/**
* main function for calling HubeRDP
*
* @param args no args needed
* @throws Exception
*/
public static void main(String[] args) {
// allocate memory
String pairsString = null, pdbpath = null;
// get command Line Arguments
CommandLineParser clp = new CommandLineParser(args);
pairsString = clp.getStringArg("--pairs");
pdbpath = clp.getStringArg("--pdb");
clp = null; // clp -> GC
// load joblist
PairFile pairfile = new PairFile(pairsString);
LinkedList<String[]> joblist = pairfile.getJoblist();
// set test data
PDBEntry templateStructure = null;
PDBEntry targetStructure = null;
// initialize PDBFileReader
PDBFileReader fr = new PDBFileReader();
// construct RDP
HubeRDP rdp = new HubeRDP();
// set scoring
Scoring scoring = new SimpleScoring();
rdp.setScoring(scoring);
// add oracles
rdp.addOracle(new RDPOracle(scoring));
LocalSequenceGotoh gotoh =
new LocalSequenceGotoh(-10.0, -2.0, bioinfo.alignment.matrices.QuasarMatrix.DAYHOFF_MATRIX);
// initialize TM stuff
TMMain tmmain = new TMMain();
// initialize output stuff
Locale.setDefault(Locale.US);
DecimalFormat df = new DecimalFormat("0.0000");
System.out.println("RDP-Scr\tRMSD\tGDT\tTM-Scr\tdepth\tGot-Scr\tRMSD\tGDT\tTM-Scr");
// INNER LOOP
for (String[] job : joblist) {
try {
// load data
templateStructure = fr.readPDBFromFile(pdbpath + job[0] + ".pdb");
targetStructure = fr.readPDBFromFile(pdbpath + job[1] + ".pdb");
// construct rdp tree
RDPProblem root = new RDPProblem(templateStructure, targetStructure.getSequence());
RDPSolutionTree t = new RDPSolutionTree(root);
// construct priority queue
RDPPriorityQueue pq = new RDPPriorityQueue(t.getRoot());
// execute rdp algorithm
rdp.rdp(t, pq);
// Solutions are now in t.getRoot();
// get HubeRDP's (first) alignment
SequenceAlignment rdpAlignment =
t.getRoot().getTA().get(0).getThreading().asSequenceAlignment();
SequenceAlignment gotohAlignment =
gotoh.align(templateStructure.getSequence(), targetStructure.getSequence());
Transformation rdptmtr =
tmmain.calculateTransformation(rdpAlignment, templateStructure, targetStructure);
Transformation gotohtmtr =
tmmain.calculateTransformation(gotohAlignment, templateStructure, targetStructure);
System.out.println(
job[0]
+ "\t"
+ job[1]
+ "\t"
+ df.format(rdpAlignment.getScore())
+ "\t"
+ df.format(rdptmtr.getRmsd())
+ "\t"
+ df.format(rdptmtr.getGdt())
+ "\t"
+ df.format(rdptmtr.getTmscore())
+ "\t"
+ (t.getDepth() / 2)
+ "\t"
+ df.format(gotohAlignment.getScore())
+ "\t"
+ df.format(gotohtmtr.getRmsd())
+ "\t"
+ df.format(gotohtmtr.getGdt())
+ "\t"
+ df.format(gotohtmtr.getTmscore()));
} catch (Exception e) {
System.err.println("Error occured: " + e.getLocalizedMessage());
e.printStackTrace();
}
}
}
