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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