java.lang.Object
com.compomics.util.experiment.identification.modification.scores.MDScore

public class MDScore
extends Object
This class estimates the MD score as described in https://www.ncbi.nlm.nih.gov/pubmed/21057138 Note: this implementation of the MD score is not restricted to phosphorylation.
Author:
Marc Vaudel
  • Constructor Details

    • MDScore

      public MDScore()
      Empty default constructor
  • Method Details

    • getMDScore

      public static Double getMDScore​(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions, Peptide peptideCandidate, ArrayList<String> ptms, SequenceMatchingParameters sequenceMatchingPreferences, Integer rounding)
      Returns the MD score for the given peptide in a spectrum match. Null if not identified by Mascot. If the peptide is the not the best scoring for Mascot the score will be negative.
      Parameters:
      mascotAssumptions - the assumptions by Mascot
      peptideCandidate - the peptide of interest
      ptms - the names of the PTMs to score
      sequenceMatchingPreferences - the sequence matching preferences
      rounding - decimal to which the score should be rounded, ignored if null
      Returns:
      the MD score