Example #1
0
  public void addModification(int zero_based_index, double modMass)
      throws UnimodRepositoryException {

    ModificationType modType = new ModificationType();
    modType.setLocation(zero_based_index + 1);

    List<String> residues = modType.getResidues();
    residues.add(String.valueOf(sequence.charAt(zero_based_index)));

    modType.setMonoisotopicMassDelta(modMass);

    // get the Unimod entry for this modification
    ModT unimod_mod =
        unimodRepository.getModification(
            sequence.charAt(zero_based_index),
            modMass,
            UnimodRepository.DELTA_MASS_TOLERANCE_1,
            true);

    if (unimod_mod != null) {

      CvParamMaker paramMaker = CvParamMaker.getInstance();
      CVParamType param =
          paramMaker.make(
              "UNIMOD:" + unimod_mod.getRecordId(), unimod_mod.getTitle(), CvConstants.UNIMOD_CV);

      modType.getCvParam().add(param);
    }

    modifications.add(modType);
  }
Example #2
0
  public static EnzymeType makeNoEnzyme() {

    EnzymeType enzymeType = new EnzymeType();
    enzymeType.setId("Enz1");
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001091", "NoEnzyme", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }
Example #3
0
  public static EnzymeType makeLysC_OR_TrypsinK() {

    /*
    	[Term]
    id: MS:1001310
    name: Lys-C/P
    is_a: MS:1001045 ! cleavage agent name
    relationship: has_regexp MS:1001336 ! (?<=K)

    */
    EnzymeType enzymeType = makeEnzymeType();
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001310", "Lys-C/P", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }
Example #4
0
  public static EnzymeType makeModifiedChymotrypsin() {

    /*
    	[Term]
    id: MS:1001306
    name: Chymotrypsin
    is_a: MS:1001045 ! cleavage agent name
    relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P)

    */
    EnzymeType enzymeType = makeEnzymeType();
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001306", "Chymotrypsin", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }
Example #5
0
  public static EnzymeType makeArgC_OR_TrypsinR() {

    // 9.  Trypsin_R              1      R           P
    /*
    	[Term]
    id: MS:1001303
    name: Arg-C
    is_a: MS:1001045 ! cleavage agent name
    relationship: has_regexp MS:1001272 ! (?<=R)(?!P)

    */
    EnzymeType enzymeType = makeEnzymeType();
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001303", "Arg-C", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }
Example #6
0
  public static EnzymeType makeCyanogenBromide() {

    // 4.  Cyanogen_Bromide       1      M           -
    /*
    	[Term]
    id: MS:1001307
    name: CNBr
    is_a: MS:1001045 ! cleavage agent name
    relationship: has_regexp MS:1001333 ! (?<=M)

    */
    EnzymeType enzymeType = makeEnzymeType();
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001307", "CNBr", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }
Example #7
0
  public static EnzymeType makeTrypsin() {

    // 1.  Trypsin                1      KR          P

    /*
    	[Term]
    id: MS:1001251
    name: Trypsin
    is_a: MS:1001045 ! cleavage agent name
    relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P)
    */
    EnzymeType enzymeType = makeEnzymeType();
    ParamListType nameParam = new ParamListType();
    nameParam
        .getParamGroup()
        .add(CvParamMaker.getInstance().make("MS:1001251", "Trypsin", CvConstants.PSI_CV));
    enzymeType.setEnzymeName(nameParam);
    return enzymeType;
  }