def test_spectrum(self):
intensity = [
100,
100,
100,
100,
100,
100
]
mz = [
#// four of the naked b/y ions
#// as well as one of the modified b and y ions ion each
350.17164, #// b
421.20875, #// b
421.20875 + 79.9657, #// b + P
547.26291, #// y
646.33133, #// y
809.39466 + 79.9657 #// y + P
]
spectrum = pyopenms.OSSpectrum()
spectrum.setMZArray(mz)
spectrum.setIntensityArray(intensity)
diascoring = pyopenms.DIAScoring()
# diascoring.set_dia_parameters(0.05, False, 30, 50, 4, 4) // here we use a large enough window so that none of our peaks falls out
p_dia = diascoring.getDefaults();
p_dia.setValue("dia_extraction_window", 0.05);
p_dia.setValue("dia_extraction_unit", "Th");
p_dia.setValue("dia_centroided", "false");
p_dia.setValue("dia_byseries_intensity_min", 30.0);
p_dia.setValue("dia_byseries_ppm_diff", 50.0);
p_dia.setValue("dia_nr_isotopes", 4);
p_dia.setValue("dia_nr_charges", 4);
diascoring.setParameters(p_dia);
a = pyopenms.AASequence.fromString(b"SYVAWDR")
bseries_score = 0.0
yseries_score = 0.0
charge = 1
bseries_score, yseries_score = diascoring.dia_by_ion_score(spectrum, a, charge, bseries_score, yseries_score)
self.assertAlmostEqual(bseries_score, 2.0)
self.assertAlmostEqual(yseries_score, 2.0)
# // now add a modification to the sequence
a.setModification(1, b"Phospho" ) #; // modify the Y
bseries_score = 0
yseries_score = 0
bseries_score, yseries_score = diascoring.dia_by_ion_score(spectrum, a, 1, bseries_score, yseries_score)
self.assertAlmostEqual (bseries_score, 1.0)
self.assertAlmostEqual (yseries_score, 3.0)
def test_spectrum(self):
intensity = [100, 100, 100, 100, 100, 100, 100]
mz = [
#// four of the naked b/y ions
#// as well as one of the modified b and y ions ion each
350.17164, #// b
421.20875, #// b
421.20875 + 79.9657, #// b + P
547.26291, #// y
646.33133, #// y
809.39466 + 79.9657 #// y + P
]
spectrum = pyopenms.OSSpectrum()
spectrum.setMZArray(mz)
spectrum.setIntensityArray(intensity)
diascoring = pyopenms.DIAScoring()
diascoring.set_dia_parameters(
0.05, False, 30, 50, 4, 4
) #; // here we use a large enough window so that none of our peaks falls out
a = pyopenms.AASequence.fromString(b"SYVAWDR", True)
bseries_score = 0.0
yseries_score = 0.0
charge = 1
bseries_score, yseries_score = diascoring.dia_by_ion_score(
spectrum, a, charge, bseries_score, yseries_score)
self.assertAlmostEqual(bseries_score, 2.0)
self.assertAlmostEqual(yseries_score, 2.0)
# // now add a modification to the sequence
a.setModification(1, b"Phospho") #; // modify the Y
bseries_score = 0
yseries_score = 0
bseries_score, yseries_score = diascoring.dia_by_ion_score(
spectrum, a, 1, bseries_score, yseries_score)
self.assertAlmostEqual(bseries_score, 1.0)
self.assertAlmostEqual(yseries_score, 3.0)