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cyclicPepTheoIdeal.py
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cyclicPepTheoIdeal.py
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# !/usr/bin/env python3
# Find a Cyclic Peptide with Theoretical Spectrum Matching an Ideal Spectrum
# University of California, Santa Cruz - BME 205
# Biomolecular Engineering and Bioinformatics
# Name: (zmmason)
# Group Members: NONE
import sys
class TheoPepCyclic:
"""
Program to find a Cyclic Peptide with a Theoretical Spectrum Matching an Ideal Spectrum
given A collection of (possibly repeated) integers Spectrum corresponding to an ideal experimental spectrum.
"""
def __init__(self, spectrum):
"""Create a constructor to hold important data and tables."""
self.spectrum = spectrum # original input spectrum
self.possiblePeptides = []
self.aaMass = {'G': 57, 'A': 71, 'S': 87, 'P': 97, 'V': 99, # dict to hold the AA masses
'T': 101, 'C': 103, 'I': 113, 'L': 113, 'N': 114,
'D': 115, 'K': 128, 'Q': 128, 'E': 129, 'M': 131,
'H': 137, 'F': 147, 'R': 156, 'Y': 163, 'W': 186}
self.aaList = list(self.aaMass) # list of the AAs
def matchTheoretical(self):
"""Create possible peptide strings given the input spectrum"""
sortedSpectrum = sorted(self.spectrum) # sorting input spectrum to be for verification of compatible peptides
parentMass = sortedSpectrum[len(self.spectrum) - 1] # gets the total mass of the input spectrum to verify
peptides = [] # list to hold valid peptides
for aa in self.aaList: # Add new amino acid and corresponding masses
newPair = [] # list to hold each sub peptide
newAA = [] # list to hold new AA
newMass = [] # list to hold each sub peptide mass
newAA.append(aa)
newMass.append(self.aaMass[aa])
newPair.append(newAA)
newPair.append(newMass)
peptides.append(newPair)
while len(peptides) > 0:
newPeptides = [] # holds all peptides that match the verification qualities
for peptideInfo in peptides:
pepList = peptideInfo[0]
stringPep = pepList[0]
pepMassList = peptideInfo[1]
pepMass = pepMassList[0]
if pepMass in self.spectrum:
newPeptides.append(peptideInfo)
if pepMass == parentMass: # mass verification
if self.getCyclicSpec(stringPep) == sortedSpectrum: # contents verification
return stringPep
peptides = self.addPeps(newPeptides) # loop to get all possible variations of the peptide spectrum
def getCyclicSpec(self, stringPep):
"""Build the mass spectrum for each possible test peptide to be used for comparison against input spectrum."""
allSubsMass = [0] # list to hold each mass for sub peptide
for i in range(1, len(stringPep) + 1):
for j in range(len(self.aaList)):
aa = self.aaList[j]
aaMass = self.aaMass[aa] # gets the mass of aa
if aa == stringPep[i-1]:
subPeptideMass = allSubsMass[i-1] + aaMass # gets the mass of each sub peptide
allSubsMass.append(subPeptideMass)
peptideMass = allSubsMass[len(stringPep)]
cyclicSpectrum = [0] # list to hold generated spectrum based on matching sub peptides
for i in range(len(stringPep)):
for j in range(i + 1, len(stringPep) + 1):
massChange = allSubsMass[j] - allSubsMass[i] # gets change in mass for each sub peptide pair (i,j)
cyclicSpectrum.append(massChange)
if i > 0 and j < len(stringPep):
subPeptideMass = peptideMass - massChange # gets the mass of combined sub peptides for calculations
cyclicSpectrum.append(subPeptideMass)
return sorted(cyclicSpectrum) # sorted for comparative verification
def addPeps(self, builtPeptides):
"""Build possible peptide sequences to be cycled for verification."""
newPeptideList = [] # list to hold new peptides
for peptideInfo in builtPeptides:
pepList = peptideInfo[0] # list to hold temporary possible peptides
stringPep = pepList[0] # list to hold temporary peptide string
pepMassList = peptideInfo[1] # list to hold temporary possible peptide masses
pepMass = pepMassList[0] # list to hold temporary peptide mass
for aa in self.aaList:
newPair = [] # list to hold new peptide
newPep = []
newStringPep = '' # string to build peptide
newStringPep += stringPep
newStringPep += aa
newPep.append(newStringPep)
newMass = [] # list to hold current peptide mass
newCalcMass = pepMass + self.aaMass[aa]
newMass.append(newCalcMass)
newPair.append(newPep)
newPair.append(newMass)
newPeptideList.append(newPair)
return newPeptideList
def getPeptideSeq(self, peptide):
"""Build list of possible peptide sequences based on the peptides built from spectrum match for final spec."""
for i in range(len(peptide)):
if i == 0:
self.possiblePeptides.append(peptide)
self.possiblePeptides.append(peptide[::-1]) # adds the reverse peptide
else:
startString = peptide[i:]
endString = peptide[:i]
newFullPep = startString + endString
self.possiblePeptides.append(newFullPep)
self.possiblePeptides.append(newFullPep[::-1]) # adds the reverse peptide
return
def formatMatchSpectrum(self):
"""Get the spectrum of the matched peptide string and prepare it for output formatting."""
allPepMasses = [] # list to hold the mass of each substring peptide for each peptide
for massSeq in self.possiblePeptides:
cirSeqMass = [] # list to hold the mass of each substring peptide for a peptide
for aminoAcid in massSeq:
mass = self.aaMass[aminoAcid] # getting mass of the substring peptides
cirSeqMass.append(mass)
allPepMasses.append(cirSeqMass)
massSets = [] # list to hold strings of each peptide spectrum calculated
for i in allPepMasses: # creating desired output formatting as a string
massString = '' # holds the output string for peptide spectrum
for j in range(len(i)):
if j < len(i) - 1:
massString += str(i[j]) + '-'
else:
massString += str(i[j])
massSets.append(massString)
return massSets
def main():
"""
Program to find a Cyclic Peptide with a Theoretical Spectrum Matching an Ideal Spectrum
given A collection of (possibly repeated) integers Spectrum corresponding to an ideal experimental spectrum.
"""
# contents = ['0 113 128 186 241 299 314 427'] # sample input
contents = sys.stdin.read().splitlines()
inputSpectrum = contents[0]
inputSpectrum = inputSpectrum.split()
spectrum = list(int(item) for item in inputSpectrum) # gets the integer value for each spectrum string
myPeptides = TheoPepCyclic(spectrum)
TheoPeptide = myPeptides.matchTheoretical()
myPeptides.getPeptideSeq(TheoPeptide)
allTheoSpec = myPeptides.formatMatchSpectrum()
print(*allTheoSpec, sep=' ') # prints the formatted output on one line with spaces between each spectrum
if __name__ == '__main__':
main()