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

import os, sys
from openeye.oechem import *

if sys.argv[1][-4:] != '.ism':
    print 'INPUT ERROR: supposed to work with ism-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=15,sc -t tracefile='+prefix+'_corina_trace.trc -i t=smiles -o t=sdf -o mdlcompact '+prefix+'.ism '+prefix+'_corina.sdf')