[Biojava-l] exception in DisplayAFP.createArtificialStructure

[Andreas Prlic]

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
>> > _______________________________________________
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>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>
>