PyMol Tkinter plugin that splits difficult multimolecule PDBs, such as those generated by SwissDock or CHARMM simulations.

multimol_split.py

"""
PyMol plugin that splits difficult multimolecule PDBs, such as those generated
by SwissDock or CHARMM simulations.

Writes a new file that treats each 'molecule' as a model which can then be parsed
by Pymol as 'states'. 

Copyright 2018 Jedd Bellamy-Carter
Released under the terms of the MIT License (https://opensource.org/licenses/MIT)
"""

from Tkinter import *
import tkFileDialog
from pymol import cmd

def __init__(self):
	self.menuBar.addmenuitem('File', 'command',
							 'Multimolecule PDB Splitter',
							 label = 'Multimolecule PDB Splitter',
							 command = lambda s=self : fileDialog(s))

def fileDialog(self):
	"""Opens a file dialog and reads data from the PDB into a list"""
	filename = tkFileDialog.askopenfilename(title='Choose PDB containing multiple molecules', 
		filetypes=[('Protein Data Bank','.pdb'),('All files','.*'),])
		
	if not filename:
		return
	
	with open(filename, 'r') as infile:
		lines = infile.readlines()
	
		fill = []
	
		for i, line in enumerate(lines):
			if line.startswith('TER'):
				fill.append(i)

	for i, e in enumerate(fill):
		lines.insert(i+e+1, 'ENDMDL\n')

	newfilename = filename.replace('.pdb', '_split.pdb')
		
	with open(newfilename, 'w') as outfile:
		outfile.writelines(lines)

	cmd.load(newfilename)