def min_mass(self):
b = mass.get_aa_mass(self.peptide[0])
if self.peptide[0] == 'C':
b += 57.02146
y = mass.get_aa_mass(self.peptide[self.length - 1])
if self.peptide[self.length - 1] == 'C':
y += 57.02146
return min(b, y)
def max_mass(self):
b = 0
y = 0
for i in range(self.length - 1):
b += mass.get_aa_mass(self.peptide[i])
if self.peptide[i] == 'C':
b += 57.02146
y += mass.get_aa_mass(self.peptide[i + 1])
if self.peptide[i + 1] == 'C':
y += 57.02146
return max(b, y)
def max_peak_mass(self, fragmentation_site, ion_type):
if fragmentation_site <= 0 or fragmentation_site >= self.length:
return 0
peak_mass = 0
if ion_type == 'b':
for i in range(fragmentation_site):
if self.peptide[i] == 'C':
peak_mass += 57.02146
peak_mass += mass.get_aa_mass(self.peptide[i])
elif ion_type == 'y':
for i in range(fragmentation_site, self.length):
if self.peptide[i] == 'C':
peak_mass += 57.02146
peak_mass += mass.get_aa_mass(self.peptide[i])
return self.max - peak_mass
def relative_peak_mass(self, fragmentation_site, ion_type):
if fragmentation_site <= 0 or fragmentation_site >= self.length:
return 0
peak_mass = 0
if ion_type == 'b':
for i in range(fragmentation_site):
if self.peptide[i] == 'C':
peak_mass += 57.02146
peak_mass += mass.get_aa_mass(self.peptide[i])
elif ion_type == 'y':
for i in range(fragmentation_site, self.length):
if self.peptide[i] == 'C':
peak_mass += 57.02146
peak_mass += mass.get_aa_mass(self.peptide[i])
# (peak_mass - min peak) / (max peak - min peak)
return (peak_mass
- self.min_peak_mass(fragmentation_site, ion_type))\
/ (self.max_peak_mass(fragmentation_site, ion_type)
- self.min_peak_mass(fragmentation_site, ion_type))