def __init__(self, sequence):
## a. parse the sequence.
match_pattern = re.compile(r'([A-Z])(?:\((\w+)\))?') # Use non-capturing group
seq_list = match_pattern.findall(sequence)
self.mass = 0.0
self.seq = []
for item in seq_list:
res = Residue()
res.bySymbol(item[0])
if item[1] != '':
mod = Modification(item[1])
# Update!!! The mod mass should not be integrated into residue mass.
#res.mass += mod.mass
self.seq.append([res, [mod]])
# Update!!! The mod mass is appended to the precursor directly.
self.mass += mod.mass
else:
self.seq.append([res, []])
self.mass += res.mass
self.length = len(self.seq)
self.mass += Composition("H2O").mass
def getStubs(self):
"""returns a list of dicts with peptide and stub glycopeptide ions """
for i in self.pep_seq:
res = Residue()
res.bySymbol(i)
if i == 'C':
self.mass += Carbamidomethyl
self.mass += res.mass
if self.mod_type == "Deamidated":
self.mass += (Deamidation * self.n_mod)
elif self.mod_type == '':
pass
stubs =[]
stubs.append({"key":"peptide", "mass": (self.mass + Proton)})
sites = self.glyco_num
if sites == 0 :
pass
elif sites>0:
if self.dHex==0:
for i in range(1,sites+1,1):
for j in range(1,3,1):
if j ==1:
key = "pep+"+str(j)+"HexNAc+"+"0Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*(j*HexNAc))
#print key, mass
stubs.append({"key":key,"mass": mass})
elif (j == 2):
for k in range(0,4,1):
key = "pep+"+str(j)+"HexNAc+"+str(k)+"Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*((j*HexNAc)+(k*Hex)))
#print key, mass
stubs.append({"key":key,"mass": mass})
else:
pass
elif self.dHex>0:
for i in range(1,sites+1,1):
for j in range(1,3,1):
if j ==1:
key = "pep+"+str(j)+"HexNAc+"+"0Hexose"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*(j*HexNAc))
#print key, mass
stubs.append({"key":key,"mass": mass})
if (j == 2):
for l in range (0,2,1):
for k in range(0,4,1):
key = "pep+"+str(j)+"HexNAc+"+str(k)+"Hexose"+str(l)+"dHex"+"-"+str(i)+"sites"
mass = self.mass+Proton+(i*((j*HexNAc)+(k*Hex)+(l*dHex)))
#print key, mass
stubs.append({"key":key,"mass": mass})
else:
pass
j +=1
return stubs
