Useful Python Scripts

On this script you will find (and can add!) Python scripts, that may be useful in any work-related way.

Converting .pdb files from vmd to xleap readable format

This script takes a filename as command line argument reads the respective .pdb file and converts it to an xleap readable format. The initial file is overwritten, but the original file is retained in filename.orig.

#!/usr/bin/env python
# -*- coding: latin1 -*-

import sys

def main():
 	fname = sys.argv[1]
 
 	fin = open( fname, "r")
 	lines = fin.readlines()
 	fin.close()

	lin2=[]

	foumod=open( fname+".orig","w")
	fomod=open( fname,"w")


	counter=1
	first=True
	oldnum=""
	for l in lines:
		if l.find( "CRYST")==-1:
			l2=l.replace( " X ", "   ")
			if len( l2)>16:
				if l2[13].isdigit():
					subs=l2[12:16]
					subs2=l2[13:17]
					l2=l2.replace( subs, subs2)

			if (not first) and len( l2)>25:
				if oldnum!=l2[25]:
					oldnum=l2[25]
					print oldnum
					lin2.append( "TER\n")
					counter+=1
			first=False
			lin2.append( l2)
		else:
			counter-=1
	lin2.insert(-1,"TER\n")

	for i in range( counter):
		lines.append( "")

	for l,l2 in zip( lines, lin2):
		foumod.write( l)
		fomod.write( l2)


if __name__ == "__main__":
	main()