Example #1
0
 /**
  * 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;
 }
Example #2
0
  /**
   * 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;
  }
Example #3
0
  /**
   * 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();
  }