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 < [email protected]> 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 <[email protected]> > 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 < >> [email protected]> 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 < >>> [email protected]> 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 <[email protected]> >>>> 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 >>>>> [email protected] >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>> >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> [email protected] >>>> 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 >
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