Function testAASequenceTutorial

src/pyOpenMS/tests/unittests/test_tutorial.py:88–169

()

@report
def testAASequenceTutorial():

    seq = AASequence.fromString("DFPIANGER")
    prefix = seq.getPrefix(4)
    suffix = seq.getSuffix(5)
    concat = seq + seq

    print(seq)
    print(concat)
    print(suffix)
    seq.getMonoWeight() # weight of M
    seq.getMonoWeight(Residue.ResidueType.Full, 2) # weight of M+2H
    mz = seq.getMonoWeight(Residue.ResidueType.Full, 2) / 2.0 # m/z of M+2H
    concat.getMonoWeight()

    print("Monoisotopic m/z of (M+2H)2+ is", mz)

    seq_formula = seq.getFormula()
    print("Peptide", seq, "has molecular formula", seq_formula)
    print("="*35)

    isotopes = seq_formula.getIsotopeDistribution( CoarseIsotopePatternGenerator(6) )
    for iso in isotopes.getContainer():
            print ("Isotope", iso.getMZ(), ":", iso.getIntensity())

    suffix = seq.getSuffix(3) # y3 ion "GER"
    print("="*35)
    print("y3 ion :", suffix)
    y3_formula = suffix.getFormula(Residue.ResidueType.YIon, 2) # y3++ ion
    suffix.getMonoWeight(Residue.ResidueType.YIon, 2) / 2.0 # CORRECT
    suffix.getMonoWeight(Residue.ResidueType.XIon, 2) / 2.0 # CORRECT
    suffix.getMonoWeight(Residue.ResidueType.BIon, 2) / 2.0 # INCORRECT
    assert str(y3_formula) == "C13H24N6O6", str(y3_formula)
    assert str(seq_formula) == "C44H67N13O15"


    print("y3 mz :", suffix.getMonoWeight(Residue.ResidueType.YIon, 2) / 2.0 )
    print(y3_formula)
    print(seq_formula)

    seq = AASequence.fromString("PEPTIDESEKUEM(Oxidation)CER")
    print(seq)
    print(seq.toString())
    print(seq.toUnmodifiedString())
    print(seq.toUniModString())
    print(seq.toBracketString())
    print(seq.toBracketString(False))

    print(AASequence.fromString("DFPIAM(UniMod:35)GER"))
    print(AASequence.fromString("DFPIAM[+16]GER"))
    print(AASequence.fromString("DFPIAM[+15.99]GER"))
    print(AASequence.fromString("DFPIAM[147]GER"))
    print(AASequence.fromString("DFPIAM[147.035405]GER"))

    s = AASequence.fromString(".(Dimethyl)DFPIAMGER.")
    print(s, s.hasNTerminalModification())
    s = AASequence.fromString(".DFPIAMGER.(Label:18O(2))")
    print(s, s.hasCTerminalModification())