Compares AA sequences of homologous proteins (ie mutant & wild-type)

aa.py

__AUTHOR__ = 'KARL HERBINE'
AA = {'LYS':'K', 'ALA':'A', 'ARG':'R', 'ASN':'N', 'ASP':'D','CYS':'C','GLU':'E', 'GLY':'G','HIS':'H', 'ILE':'I','LEU':'L','MET':'M', 'PHE':'F', 'PRO':'P', 'SER':'S', 'THR':'T', 'TRP':'W', 'TYR':'Y','VAL':'V','GLN':'Q'}
CHAINS = list('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
print 'Amino Acid Sequence differences'.center(100,' ')
print 'This Python script is useful for comparing AA sequences between two polypeptides (eg. Mutant vs Wild-Type)'
print 'NOTE: SOME HOMOLOGOUS STRUCTURES MAY NOT CONTAIN SAME NUMBER OF RESIDUES'.center(100,' ')


pdb1 = str(raw_input("Enter the name of the first pdb file (name.pdb): "))
pdb2 = str(raw_input("Enter the name of the second pdb file (name.pdb): "))

chain1 = ['' for x in range(0,len(CHAINS))]
chain2 = ['' for x in range(0,len(CHAINS))]

for letter in range(0,len(CHAINS)):
	with open(pdb1,'r') as file1:
		for line in file1:
			if 'SEQRES' in line:
				if ' %s ' % CHAINS[letter] in line:
					for word in line.split():
						for i in AA.keys():
							if word == i:
								chain1[letter] += AA.get(word)

for letter in range(0,len(CHAINS)):								
	with open(pdb2,'r') as file2:
		for line in file2:
			if 'SEQRES' in line:
				if ' %s ' % CHAINS[letter] in line:
					for word in line.split():
						for i in AA.keys():
							if word == i:
								chain2[letter] += AA.get(word)
def sequences(s1,s2):
	if len(s1) > len(s2):
		length = len(s2)
	else:
		length = len(s1)
	l = [int(i) for i in range(0,length)]
	nomatch = []
	for i in l:
		if s1[i] != s2[i]:
			nomatch.append(i)
	for i in nomatch:
		print 'Amino Acid: %s%d substituted for %s%d' % (s1[i], i+1, s2[i], i+1)
	if len(nomatch) == 0:
		print
		print "Total Amino Acid Substitutions".center(60,'-')
		print "%d".center(60,' ') % len(nomatch)
		print "These two sequences are identical."
		print
	else:
		print
		print "Total Amino Acid Substitutions".center(60,'-')
		print "%d".center(60,' ') % len(nomatch)
		print "".center(60,'-')
		print
	polar = 'STCYNQ'
	non_polar = 'GAVLIMFWP'
	acid = 'ED'
	base = 'KRH'
	aromatic = 'WFY'
	for i in nomatch:
		if s1[i] in polar and s2[i] not in polar:
			if s2[i] in aromatic:
				print "Amino Acid %s%d is POLAR and has been substituted for %s%d which has an AROMATIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in acid:
				print "Amino Acid %s%d is POLAR and has been substituted for %s%d, a POLAR aa with an ACIDIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in non_polar:
				print "Amino Acid %s%d is POLAR and has been substituted for %s%d, a NON-POLAR aa" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in base:
				print "Amino Acid %s%d is POLAR and has been substituted for %s%d, a POLAR aa with a BASIC R-group" % (s1[i], i+1, s2[i], i+1)
		elif s1[i] in non_polar and s2[i] not in non_polar:
			if s2[i] in aromatic:
				print "Amino Acid %s%d is NON-POLAR and has been substituted for %s%d which has an AROMATIC R-group"% (s1[i], i+1, s2[i], i+1)
			elif s2[i] in acid:
				print "Amino Acid %s%d is NON-POLAR and has been substituted for %s%d, a POLAR aa with an ACIDIC R-group"% (s1[i], i+1, s2[i], i+1)
			elif s2[i] in base:
				print "Amino Acid %s%d is NON-POLAR and has been substituted for %s%d, a POLAR aa with a BASIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in polar:	
				print "Amino Acid %s%d is NON-POLAR and has been substituted for %s%d, a POLAR aa" % (s1[i], i+1, s2[i], i+1)
		elif s1[i] in aromatic and s2[i] not in aromatic:
			if s2[i] in base:
				print "Amino Acid %s%d is AROMATIC and has been substituted for %s%d, a POLAR aa with a BASIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in acid:
				print "Amino Acid %s%d is AROMATIC and has been substituted for %s%d, a POLAR aa with an ACIDIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in non_polar:
				print "Amino Acid %s%d is AROMATIC and has been substituted for %s%d, a NON-POLAR aa"  % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in polar:
				print "Amino Acid %s%d is AROMATIC and has been substituted for %s%d, a POLAR aa" % (s1[i], i+1, s2[i], i+1)	
		elif s1[i] in base and s2[i] not in base:
			if s2[i] in aromatic:
				print "Amino Acid %s%d is BASIC and has been substituted for %s%d which has an AROMATIC R-group " % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in acid:
				print "Amino Acid %s%d is BASIC and has been substituted for %s%d, a POLAR aa with an ACIDIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in non_polar:
				print "Amino Acid %s%d is BASIC and has been substituted for %s%d, a NON-POLAR aa"  % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in polar:
				print "Amino Acid %s%d is BASIC and has been substituted for %s%d, a POLAR aa" % (s1[i], i+1, s2[i], i+1)
		elif s1[i] in acid and s2[i] not in acid:	
			if s2[i] in aromatic:
				print "Amino Acid %s%d is ACIDIC and has been substituted for %s%d which has an AROMATIC R-group " % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in base:
				print "Amino Acid %s%d is ACIDIC and has been substituted for %s%d, a POLAR aa with a BASIC R-group" % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in non_polar:
				print "Amino Acid %s%d is ACIDIC and has been substituted for %s%d, a NON-POLAR aa"  % (s1[i], i+1, s2[i], i+1)
			elif s2[i] in polar:
				print "Amino Acid %s%d is ACIDIC and has been substituted for %s%d, a POLAR aa" % (s1[i], i+1, s2[i], i+1)
		else:
			print "Amino Acid %s%d has been substituted for %s%d with an equally functional R-Group" % (s1[i], i+1, s2[i], i+1)

def chains():
	total_chains = [i for i in chain1 if len(i)>1]
	for a in range(len(total_chains)):
		print ''.center(60,'-')
		print 'CHAIN %s'.center(60,' ') % (CHAINS[a])
		print ''.center(60,'-')
		print "Total Amino Acids in %s is: %d" % (pdb1, len(chain1[a]))
		print "Total Amino Acids in %s is: %d" % (pdb2, len(chain2[a]))
		print
		print "Amino Acid Sequence for CHAIN %s in %s: %s" % (CHAINS[a], pdb1, chain1[a])
		print "Amino Acid Sequence for CHAIN %s in %s: %s" % (CHAINS[a], pdb2, chain2[a])
		print
		sequences(chain1[a],chain2[a])
chains()