exception in DisplayAFP.createArtificialStructure

Daniel Asarnow <[email protected]>
Newsgroups gmane.comp.java.bio.general
Message-ID <CANBcHWrdVZF66jVtp3pq4K32XtAA4riNMidauJf-BgZZtL7JNw@mail.gmail.com>
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
lmpx.com only provides a reader for public news (NNTP) servers. It is not affiliated with the servers or forums shown here and is not responsible for the content of articles, which is written by their respective authors.