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.
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