So I think it's here: https://github.com/cdk/cdk/blob/cdk-1.4.19/src/main/org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java#L398
Which is deep in the algorithm rather than in the reader. Can you also send the V2000 that you say works and I'll see if there is anything obvious you can do to make the V3000 work. Testing the current version I don't see the error, the only significant change was in 2013: https://github.com/cdk/cdk/commit/0aa0b794f48cdc057db133eabbcd865775a0730b On Thu, 11 Jan 2024 at 09:53, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > skip=true doesn't help. > > On Thu, Jan 11, 2024 at 8:56 AM John Mayfield <john.wilkinson...@gmail.com> > wrote: > >> Hi Tim, >> >> Why are you forced to use 1.4? I remember I made lots of improvements to >> the SDF reading over a decade ago (1.4 is now 10.5 years old) but these >> would have been in 1.5 onwards. It doesn't look like you're doing anything >> wrong but you could try adding skip=true to your constructor. This means if >> it sees something it doesn't like it continues rather than stops iterating. >> >> Best, >> John >> >> On Wed, 10 Jan 2024 at 16:31, Tim Dudgeon <tdudgeon...@gmail.com> wrote: >> >>> I'm having difficulty reading V3000 SDF files. >>> The IteratingMDLReader docs ( >>> https://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/io/iterator/IteratingMDLReader.html) >>> seem to suggest that it will read V3000, but maybe it has to be >>> specifically told to use V3000 format (which would be a pain to work out)? >>> >>> I'm using it like this: >>> >>> File sdfFile = new File(file); >>> IteratingMDLReader reader = new IteratingMDLReader( >>> new FileInputStream(sdfFile), >>> DefaultChemObjectBuilder.getInstance() >>> ); >>> >>> BTW, I'm forced into using an old 1.4 version for reasons out of my >>> control. >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk-user@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>
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