#!/usr/bin/perl

# --- (c) Molinspiration Cheminformatics 2006
# --- script automatizing screening by miscreen toolkit
#
# --- run as: screen.pl act.smi ina.smi|ina.frag toscreen.smi
# --- as inactives either molecules, or fragments may be used (i.e. 100k.frag)
# --- if provideing fragmnet file, it must end by '.frag'

# --- edit the following parameters
$miscreen = "java -jar miscreen.jar";
$name = "run"; # --- filename of output files
$minscore = 0.3; # molecules with score < minscore will be discarded

if ($#ARGV < 2) {
  print "Usage: screen.pl act.smi ina.smi toscreen.smi\n";
  print "(you can use your own file names)\n";
  exit;
}
$actdata = $ARGV[0]; # --- file with active molecules
$inadata = $ARGV[1]; # --- file with inactive molecules

# --- start of the run
open (ACT,"$actdata") || die "Cannot open file $actdata\n";
open (INA,"$inadata") || die "Cannot open file $inadata\n";

# --- generation of active fragments
print "generating active fragments ...\n";
$actfragments = $name.".af";
`$miscreen -fragment $actdata > $actfragments`;
print "file $actfragments created\n";

# --- generation of inactive fragments (if file does not end by 'frag')
print "generating inactive fragments ...\n";
$inafragments = $name.".if";
`$miscreen -fragment $inadata > $inafragments`;
print "file $inafragments created\n";

# --- calculation of scores;
print "creating model ...\n";
$model = $name.".model";
`$miscreen -createmodel -af $actfragments -if $inafragments > $model`;
print "model $model created\n";

# --- screening
print "screening ...\n";
$tmppred = $name.".tmp";
$test = $ARGV[2];
`$miscreen -screen $test -model $model -minscore $minscore > $tmppred`;

# --- sorting based on the calculated activity
# --- this requires UNIX or cygwin sort (will not run on Windows) !
$pred = $name.".pred";
`sort +1 -2 -rn $tmppred > $pred`;

print "Screened molecules sorted according to activity in $pred\n";