[Biojava-l] exception in DisplayAFP.createArtificialStructure

[Andreas Prlic]

Hi Daniel,

having problems to reproduce this... What is the algorithmName you are
using and any non standard parameters? Also, any parameters you are
setting on AtomCache?

Andreas


On Sun, Aug 14, 2011 at 12:08 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Hello again,
> I'm getting a null value from DisplayAFP.createArtificialStructure after a
> successful alignment.  It appears that the Groups in hetatms aren't set or
> are missing their Atom; There is a StructureException ("no atom found at
> position 0") thrown from the Group.getAtom call at DisplayAFP line 487
> (inside the getAtomArray call at line 679).
>
> Here is my code:
>
> Structure structure1 = cache.getStructure("2hhb.A"); // Hb A chain
> Structure structure2 = cache.getStructure("2v1k.A"); // Mb
> Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
> Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
> StructureAlignment alignment =
> StructureAlignmentFactory.getAlgorithm(algorithmName);
> AFPChain afpChain = alignment.align(ca1, ca2, params); // successful w/
> correct alignment score
> artificial = DisplayAFP.createArtificalStructure(afpChain, ca1, ca2); //
> returns null
>
> This is with the 3.0.2 snapshot JARs.
> I'm a missing something or is this a bug?
>
> Thanks!
>
> -da
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