Hi Steve,
Without an example it's difficult to diagnose. Are you coming from Molfile,
does the molfile have 2D wedge bonds already? On read we deliberately pass
through whatever information is present even if it was symmetric - correct
stereochemistry cleaner is a lot harder than you might think, consider
inositols <https://en.wikipedia.org/wiki/Inositol> (we do have some basic
utilities such as the StereoElementFactory which are good enough in
practise). The passing through is easier to demonstrate from SMILES:
*CC[C@@H](CC)O*
[image: Inline images 1]
To remove that you need to manually touch the stereoelements
(setStereoElements). If you only want stereochemistry perceived from 3D you
can do something like the following:
>
>
>
> *if (checkHas3D(mol)) { mol.setStereoElements(
> StereoElementFactory.using3DCoordinates(atomContainer).createAll()) }
> else { mol. setStereoElements(Collections.<IStereoElemenet>emptyList());}*
However the molfile (presuming that's your input) should be doing this
already.
In practise it shouldn't matter but your 3D should also probably be
inverted - you need all atoms to have Point3d and non-zero z not just one!
John
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