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

import os, sys, string
from openeye.oechem import *

try:
    if sys.argv[1][-4:] == '.ism':
        suffix = '.ism'
        t = 'smiles'
    elif sys.argv[1][-4:] == '.smi':
        suffix = '.smi'
        t = 'smiles'
    elif sys.argv[1][-4:] == '.sdf':
        suffix = '.sdf'
        t = 'sdf'
    else:
        print 'INPUT ERROR: supposed to work with ism-,smi- or sdf-files'
        print sys.argv[1][-4:]
        raise SystemExit()
except IndexError:
    print 'usage: cysprot_91rxn_corina.py filename'
    raise SystemExit()


prefix = 'cysprot_91rxn'+sys.argv[1][string.find(sys.argv[1], 'rxn')+3:-4]


if 'db':
    # create 3d coordinates from ring_confs and stereoisomers
    # recommended mc=10, but in study used mc=25 -> typing error?
    print 'DB-params are used....ringconfs, stereoisomers...'
    os.system('corina -d errorfile='+prefix+'_corina_error.sdf,r2d,wh,stergen,msc=5,msi=13,names,preserve,rc,flapn,mc=10,sc -t tracefile='+prefix+'_corina_trace.trc -i t='+t+' -o t=sdf -o mdlcompact '+sys.argv[1]+' '+prefix+'.sdf')