#!/usr/bin/python
import os, sys
from openeye.oechem import *

#*************************************************************
def start_and_end_with(strng, startpattern, endpattern):
    l_startpattern = len(startpattern)
    l_endpattern = len(endpattern)
    if strng[:l_startpattern] == startpattern and strng[-l_endpattern:] == endpattern:
        return 1
    else:
        return 0
#*************************************************************

try:
    start = sys.argv[1]
    end = sys.argv[2]
except IndexError:
    print 'usage: c1_corina.py start-file-pattern end-file-pattern'
    raise SystemExit()

for file in os.listdir('.'):
    if start_and_end_with(file, start, end):
        prefix = 'c1_'+file[:-8]
        if file[-3:] != 'ism':
            print 'Skip '+file+' ism-file needed as input'
            continue
        elif os.path.exists('./'+prefix+'_out.sdf'):
            print prefix+'_out.sdf exists already, skip '+file
            continue
        else:
            pass
        # create 3d coordinates from ring_confs and stereoisomers
        # recommended mc=10, but in study used mc=25 -> typing error?
        print 'run corina for '+file+'; DB-params are used ....ringconfs, stereoisomers....'
        os.system('corina -d errorfile='+prefix+'_error.sdf,r2d,wh,stergen,msc=5,msi=13,names,preserve,rc,flapn,mc=10,sc -t tracefile='+prefix+'_trace.trc -i t=smiles -o t=sdf -o mdlcompact '+prefix[3:]+'_out.ism '+prefix+'_out.sdf')