/**
* 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;
*/
}
