#!/usr/local/bin/python2.3
import os, sys, socket
from var_functions import start_and_end_with


if socket.gethostname() != 'bjork.compbio.ucsf.edu':
    print '\nRun on bjork!\n'
    raise SystemExit()

try:
    start = sys.argv[1]
    end = sys.argv[2]
except IndexError:
    print '\nUsage: c2_ionizer.py start-file-pattern end-file-pattern\n'
    raise SystemExit()

for file in os.listdir('.'):
    prefix = 'c2_'+file[3:-8]
    if start_and_end_with(file, start, end):
        if os.path.exists('./'+prefix+'_out.sdf'):
            print prefix+'_out.sdf exists already, skip '+file
            continue
        pass
    else:
        continue

    # Just run ionizer
    os.system('sdconvert -st -isd c1_'+prefix[3:]+'_out.sdf -omae c1_'+prefix[3:]+'_out.mae')
    os.system('ionizer -i 2 -ph 7 -s ~joha/PETC/PYTHON/DATABASE_SCRIPTS/ionizer_ti_O-vS-OH_exclude.ini -i c1_'+prefix[3:]+'_out.mae -l '+prefix+'.log -b '+prefix+'_bad.mae -o '+prefix+'_out.mae')
    os.system('sdconvert -imae '+prefix+'_out.mae -osd '+prefix+'_out.sdf')