#!/usr/local2/bin/python2.3

import os, sys
from openeye.oechem import *

if sys.argv[1][-4:] != '.sdf':
    print 'INPUT ERROR: works only with sdf-files'
    raise SystemExit()

prefix = sys.argv[1][:-4]

# Just run ionizer
os.system('sdconvert -st -isd '+sys.argv[1]+' -omae '+prefix+'.mae')
os.system('ionizer -i 2 -ph 7 -s ~joha/PETC/PYTHON/DB/ionizer_ti_O-vS-OH_exclude.ini -i '+prefix+'.mae -l '+prefix+'_ionizer.log -b '+prefix+'_ionizer_bad.mae -o '+prefix+'_ionizer.mae')
os.system('sdconvert -imae '+prefix+'_ionizer.mae -osd '+prefix+'_ionizer.sdf')