I'm using 1.4 because I'm using SmartCYP that was from that generation. >From memory there was a reason why I had to stick with 1.4, but I can't recall the details. The error I'm seeing with the attached molecule is this:
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1 at org.openscience.cdk.graph.invariant.EquivalentClassPartitioner.checkDiffNumber(EquivalentClassPartitioner.java:398) at org.openscience.cdk.graph.invariant.EquivalentClassPartitioner.findTopoEquivClass(EquivalentClassPartitioner.java:470) at org.openscience.cdk.graph.invariant.EquivalentClassPartitioner.getTopoEquivClassbyHuXu(EquivalentClassPartitioner.java:98) at smartcyp.MoleculeKU.setSymmetryNumbers(MoleculeKU.java:643) at smartcyp.MoleculeKU.sortAtoms(MoleculeKU.java:564) at squonk.jobs.smartcyp.Predictor.calculateMol(Predictor.java:303) at squonk.jobs.smartcyp.Predictor.lambda$run$0(Predictor.java:226) at java.base/java.util.stream.ReferencePipeline$11$1.accept(ReferencePipeline.java:441) at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133) at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474) at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913) at java.base/java.util.stream.ReduceOps$5.evaluateSequential(ReduceOps.java:257) at java.base/java.util.stream.ReduceOps$5.evaluateSequential(ReduceOps.java:248) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.count(ReferencePipeline.java:605) at squonk.jobs.smartcyp.Predictor.run(Predictor.java:244) at squonk.jobs.smartcyp.PredictorTest.test ibuprofen v3000(PredictorTest.groovy:55) Using the same molecule in V2000 format works OK. 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_V3000.sdf
Description: Binary data
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