private void checkAddHBond(int i, int j) {
SecStrucGroup one = groups[i];
SecStrucGroup two = groups[j];
if (!two.hasAtom("H")) {
System.err.println("two has no H " + j);
return;
}
if (one.getPDBName().equals("PRO")) {
if (debug) System.out.println(" ignore: PRO " + one.getPDBCode());
return;
}
double energy = 0;
try {
energy = calculateHBondEnergy(one, two);
} catch (Exception e) {
e.printStackTrace();
return;
}
// System.out.println(" " + energy);
trackHBondEnergy(i, j, energy);
}
/**
* calculate HBond energy of two groups in cal/mol ... see Creighton page 147 f
*
* <p>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.
* categorizes hbonds with donor-acceptor distances of 2.2-2.5 å as "strong, mostly
* covalent", 2.5-3.2 å as "moderate, mostly electrostatic", 3.2-4.0 å as "weak,
* electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively.
*/
public double calculateHBondEnergy(SecStrucGroup one, SecStrucGroup two)
throws StructureException {
// System.out.println("calcHBondEnergy" + one + "|" + two);
Atom N = one.getN();
Atom H = one.getH();
Atom O = two.getO();
Atom C = two.getC();
double dno = Calc.getDistance(O, N);
double dhc = Calc.getDistance(C, H);
double dho = Calc.getDistance(O, H);
double dnc = Calc.getDistance(C, N);
if (debug) {
System.out.println(
" cccc: "
+ one.getPDBCode()
+ " "
+ one.getPDBName()
+ " "
+ two.getPDBCode()
+ " "
+ two.getPDBName()
+ String.format(
" O ("
+ O.getPDBserial()
+ ")..N ("
+ N.getPDBserial()
+ "):%4.1f | ho:%4.1f - hc:%4.1f + nc:%4.1f - no:%4.1f ",
dno,
dho,
dhc,
dnc,
dno));
}
// System.out.println( cn > ch && oh < 3.0f);
double contact = MINDIST;
// there seems to be a contact!
if ((dno < contact) || (dhc < contact) || (dnc < contact) || (dno < contact)) {
// System.out.println("!!! contact " + one + " " + two);
return HBONDLOWENERGY;
}
double e1 = Q / dho - Q / dhc;
double e2 = Q / dnc - Q / dno;
double energy = e1 + e2;
if (debug)
System.out.println(
String.format(
" N (%d) O(%d): %4.1f : %4.2f ",
N.getPDBserial(), O.getPDBserial(), (float) dno, energy));
// bond too weak
if (energy > HBONDHIGHENERGY) return 0;
// test to avoid bond too strong
if (energy > HBONDLOWENERGY) return energy;
return HBONDLOWENERGY;
}
