If you have that discussion here, I can update
https://egonw.github.io/cdkbook/migration.html accordingly.
Egon
On Sat, 23 Sept 2023 at 11:43, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> 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
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>>>
>>
>>
>> --
>> 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
>>
>
--
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
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