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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