I have no idea what CDKMolDepict is, a Knime thing?
It's probably just not being updated. Testing the following on master/main
works as expected (DepictionGenerator computes the 2D as needed, no need to
clear the 3D):
public static void main(String[] args) {
String molfile = "\n" +
" MJ231200 \n" +
"\n" +
" 5 4 0 0 1 0 0 0 0 0999 V2000\n" +
" 0.9718 -0.1139 0.6193 O 0 0 0 0 0 0 0 0 0
0 0 0\n" +
" 0.9448 0.0189 -0.2285 S 0 0 0 0 0 0 0 0 0
0 0 0\n" +
" -0.0042 0.1584 -0.4371 C 0 0 0 0 0 0 0 0 0
0 0 0\n" +
" -0.2882 0.8589 -0.1053 C 0 0 0 0 0 0 0 0 0
0 0 0\n" +
" 1.1863 -0.8418 -0.6272 C 0 0 0 0 0 0 0 0 0
0 0 0\n" +
" 1 2 2 0 0 0 0\n" +
" 2 3 1 0 0 0 0\n" +
" 3 4 1 0 0 0 0\n" +
" 2 5 1 0 0 0 0\n" +
"M END\n";
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
try (MDLV2000Reader mdlr = new MDLV2000Reader(new
StringReader(molfile))) {
IAtomContainer mol = mdlr.read(bldr.newAtomContainer());
new DepictionGenerator().depict(mol).writeTo("/tmp/tmp.svg");
} catch (IOException e) {
throw new RuntimeException(e);
} catch (CDKException e) {
throw new RuntimeException(e);
}
}
On Tue, 19 Sept 2023 at 18:15, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> I'm using StructureDiagramGenerator.generateCoordinates() to create a
> layout before using CDKMolDepict to generate images for molecules, and I've
> hit a problem when using molecules that already have 3D coordinates as
> StructureDiagramGenerator.generateCoordinates() does not generate a new 2D
> layout if 3D coordinates are present, and passing in a molecule with 3D
> coordinates seems to make CDKMolDepict crash badly.
>
> So, what is the best way to clear the 3D coordinates for a molecule, so
> that StructureDiagramGenerator.generateCoordinates() can do its job?
> _______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
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>
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