private static boolean isTrypsin(MsEnzymeIn enzyme) {
// 1. Trypsin 1 KR P
return (("RK".equals(enzyme.getCut()) || "KR".equals(enzyme.getCut()))
&& "P".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}
private static boolean isCynanogenBromide(MsEnzymeIn enzyme) {
// 4. Cyanogen_Bromide 1 M -
return ("M".equals(enzyme.getCut())
&& "-".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}
/** Only some enzymes are supported. */
public static EnzymeType makeEnzymeType(MsEnzymeIn enzyme) {
// !----------------------------------------------------------
// TODO This method should be tested and other enzymes should be supported.
// !----------------------------------------------------------
if (enzyme == null || enzyme.getName().equalsIgnoreCase("No_Enzyme")) {
return makeNoEnzyme();
}
// found entries for these in the controlled vocabulary:
if (isTrypsin(enzyme)) {
return makeTrypsin();
} else if (isCynanogenBromide(enzyme)) {
return makeCyanogenBromide();
} else if (isLysCNoCutP(enzyme)) {
return makeLysC_OR_TrypsinK_nocutP();
} else if (isLysC(enzyme)) {
return makeLysC_OR_TrypsinK();
} else if (isArgC(enzyme)) {
return makeArgC_OR_TrypsinR();
} else if (isModifiedChymotrypsin(enzyme)) {
return makeModifiedChymotrypsin();
}
// could not find and entry for these:
else if (enzyme.getName().equalsIgnoreCase("Chymotrypsin")) {
return null; // NOTE: can't find a term for this in PSI-MS vocabulary
// There is an entry for Chymotrypsin but the given regex does not match
// the "cut" residues in sequest.params
}
return null;
}
private static boolean isArgC(MsEnzymeIn enzyme) {
// 9. Trypsin_R 1 R P
return ("R".equals(enzyme.getCut())
&& "P".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}
private static boolean isLysCNoCutP(MsEnzymeIn enzyme) {
// 8. Trypsin_K 1 K P
return ("K".equals(enzyme.getCut())
&& "P".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}
private static boolean isModifiedChymotrypsin(MsEnzymeIn enzyme) {
// 11. Cymotryp/Modified 1 FWYL P
return (enzyme.getCut() != null
&& enzyme.getCut().length() == 4
&& enzyme.getCut().contains("F")
&& enzyme.getCut().contains("W")
&& enzyme.getCut().contains("Y")
&& enzyme.getCut().contains("L")
&& "P".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}
private static boolean isLysC(MsEnzymeIn enzyme) {
return ("K".equals(enzyme.getCut())
&& "-".equals(enzyme.getNocut())
&& enzyme.getSense() == Sense.CTERM);
}