/**
* voronoi data container for multiple sequence scoring on model will be initialized
*
* @param model
* @return voronoi data reuced and decomposited by given pdbmodel grid will be used and generated
*/
@Override
public void prepareSequenceScoring(Object model) {
PDBEntry entry = (PDBEntry) model;
data = new VoronoiData(entry.getId());
data.reducePDB(entry);
data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
voro.decomposite(data);
data.detectOuterGrid(minContact);
}
/**
* @param pdb
* @param type
* @return voronoi data reuced and decomposited by given pdbmodel no grid will be used
*/
public VoronoiData prepareSimple(PDBEntry pdb, VoroPrepType type) {
VoronoiData data;
data = new VoronoiData(pdb.getId());
data.reducePDB(type, pdb);
voro.decomposite(data);
return data;
}
/**
* for whenever we need to only make sequence fragments
*
* @param pdb the entry to disassemble
* @param l a list of protein fragments
* @param fLength the desired length of protein fragments
* @return the new list of fragments
*/
public static LinkedList<char[]> disassemble(
PDBEntry pdb, LinkedList<char[]> l, int fragmentLength) {
char[] pdbChar = new char[pdb.length()];
for (int i = 0; i < pdb.length(); i++) {
pdbChar[i] = pdb.getAminoAcid(i).getName().getOneLetterCode().charAt(0);
}
for (int i = 0; i < pdb.length() - fragmentLength; i++) {
char[] temp = new char[fragmentLength];
for (int j = 0; j < fragmentLength; j++) {
temp[j] = pdbChar[i + j];
}
l.add(temp);
}
return l;
}
/**
* normal preparation of data in solvent
*
* @param pdb
* @param gridExtend
* @param gridDensity
* @param gridClash
* @param minContact
* @return voronoi data reuced and decomposited by given pdbmodel grid will be used and generated
*/
public VoronoiData prepareWithGrid(
PDBEntry pdb, double gridExtend, double gridDensity, double gridClash, double minContact) {
VoronoiData data;
data = new VoronoiData(pdb.getId());
data.reducePDB(pdb);
data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
voro.decomposite(data);
data.detectOuterGrid(minContact);
return data;
}
/**
* goes through a PDB Entry and reads protein fragments using the CA atoms
*
* @param pdb the entry to crunch
* @param l a list of protein fragments
* @param fLength the desired length of protein fragments
* @return the new list of fragments
*/
public static LinkedList<ProteinFragment> crunchBackboneN(
PDBEntry pdb, String secStruct, LinkedList<ProteinFragment> l, int fLength) {
try {
String curSecStruct = "";
for (int i = 0; i < pdb.length() - fLength; i++) {
Atom[] temp = new Atom[fLength];
for (int j = i; j < i + fLength; j++) {
temp[j - i] = pdb.getAminoAcid(j).getAtomByType(AtomType.CA);
}
curSecStruct = secStruct.substring(i, i + fLength);
ProteinFragment tempFrag =
new ProteinFragment(pdb.getId() + "_" + i, curSecStruct, temp, fLength);
l.add(tempFrag);
}
return l;
} catch (Exception e) {
System.out.println("Entry " + pdb.getId() + " probably has incomplete records.");
}
return null;
}
/**
* alternative version that returns the sequence along with the other stuff.
*
* @param pdb the entry to crunch
* @param l a list of protein fragments
* @param fLength the desired length of protein fragments
* @return the new list of fragments
*/
public static List<ProteinFragment> crunchBackboneSeq(
PDBEntry pdb, List<ProteinFragment> l, int fLength) {
try {
AminoAcid tempAA = new AminoAcid("ALA", 0);
StringBuilder seq = new StringBuilder();
for (int i = 0; i < pdb.length() - fLength; i++) {
Atom[] temp = new Atom[fLength];
seq.delete(0, fLength);
for (int j = i; j < i + fLength; j++) {
tempAA = pdb.getAminoAcid(j);
seq.append(tempAA.getName().getOneLetterCode());
temp[j - i] = tempAA.getAtomByType(AtomType.CA).clone();
}
ProteinFragment tempFrag =
new ProteinFragment(pdb.getId() + "_" + i, seq.toString(), temp, fLength);
l.add(tempFrag);
}
return l;
} catch (Exception e) {
System.out.println("Entry " + pdb.getId() + " probably has incomplete records.");
e.printStackTrace();
}
return null;
}
/**
* 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();
}
}
}