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));
}*/
}
}
}
/** 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;
}
}
}
}
}
/** 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;
}
private static SecStrucGroup[] initGroupArray(Structure s) {
List<SecStrucGroup> groupList = new ArrayList<SecStrucGroup>();
// GroupIterator iter = new GroupIterator(s);
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
// System.out.println(g);
// we can also calc secstruc if hetatom is a modified amino acid.
if (g.hasAminoAtoms()) {
SecStrucGroup sg = new SecStrucGroup();
sg.setPDBCode(g.getPDBCode());
sg.setPDBFlag(true);
try {
sg.setPDBName(g.getPDBName());
} catch (PDBParseException e) {
e.printStackTrace();
}
sg.setParent(g.getChain());
try {
sg.setN((Atom) g.getAtomByPDBname(" N ").clone());
sg.setCA((Atom) g.getAtomByPDBname(" CA ").clone());
sg.setC((Atom) g.getAtomByPDBname(" C ").clone());
sg.setO((Atom) g.getAtomByPDBname(" O ").clone());
sg.setOriginal(g);
// create H in calc_H
} catch (StructureException e) {
e.printStackTrace();
// one of these atoms is not found!
continue;
}
SecStrucState state = new SecStrucState();
Map m = sg.getProperties();
if (m == null) {
m = new HashMap();
sg.setProperties(m);
}
m.put("secstruc", state);
groupList.add(sg);
} else {
// System.out.println("not an amino group");
}
}
}
return (SecStrucGroup[]) groupList.toArray(new SecStrucGroup[groupList.size()]);
}
