Hi Tim,
It looks like you're using 5 year old CDK 2.2, is that correct?
build.gradle:
> project.ext.set('cdkVersion', '2.2')
It's likely just updating will fix the issue. It should be relatively
seamless but let me know if there are any issues and I'll tell you how to
fix it.
On Sat, 23 Sept 2023 at 06:38, Egon Willighagen <egon.willigha...@gmail.com>
wrote:
>
> Tim,
>
> I guess you are referring to
> https://github.com/InformaticsMatters/squonk/blob/master/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMolDepict.java
>
> I also looked at the molfile reading in CDKMoleculeIOUtils and it looks
> correct to me, but the hydrogen adding may be a conflicting issue here.
> What is the actual exception (stacktrace) you get?
>
> Like John set, removing the 3D coordinates should not be needed (the CDK
> is designed to allow having both of them in parallel), but if you have to,
> run .setPoint3d(null) on each atom. That should do the trick.
>
> Egon
>
>
>
>
>
> On Wed, 20 Sept 2023 at 12:05, John Mayfield <john.wilkinson...@gmail.com>
> wrote:
>
>> 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
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>> _______________________________________________
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>
>
> --
> Inherited disorders can be hard to interpret when multiple biomarkers are
> involved. A network approach can help bring insight:
> https://doi.org/10.1186/s13023-023-02683-9
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Blog: https://chem-bla-ics.blogspot.com/
> Mastodon: https://scholar.social/@egonw
> PubList: https://orcid.org/0000-0001-7542-0286
>
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
