On Wednesday 08 February 2006 14:53, Egon Willighagen wrote:
> Now, I strongly believe we should remove the second option from the
> interfaces.
Stefan reported that the SMILES generator does not use it, and the only use in
CDK seems to be in ModelBuilder3D:
if (atomA.getStereoParity() != 0 ||
(Math.abs((molecule.getBond(atomA,
unplacedAtom)).getStereo()) < 2
&& Math.abs((molecule.getBond(atomA,
unplacedAtom)).getStereo()) != 0)
&& molecule.getMaximumBondOrder(atomA) < 1.5) {
if (atomNeighbours.getAtomCount() > 1) {
stereo =
atlp3d.makeStereocenter(atomA.getPoint3d(),
molecule.getBond(atomA, unplacedAtom),
(atomNeighbours.getAtomAt(0)).getPoint3d(),
(atomNeighbours.getAtomAt(1)).getPoint3d(), branchPoints);
}
}
And even in this case, I think it can be savely removed (note the ||).
If nobody shows disagreement, I will remove the two methods from IAtom this
weekend.
Egon
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