I don't thank that's possible with the current API. Egon might know of a way
though. Having a look at the javadoc though I think you're right and the
ILigancyFour… was either meant to be public or at least not exported by the
method.
J
On 4 Sep 2013, at 14:39, "Nick Vandewiele" <[email protected]> wrote:
> OK, thanks for the help.
>
> And how do I use :
>
> ILigand [] ligands = CIPTool.order(chirality.getLigands());
>
> I need a way to get an array of the ligand atoms, ordered according to CIP.
>
> Since ITetrahedralChirality can’t return an array of ILigand anymore, I can’t
> fill in that array as a parameter in CIP.order(…) .
>
> Regards,
> Nick
>
> From: John May [mailto:[email protected]]
> Sent: Wednesday, September 04, 2013 2:28 PM
> To: Nick Vandewiele
> Subject: Re: [Cdk-user] use of protected class
> org.openscience.cdk.geometry.cip.LigancyFourChirality
>
> Didn't write the API so can't comment on why but I think you probably want
> the ITetrahedralChirality. Stereochemistry in the CDK is a bit of a mess
> (currently) but TetrahedralChirality is how stuff should be stored. Note
> InChI currently loads 'AtomParity' class which is basically exactly the same.
> SMILES will load ITetrahedralChirality though.
>
> IAtomContainer container = …
> ITetrahedralChirality tc = new TetrahedralChirality();
>
> CIPTool.getCIPChirality(container, tc);
>
> J
>
> On 4 Sep 2013, at 13:20, Nick Vandewiele <[email protected]> wrote:
>
>
> Hi,
>
> I’d like to use org.openscience.cdk.geometry.cip.LigancyFourChirality as in:
>
> LigancyFourChirality chirality = CIPTool.defineLigancyFourChirality(
> mol, 0, 1, 2, 3, 4, stereo);
>
> Why is that class protected? What should I use instead? The tests of
> org.openscience.cdk.geometry.cip all use that class too, so I don’t see why
> that class should be protected.
>
> Regards,
> Nick
>
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