The old StructurePairAligner is unpublished and is probably slower than the CE and FATCAT implementations. Try e.g. CE:
http://biojava.org/wiki/BioJava:CookBook:PDB:CE_Algorithm Andreas On Wed, Jan 19, 2011 at 2:49 PM, Jay Vyas <[email protected]> wrote: > Hi guys : > > The following code snippet, for two 150 amino acid proteins, is taking a > somewhat long time, that is, well over 4 minutes, .... > > long t=(System.currentTimeMillis()); > StructurePairAligner aligner = new StructurePairAligner(); > aligner.align(s1, s2); > aligner.setDebug(false); > System.out.println("time = " + (System.currentTimeMillis()-t)/1000+" > sec"); > > Strangely, Im running biojava on a 2x28 GHz Quad Core Intel Xeon chip, Mac > OS 10.5.8, with aggressiveheap enabled, and 6 Gigs of RAM. > This suprises me since the tests on the biojava wiki page for structural > alignments seem to be quite efficient. > > -- > Jay Vyas > MMSB/UCHC > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
