/**
* Sets to all amino acids atoms in a protein their associated XlogP values.
*
* @return float value representing the sum of XlogP values for the protein complex.
*/
private float setAtomicXlogP() {
Hashtable<AminoAcidType, Hashtable<AtomType, Float>> xlogPs =
ParameterReader.getXlogPparameterSet();
float sum = 0;
for (PolyPeptide polyPeptide : this.polyPeptideComplex) {
for (AminoAcid aa : polyPeptide) {
for (Atom atom : aa.getAllAtoms()) {
if (!atom.getElement().getSymbol().equals("H")) {
Hashtable<AtomType, Float> atomicXlogPs = xlogPs.get(aa.getType());
float xlogP = atomicXlogPs.get(atom.getType());
atom.setXlogP(xlogP);
sum += xlogP;
} else {
// hydrogen atoms have always a XlogP value of 0.
atom.setXlogP(0);
}
}
}
}
return sum;
}