Can you point us (well, John particularly) to the SMSD code you are using? I think if he can find the time, he can make some suggestions on how to replace it with more modern code.
Egon On Sat, 23 Sept 2023 at 12:55, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > Sorry for the late reply. I've been distracted. > Sorry, I meant DepictionGenerator. CDKMolDepict is my class that's > running this! Egon found it correctly. > > Regarding the version, yes, this is old code, and I can't remember all the > details. > I'm not able to update to the latest as I have a dependency on the > deprecated org.openscience.cdk:cdk-smsd module. > I did have a discussion some time ago with Egon about removing the > dependency on the deprecated code, but we never got that resolved. > So this means that I can only update to version 2.5. which I've now done. > > I still find problems with that version. For some reason that I can't > recall I'm using: > > StructureDiagramGenerator g = new StructureDiagramGenerator(); > g.generateCoordinates(mol); > > to do the layout prior to calling DepictionGenerator().depict(mol) > > This is causing me problems when handling 2D or 3D molfiles. > I find I can work around it by doing IAtomContainer -> SMILES -> > IAtomContainer, which works for now. > I'll need to look more deeply at the code to work out better options. > There's a lot going on like MCS alignment and highlighting. > > Thanks for your help. > > > On Sat, Sep 23, 2023 at 10:45 AM Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> 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 >>>>> 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 >>>> >>> >> >> -- >> 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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