Here is the V2000 file. On Thu, Jan 11, 2024 at 10:13 AM John Mayfield <john.wilkinson...@gmail.com> wrote:
> 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 >>>> >>>
Ibuprofen_V2000.sdf
Description: Binary data
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