[Biojava-l] exception in DisplayAFP.createArtificialStructure

[Daniel Asarnow]

I create the AtomCache as follows:

AtomCache cache = new AtomCache(pdbPath, divided);
FileParsingParameters params = new FileParsingParameters();
params.setAlignSeqRes(false);
params.setParseSecStruc(false);
params.setLoadChemCompInfo(false);
params.setParseCAOnly(true);
cache.setFileParsingParams(params);

My algorithmName is simply from CeMain.algorithmName or
FatCatFlexible.algorithmName, and I use the default CeParameters or
FatCatParameters.

I get the StructureException I described, and then a NullPointerException
when trying to access the artificial structure (I also test specifically
that the artificial structure is null).

My apologies for not adding that (about the NPE) previously, I made a bare
bones version of my method to remove my application-specific code and
looking at the output made me realize I hadn't mentioned it.

-da

On Sun, Aug 14, 2011 at 22:09, Andreas Prlic <andreas at sdsc.edu> wrote:

> 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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> >
>