#!/usr/bin/python
"""
(c) Molinspiration Cheminformatics 2010
script to automatize model generation and screening by the miscreen engine

run as:
screen.py act.smi|act.sdf ina.smi|ina.sdf|ina.frag toscreen.smi > out.smi
as inactives either molecules, or "background" fragments may be used
(i.e. 100k.frag provided by Molinspiration)
if using the fragmnet file, it must end by '.frag'
"""

import sys
import os
import commands

# --- edit the following parameters
miscreen = "java -jar miscreen.jar"
jobname = "run" # --- filename of output files
minscore = -9999 # only molecules with score > minscore will be printed

if (len(sys.argv) < 2):
  print "Usage: screen.py actives inactives toscreen > out"
  print "(you can use, of course, your own file names)"
  sys.exit()
actdata = sys.argv[1] # --- file with active molecules
inadata = sys.argv[2] # --- file with inactive molecules or fragments
toscreen = sys.argv[3] # --- file to screen

# --- checking miscreen jar
d,out = commands.getstatusoutput(miscreen)
if (out.find("Unable") > -1):
  print "Cannot access miscreen.jar"
  print "check miscreen.jar path and modify the respective parameter in the screen.py"
  sys.exit()

def screenrun():
  
  # --- checking file availability
  if not os.path.exists(actdata):
    print "Cannot open file",actdata
    sys.exit()
  if not os.path.exists(inadata):
    print "Cannot open file",inadata
    sys.exit()
  if not os.path.exists(toscreen):
    print "Cannot open file",toscreen
    sys.exit()
  
  # --- start of the run
  print "Running Molinspiration virtual screening protocol"
  # --- generation of active fragments
  print "generating active fragments ...";
  actfragments = jobname+".af";
  os.system(miscreen + " -fragment " + actdata + " > " + actfragments)
  print "file",actfragments,"with active fragments created";
  
  # --- generation of inactive fragments (if file does not end by 'frag')
  if not inadata.endswith(".frag"):
    print "generating inactive fragments ...";
    inafragments = jobname+".if";
    os.system(miscreen + " -fragment " + inadata + " > " + inafragments)
    print "file",inafragments,"with inactive fragments created";
  else:
    inafragments = inadata 
    print "using supplied fragment set " + inafragments + " as inactives"
  
  # --- calculation of scores
  print "creating bioactivity model ..."
  model = jobname+".model"
  os.system(miscreen + " -createmodel -af " + actfragments + " -if " + inafragments + " > " + model)
  print "model " +  model + " created"
  
  # --- screening
  print "screening ..."
  out = jobname+".out"
  os.system(miscreen + " -screen " + toscreen + " -model " + model + " -minscore " + str(minscore) + " > " + out)
  
# main
screenrun()
print "Screened molecules with predicted activity in " + jobname+".out";