#!/usr/local2/bin/python2.3
# !!!! RUN ON BJORK !!!!!
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]

if sys.argv[2] == 'O': ini = 'ionizer_tiOH_exclude.ini'
elif sys.argv[2] == 'S': ini = 'ionizer_tiSHO_exclude.ini'

# Just run ionizer
if not os.path.exists(prefix+'.mae'):
    os.system('sdconvert -st -isd '+prefix+'.sdf -omae '+prefix+'.mae')
else:
    pass
os.system('ionizer -i 2 -ph 7 -s ~/PETC/PYTHON/DB/'+ini+' -i '+prefix+'.mae -l '+prefix+'_ionizer.log -b '+prefix+'_ionizer_bad.mae -o '+prefix+'_ionizer.mae')
#print 'ionizer -i 2 -ph 7 -s ionizer_tiOH_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')