Hi Björn,
The segfault with FP4 is known and was fixed back in Nov 2011. I just
checked with your specific molecule. I recommend that you use the
development version.
I can't see any error in the stereochemistry with 2.3.1.
- Noel
2012/3/9 Björn Grüning <bjoern.gruen...@pharmazie.uni-freiburg.de>
> Hi,
>
> in one of your tests we downloaded the chembl Compound CHEMBL7225 as
> SMILES converted it to canonical SMILES and tried to create
> FP4-fingerprints out of it. Unfortunately it crashed.
>
> Is that a known bug? Also the sterochemical information seems to be
> lost, or changed during conversion. Maybe that the gut behind the crash
> afterwards?
> All tests are done with openbabel-2.3.1.
>
> Here is a small code to reproduce.
>
> import pybel
>
> mol = pybel.readstring('smi',
> 'CN[C@H]1[C@H](O)CO[C@H](OC2[C@H](N)CC(N)[C@@H](O[C@H]3OC(CO)[C@@H](O)[C@H
> ](O)C3NO)[C@@H]2O)C1O')
>
> can = mol.write('can')
>
> mol.calcfp('FP4')
> mol2 = pybel.readstring('smi', can)
> mol2.calcfp('FP4')
> --> Allocation error
>
> Any advise? Should i fill a bug-report?
>
> Thanks and kind regards,
> Bjoern
>
>
> --
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
>
> Tel.: +49 761 203-4872
> Fax.: +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
>
>
>
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Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
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