#!/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 '+prefix+'.sdf -omae '+prefix+'.mae')
os.system('ionizer -i 2 -ph 7 -s '+sys.argv[2]+' -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')

raise SystemExit()

titles = []
ifs = oemolistream()
ofs = oemolostream()
ifs.open(prefix+'_ionizer_out.sdf')
ofs.open(prefix+'_corina_ionizer_out.sdf')
for mol in ifs.GetOEMols():
    num = 1
    title = mol.GetTitle()+'_lp'+str(num)
    while title in titles:
        num+=1
        title = mol.GetTitle()+'_lp'+str(num)
    mol.SetTitle(title)
    titles.append(title)
    OEWriteMolecule(ofs, mol)
ofs.close()
ifs.close()

os.system('rm -rf '+prefix+'_corina_out.mae '+prefix+'_ionizer_out.mae '+prefix+'_ionizer_out.sdf')