3.1 Compute isoelectric point of all peptide sequences - PRIDE-Utilities/ms-data-core-api GitHub Wiki

import uk.ac.ebi.pride.utilities.mol.IsoelectricPointUtils;
....

MzIdentMLControllerImpl mzIdentMlController new MzIdentMLControllerImpl(inputFile, true);
Collection<Comparable> proteinIds = mzIdentMlController.getProteinIds();
   for(Comparable proteinID: proteinIds){
          Collection<Comparable> peptideIds = mzIdentMlController.getPeptideIds(proteinID);
          for(Comparable peptideId: peptideIds)
             System.out.println(IsoelectricPointUtils.calculate(mzIdentMlController.getPeptideSequence(proteinID,peptideId)));
   }