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kiyoko / eurocarb

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Importing CFG format glycan #51

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi, it a question about the "importing from sequence format" function in 
GLycoWorkbench. The 
software interface is great. I tried some hand drawn glycans and it worked 
perfectly. I then tried 
to use it on some CFG glycans by importing glycans named using CFG 
nomenclature, but it didn't 
work. I guess the problem I have is which importing format should be used for 
the CFG 
nomenclature? Or how could I convert it to a proper format for GlycoWorkbench? 
Thanks.

Best Regards,

Yong Li

School of Informatics and Computing
Indiana University Bloomington
Bloomington, IN, 47408

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Original issue reported on code.google.com by fuga...@gmail.com on 21 Oct 2009 at 3:39

GoogleCodeExporter commented 9 years ago 
Hi Yong,

We currently don't support importing of sequences from the CFG nomenclature in 
GlycoWorkBench.

Right now, the best advice for converting structures from the CFG format, is to 
do some programming:

You'll need to check out the trunk of the eurocarb source, and compile it. In 
the top level lib directory, you 
should find a MolecularFramework.jar (or something named similarly). Using all 
the jars in the lib directory as 
your classpath, compile and run this program:

http://code.google.com/p/eurocarb/source/browse/trunk/application/MolecularFrame
work/src/org/eurocar
bdb/MolecularFramework/examples/CarbbankToLinucs.java

If that works, you should be able to change the class that performs the 
importing from 
SugarImporterCarbbank to SugarImporterCFG, compile again, and use this as a 
stub to develop a more generic 
converter program. Unfortunately not the simplest way to do this, but we're a 
bit short of active developers at 
the moment.

Cheers,

Hiren

Original comment by hir...@gmail.com on 21 Oct 2009 at 10:11

GoogleCodeExporter commented 9 years ago 
Hi Yong,

I've just been told by one of the developers that I'm wrong, and that you 
should be using the "Import from 
Glycomindes" option for importing CFG nomenclature sequences.

I'm marking this as a bug so that the menu-label is changed to reflect that it 
can import CFG structures.

Thanks,

Hiren

Original comment by hir...@gmail.com on 9 Nov 2009 at 7:20