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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