/** Sets the probability of observing this cross-link with its SAS distance. */
public final void setSASDprobability() {
float preProb = -1;
TreeSet<Float> sortedBins =
new TreeSet<Float>(ParameterReader.getSASdistanceProbabilitySet().keySet());
for (float bin : sortedBins) {
float prob = ParameterReader.getSASdistanceProbabilitySet().get(bin);
if (bin > this.solventPathDistance) {
this.sasdDistProbability = preProb;
break;
}
preProb = prob;
}
if (this.sasdDistProbability == -1 && this.solventPathDistance != -1) {
this.sasdDistProbability = 0;
}
this.doProbability = true;
}
/** Sets the probability of observing this cross-link with its Euclidean distance. */
public final void setEucProbability() {
float preProb = -1;
TreeSet<Float> sortedBins =
new TreeSet<Float>(ParameterReader.getEuclideanDistanceProbabilitySet().keySet());
for (float bin : sortedBins) {
float prob = ParameterReader.getEuclideanDistanceProbabilitySet().get(bin);
if (bin > this.eucDist) {
this.eucDistProbability = preProb;
break;
}
preProb = prob;
}
if (this.eucDistProbability == -1 && this.eucDist != -1) {
this.eucDistProbability = 0;
}
this.doProbability = true;
}
/**
* Constructor. Reads in the XlogP parameter file and assigns the values to the protein atoms.
*
* @param complex Protein complex object holding all amino acids to which atomic XlogP values will
* be calculated.
*/
public Hydrophobicity(final PolyPeptideList complex) {
// if (ParameterReader.getXlogPparameterSet() == null) {
try {
ParameterReader.setParameterReader(Constants.ParameterSets.XLOGP);
} catch (IOException e) {
System.err.print(
e.getMessage()
+ Constants.LINE_SEPERATOR
+ "ERROR: While reading the XlogP parameter file"
+ Constants.LINE_SEPERATOR);
}
// }
this.polyPeptideComplex = complex;
this.setAtomicXlogP();
}
/**
* 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;
}