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 <[email protected]> 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 <[email protected]> > 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 - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
