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 the coordinates for the H atoms. They are usually missing in the PDB files as only
* few experimental methods allow to resolve their location
*/
private void calculateHAtoms() throws StructureException {
for (int i = 0; i < groups.length - 1; i++) {
SecStrucGroup a = groups[i];
SecStrucGroup b = groups[i + 1];
if (!b.hasAtom("H")) {
// System.out.println(cur);
// calculate the coordinate for the H atom
// Atom H = calc_H(a.getC(), b.getN(), b.getCA());
// alternative:
Atom H = calcSimple_H(a.getC(), a.getO(), b.getN());
b.setH(H);
/*System.out.println("added H for " + i + " " + H);
for ( int aa = 0 ; aa < b.size() ; aa++){
Atom at = b.getAtom(aa);
System.out.println(aa + " " + at.getFullName() + " "+ Calc.getDistance(at,H));
}*/
}
}
}
/** calculate the HBonds between different groups ... see Creighton page 147 f */
private void calculateHBonds() throws StructureException {
System.out.println("groups length: " + groups.length);
// skip the first residue , unable to calc H for it ...
for (int i = 1; i < groups.length; i++) {
SecStrucGroup one = groups[i];
if (!one.hasAtom("H")) {
System.out.println(" no H at " + i);
continue;
}
for (int j = i + 1; j < groups.length; j++) {
SecStrucGroup two = groups[j];
// check if distance is too large.
// if too big - for sure no HBonds ...
double dist = Calc.getDistance(one.getCA(), two.getCA());
// speed up...
if (dist >= CA_MIN_DIST) continue;
// System.out.println("calc " + i + " " + j + " "+ dist);
checkAddHBond(i, j);
// "backwards" hbonds are not allowed
if (j != (i + 1)) {
checkAddHBond(j, i);
}
// System.out.println(" ");
}
}
}
