protein_split_backbone_sidechain.py

# Requires Python2.7
import sys
import subprocess

# This script highlights all possible backbone atoms and divides residues in protein into abckbone and sidechain groups via index

atominterest = ["H1 ", "H2 ", "H3 ", "HA ","O ", "OT1 ", "OT2 ", "HN ", "HA ", "CA ","C ","N "]

# Name of structure to be split
filename = str(sys.argv[1])
# Where files will be output to
fileout = str(sys.argv[2])
# First residue number
initialnumber = int(sys.argv[3])
count = 0
writeoutbb = ""
writeoutsc = ""
with open(filename) as f:
	for line in f:
		splitline = line.split()
		if (splitline[0] == "ATOM"):
			if initialnumber == int(splitline[5]):	
				if ((splitline[2]) + " ") in atominterest:
					writeoutbb = writeoutbb + line
					filetowrite = open(str(fileout) + str(splitline[3]) + str(splitline[5]) + "_backbone.pdb", 'w')
					filetowrite.write(writeoutbb)
					print line
				elif ((splitline[2]) + " ") not in atominterest:
					writeoutsc = writeoutsc + line
					filetowrite = open(str(fileout) + str(splitline[3]) + str(splitline[5]) + "_sidechains.pdb", 'w')
					filetowrite.write(writeoutsc)
					print line
			else:
				writeoutsc = ""
				writeoutbb = line
				initialnumber = initialnumber+1