residue_atom_pull.py

# Requires Python2.7
import subprocess
import sys
import os
import math

# This script takes the amino acid side chain atoms (or those not listed in aainterest) for each residue of interest in list residueinterest and writes them into their own file

# Can add other atoms to exlude
aainterest = ["CA","C","N","O","HN","HA"]
# Residues wanted to target
residueinterest = ["71","72","73","75","76","89","93","99","101","104","107","108","111","135","138","142","146",]
# Pdb file being read
pdbread = str(sys.argv[1])
# Identifier of molecule
molid = "MB"
emptynumbers = []
# Collection of atoms selected into this file
file = open('proteinsidechain.txt','w')
thestring = ""
with open(pdbread+".pdb") as f:
	for line in f:
		splitline = line.split()
		if len(splitline) > 5:
			if splitline[2] not in aainterest:
				if splitline[4] in residueinterest:
					if splitline[10] == molid:
						thestring = thestring+splitline[1] + " "

file.write(thestring)