
> while (itatoms.hasNext())
> itatoms.next().setPoint3d(point3d);
What are you trying to achieve with this code? It has nothing to do
with the StructureDiagramGenerator which does not create 3D
coordinates, but 2D.
The first bit of code should set 2D coordinates which you can check with:
for (IAtom atom : mol.atoms()) {
Point2d coord2d = atom.getPoint2d();
}
Egon
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