[Biojava-l] exception in DisplayAFP.createArtificialStructure

[Daniel Asarnow]

Sorry for the delay in replying, but I can confirm your fix is working.

Thanks again for all your help.

-da

On Mon, Aug 15, 2011 at 07:15, Andreas Prlic <andreas at sdsc.edu> wrote:

> Ok, got it. This happened, since you are using a Calpha-only
> representation of the molecule. If you update the DisplayAFPChain
> class, this should be fixed now. Since you are not using all atoms for
> the alignment, ligands won't get superimposed This is something that
> some users find useful...
>
> Andreas
>
>
> On Mon, Aug 15, 2011 at 1:02 AM, Daniel Asarnow <dasarnow at gmail.com>
> wrote:
> > 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
> >> > _______________________________________________
> >> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >
> >
> >
>