According to the CTFile spec there should be two spaces before the first 0. https://www.daylight.com/meetings/mug05/Kappler/ctfile.pdf So it's strange that the latest version has that behaviour.
BTW the 1.4 versions are available from Maven from https://nexus.ideaconsult.net/content/repositories/thirdparty I tried using 1.4 but that failed as SmartCyp uses classes such as org.openscience.cdk.interfaces.IMolecule that disappeared in 1.5. On Fri, Jan 12, 2024 at 9:11 PM Velusamy Velu <vv...@peruselab.com> wrote: > I tried to use cdk version 1.42 | 1.4.19 etc but no luck downloading them. > So, I used version 2.9 (the latest I guess). Yet, there was an error. > > After that I inspected your SDF and found it to have an extra space in the > 4th line. > Originally: > > 123456789012345678901234567890123456789012345678901234567890 > 0 0 0 0 0 0 V3000 > > After correction: > > 123456789012345678901234567890123456789012345678901234567890 > 0 0 0 0 0 0 V3000 > > After removing that extra space it worked fine with CDK 2.9. I have > attached the image created from the parsed molecule. > > Sorry, this may not be the answer you need but probably can help you yet. > > Thanks > > Velusamy K. Velu > (614) 323-9649 > <https://peruselab.com> <https://www.linkedin.com/company/peruselab/> > <https://twitter.com/PeruseLab> <https://www.facebook.com/PeruseLab/> > > > On Thu, Jan 11, 2024 at 11:14 AM Youyi Peng via Cdk-user < > cdk-user@lists.sourceforge.net> wrote: > >> Hi, >> >> Could you please remove my name from the email list? >> >> Thank you, >> >> >> >> Youyi >> >> >> >> *From: *John Mayfield <john.wilkinson...@gmail.com> >> *Date: *Thursday, January 11, 2024 at 5:14 AM >> *To: *Tim Dudgeon <tdudgeon...@gmail.com> >> *Cc: *CDK users list <cdk-user@lists.sourceforge.net> >> *Subject: *Re: [Cdk-user] Reading V3000 SDF >> >> 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 >> >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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