#!/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]

# create 3d coordinates from ring_confs and stereoisomers
# recommended mc=10, but in study used mc=25 -> typing error?
os.system('corina.nirvana -d errorfile='+prefix+'_corina_error.sdf,r2d,wh,stergen,msc=5,msi=13,names,preserve,rc,flapn,mc=25,sc -t tracefile='+prefix+'_corina_trace.trc -i t=sdf -o t=sdf -o mdlcompact '+prefix+'.sdf c_'+prefix[2:]+'_corina.sdf')

# Just run ionizer
os.system('sdconvert -st -isd c_'+prefix[2:]+'_corina.sdf -omae c_'+prefix[2:]+'_corina.mae')
os.system('ionizer -i 2 -ph 7 -s ionizer_reduced_ti.ini -i c_'+prefix[2:]+'_corina.mae -l c_'+prefix[2:]+'_corina.log -b c_'+prefix[2:]+'_corina.mae -o c_'+prefix[2:]+'_corina.mae')
os.system('sdconvert -imae c_'+prefix[2:]+'_ionizer.mae -osd c_'+prefix[2:]+'_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')