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 >
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