/**
* Sets both peptide object that are interconnected by this cross-linker.
*
* @param prePeptide - PolyPeptide object of the preAtom.
* @param postPeptide - PolyPeptide object of the postAtom.
* @return {@code TRUE} if both peptides contain both cross-linked atoms, {@code FALSE} otherwise.
*/
public final boolean setPeptides(final PolyPeptide prePeptide, final PolyPeptide postPeptide) {
for (AminoAcid aa : prePeptide) {
if (aa.getAllAtoms().contains(this.preAtom)) {
this.preAtomPeptide = prePeptide;
}
if (aa.getAllAtoms().contains(this.postAtom)) {
this.postAtomPeptide = prePeptide;
}
}
// here the order must be inverse, i.e. first check for post than for
// pre atom to allow for "self-cross-links". Self-cross-links are
// cross-links between two identical atom, which is physically
// incorrect but might be requested over a distance file.
for (AminoAcid aa : postPeptide) {
if (aa.getAllAtoms().contains(this.postAtom)) {
this.postAtomPeptide = postPeptide;
}
if (aa.getAllAtoms().contains(this.preAtom)) {
this.preAtomPeptide = postPeptide;
}
}
if (this.preAtomPeptide != null && this.postAtomPeptide != null) {
return true;
}
return false;
}
/**
* 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;
}
/**
* Returns a String representation of this cross-link in distance file format.
*
* @return String object holding the representation of this cross-link in distance file format.
*/
public final String toString() {
String atomId1 = AminoAcid.getAminoAcidId(preAtom) + "-" + preAtom.getName().trim();
String atomId2 = AminoAcid.getAminoAcidId(postAtom) + "-" + postAtom.getName().trim();
if (preAtom.getAlternativeLocation() != ' ') {
atomId1 += "-" + preAtom.getAlternativeLocation();
}
if (postAtom.getAlternativeLocation() != ' ') {
atomId2 += "-" + postAtom.getAlternativeLocation();
}
StringBuffer output = new StringBuffer();
int maxPeptideLength = xwalk.constants.Constants.MAX_PEPTIDE_LENGTH;
int minPeptideLength = xwalk.constants.Constants.MIN_PEPTIDE_LENGTH;
boolean outputPeptide = false;
if (preAtomPeptide != null && postAtomPeptide != null) {
outputPeptide =
preAtomPeptide.size() <= maxPeptideLength
&& preAtomPeptide.size() >= minPeptideLength
&& postAtomPeptide.size() <= maxPeptideLength
&& postAtomPeptide.size() >= minPeptideLength;
}
output.append(
this.filePath
+ "\t"
+ atomId1
+ "\t"
+ atomId2
+ "\t"
+ this.seqDist
+ "\t"
+ this.getEuclideanDistance()
+ "\t");
if (this.getSolventPathDistance() > -0.1 || this.getSolventPathDistance() < -0.9) {
output.append(this.getSolventPathDistance() + "\t");
} else {
output.append("-\t");
}
if (this.doProbability) {
output.append(this.getEuclideanDistanceProbability() + "\t");
if (this.getSolventPathDistance() > -0.1 || this.getSolventPathDistance() < -0.9) {
output.append(this.getSolventPathDistanceProbability() + "\t");
} else {
output.append("-\t");
}
} else {
output.append("-\t-\t");
}
if (outputPeptide) {
output.append(
this.preAtomPeptide.toStringOneLetterCode()
+ "-"
+ this.postAtomPeptide.toStringOneLetterCode());
} else {
output.append("-");
}
output.append(Constants.LINE_SEPERATOR);
return output.toString();
}