private static Atom calcSimple_H(Atom c, Atom o, Atom n) throws StructureException {
Atom h = Calc.substract(c, o);
double dist = Calc.getDistance(o, c);
// System.out.println(dist);
double x = n.getX() + h.getX() / dist;
double y = n.getY() + h.getY() / dist;
double z = n.getZ() + h.getZ() / dist;
h.setX(x);
h.setY(y);
h.setZ(z);
h.setName("H");
h.setFullName(" H ");
return h;
}
/**
* Use unit vectors NC and NCalpha Add them. Calc unit vector and substract it from N. C
* coordinates are from amino acid i-1 N, CA atoms from amino acid i
*
* <p>see also:
*
* @link
* {http://openbioinformatics.blogspot.com/2009/08/how-to-calculate-h-atoms-for-nitrogens.html}
*/
private static Atom calc_H(Atom C, Atom N, Atom CA) throws StructureException {
Atom nc = Calc.substract(N, C);
Atom nca = Calc.substract(N, CA);
Atom u_nc = Calc.unitVector(nc);
Atom u_nca = Calc.unitVector(nca);
Atom added = Calc.add(u_nc, u_nca);
Atom U = Calc.unitVector(added);
// according to Creighton distance N-H is 1.03 +/- 0.02A
Atom H = Calc.add(N, U);
H.setName("H");
H.setFullName(" H ");
// this atom does not have a pdbserial number ...
return 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(" ");
}
}
}
/**
* 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;
}