Exemple #1
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  private static EnzymeType makeEnzymeType() {

    EnzymeType enzymeType = new EnzymeType();
    enzymeType.setId("Enz1");
    enzymeType.setCTermGain("OH");
    enzymeType.setNTermGain("H");
    enzymeType.setMinDistance(1);
    return enzymeType;
  }
Exemple #2
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  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;
  }
Exemple #3
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  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;
  }
Exemple #4
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  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;
  }
Exemple #5
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  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;
  }
Exemple #6
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  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;
  }
Exemple #7
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  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;
  }