snippet.sc

#!/usr/bin/env python
# encoding: utf-8
"""Extract cartesian geometries from gaussian log files using openbabel.

Reads all files that end '.log' in the current working directory.
Puts corresponding .mol files in the 'Geometries' subdirectory.

Created by Richard West on 2009-10-15.
Copyright (c) 2009 MIT. All rights reserved.
"""

import sys
import os
import pybel
import re


if __name__ == '__main__':
	outfolder='Geometries'
	(os.path.exists(outfolder) and os.path.isdir(outfolder)) or os.mkdir(outfolder)
	
	finder = re.compile('.*\.log')
	for possible in os.listdir('.'):
		if finder.match(possible):
			filename=possible
			try:
				reader = pybel.readfile('g03',filename)
				try:
					molecule = reader.next()
				finally:
					reader.close()
				outname = os.path.join(outfolder,filename+'.mol')
				molecule.write(format='mol',filename=outname)
			except:
				print "failed to read",possible