/*
*
* (non-Javadoc)
* @see java.lang.Object#toString()
*/
public String toString() {
StringBuffer buf = new StringBuffer();
String nl = System.getProperty("line.separator");
buf.append(
" # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA ");
buf.append(nl);
for (int i = 0; i < groups.length; i++) {
Group g = groups[i];
SecStrucState state = (SecStrucState) g.getProperty("secstruc");
// System.out.println("XX"+i+" "+g.getPDBCode() + " " + g.getPDBName() +
// iter.getCurrentChain().getName() + " " + state);
buf.append((i + 1) + "\t");
buf.append(g.getPDBName() + " ");
buf.append(g.getPDBCode() + "\t");
boolean[] turns = state.getTurn();
for (int t = 0; t < 3; t++) {
if (turns[t]) {
buf.append('>');
} else {
buf.append(' ');
}
}
// tmp filler
buf.append(" ");
int p1 = state.getAccept1().getPartner();
if (p1 != 0) p1 -= i;
double e1 = (state.getAccept1().getEnergy() / 1000.0);
buf.append(String.format("%6d,%4.1f\t", p1, e1));
int p2 = state.getDonor1().getPartner();
if (p2 != 0) p2 -= i;
double e2 = (state.getDonor1().getEnergy() / 1000.0);
buf.append(String.format("%6d,%4.1f\t", p2, e2));
int p3 = state.getAccept1().getPartner();
if (p3 != 0) p3 -= i;
double e3 = (state.getAccept2().getEnergy() / 1000.0);
buf.append(String.format("%6d,%4.1f\t", p3, e3));
int p4 = state.getDonor2().getPartner();
if (p4 != 0) p4 -= i;
double e4 = (state.getDonor2().getEnergy() / 1000.0);
buf.append(String.format("%6d,%4.1f\t", p4, e4));
buf.append(nl);
}
return buf.toString();
}
/** detect helical turn patterns */
private void calculateTurns() {
int l = groups.length;
for (int i = 0; i < l; i++) {
for (int turn = 3; turn <= 5; turn++) {
if (i + turn >= l) continue;
if (isBonded(i + turn, i)) {
// System.out.println("is bondend " + (i+turn) + i );
for (int j = i; j < i + turn + 1; j++) {
// System.out.println("turn at i:" + i + " j:" + j + " turn" + turn);
SecStrucGroup group = groups[j];
SecStrucState state = (SecStrucState) group.getProperty("secstruc");
boolean[] turns = state.getTurn();
turns[turn - 3] = true;
}
}
}
}
}
/**
* test if two groups are forming an H-Bond DSSP defines H-Bonds if the energy < -500 cal /mol
*
* @param one group one
* @param two group two
* @return flag if the two are forming an Hbond
*/
private boolean isBonded(int i, int j) {
Group one = groups[i];
// Group two = groups[j];
SecStrucState stateOne = (SecStrucState) one.getProperty("secstruc");
// SecStrucState stateTwo = (SecStrucState)two.getProperty("secstruc");
System.out.println("*** bonded? " + i + " " + j + " " + stateOne);
double acc1e = stateOne.getAccept1().getEnergy();
double acc2e = stateOne.getAccept2().getEnergy();
int partnerAcc1 = stateOne.getAccept1().getPartner();
int partnerAcc2 = stateOne.getAccept2().getPartner();
if (((partnerAcc1 == j) && (acc1e < HBONDHIGHENERGY))
|| ((partnerAcc2 == j) && (acc2e < HBONDHIGHENERGY))) {
System.out.println("*** yes is bonded " + i + " " + j);
return true;
}
return false;
}
/**
* store Hbonds inamino acids DSSP allows two HBonds / aminoacids to allow bifurcated bonds ...
*/
private void trackHBondEnergy(int i, int j, double energy) {
Group one = groups[i];
Group two = groups[j];
SecStrucState stateOne = (SecStrucState) one.getProperty("secstruc");
SecStrucState stateTwo = (SecStrucState) two.getProperty("secstruc");
double acc1e = stateOne.getAccept1().getEnergy();
double acc2e = stateOne.getAccept2().getEnergy();
double don1e = stateTwo.getDonor1().getEnergy();
double don2e = stateTwo.getDonor2().getEnergy();
// if ( energy < 0)
// System.out.println("--- tracking Hbond " + i + " " + j + " " + energy + " (accept: " +
// acc1e + " " + acc2e +") (donor: "+don1e + " " + don2e+")");
if (energy < acc1e) {
// System.out.println(energy +"<"+acc1e) ;
stateOne.setAccept2(stateOne.getAccept1());
HBond bond = new HBond();
bond.setEnergy(energy);
bond.setPartner(j);
stateOne.setAccept1(bond);
} else if (energy < acc2e) {
// System.out.println(energy +"<"+acc2e) ;
HBond bond = new HBond();
bond.setEnergy(energy);
bond.setPartner(j);
stateOne.setAccept2(bond);
}
// and now the other side of the bond ..
if (energy < don1e) {
stateTwo.setDonor2(stateTwo.getDonor1());
HBond bond = new HBond();
bond.setEnergy(energy);
bond.setPartner(i);
stateTwo.setDonor1(bond);
} else if (energy < don2e) {
// System.out.println(energy +"<"+don2e) ;
HBond bond = new HBond();
bond.setEnergy(energy);
bond.setPartner(i);
stateTwo.setDonor2(bond);
}
// System.out.println(stateOne);
// one.setProperty("secstruc", stateOne);
// two.setProperty("secstruc", stateTwo);
/*groups[i] = one;
groups[j] = two;
*/
}