#!/usr/bin/perl -w
use Getopt::Std;
use strict;
my $debug = 0;
my $spec;
my $method; #1 -- use symmetry, 2 -- no symm

main();

sub main {
  my $cmd;
  my ($atomdef,$residef,$stdvol,$symfile,$namfile,$outfile) = getINPUT();

  if($method == 1) {
    $cmd = mkCMD($atomdef,$residef,$stdvol,$symfile,In2Out($symfile));
  } else {
    $cmd = mkCMD($atomdef,$residef,$stdvol,$namfile,$outfile);
  }
  if($debug) { print STDERR $cmd,"\n"; } else { system($cmd); }

  if($method == 1) {
    $cmd = Truncate2(In2Out($symfile),$namfile,$outfile);
    if($debug) { print STDERR $cmd,"\n"; } else { system($cmd); }
    
    system("rm -f ".In2Out($symfile));
  } 

  print STDERR "\n\n\n\n\n$outfile created\n";
};

sub getUname {
  system("uname > temp.$spec");
  open(TEMP, "< temp.$spec") or die;
  if(defined(my $line = <TEMP>)) {
    $line =~ s/\s+$//; $line =~ s/^\s+//;
    close(TEMP);
    system("rm -f temp.$spec");
    return lc($line);
  }
  close(TEMP);
  system("rm -f temp.$spec");
  return "";
}

sub Truncate {
  my ($symfile,$infile,$outfile) = @_;
  my $path = getPath();
  my $exefile = $path."truncate2.pl";
  if(!stat($exefile)) { die; }
  return "perl $exefile -s $symfile -i $infile -o $outfile";
};

sub Truncate2 {
  my ($symfile,$infile,$outfile) = @_;
  my $path = getPath();
  my $exefile = $path."truncate3.pl";
  if(!stat($exefile)) { die; }
  return "perl $exefile -s $symfile -i $infile -o $outfile";
};

sub In2Out {
  my ($infile) = @_;
  my @chunks = split('/',$infile);
  substr($chunks[$#chunks],-4) = "-temp-$spec\.out";
  return $chunks[$#chunks];
};

sub mkCMD {
  my ($atomdef,$residef,$stdvol,$infile,$outfile) = @_;
  my $path = getPath();
  my $uname = getUname();
  my $exefile =       "/usr/local/bin/packing-eff.exe";
  #my $exefile =       "./packing-eff.exe.$uname";
  #my $exefile = "/bh0/vossman/bin/packing-eff";
  if(!stat($exefile)) { die; }
  return "$exefile -types-file $atomdef -residue-file $residef "
        ."-stdvols $stdvol -i $infile > $outfile";
};

sub getPath {
  use Cwd;
  my $dir = cwd();
  $dir =~ s/$/\//;
  my $path = "/home/vossman/phos/"; 
  #my $path = "/bh0/vossman/phosphate/";
  if(!stat($path)) { die; }
  if($path eq $dir) { $path = ""; }
  return $path;
};  

sub getINPUT {
  my %args;
  my ($atomdef,$residef,$stdvol,$symfile,$namfile,$outfile);
  getopt("uspoarm",\%args);
  my $path = getPath();
  $method = $args{'m'} || 1;
  $spec = $args{'u'} || int(rand(1000000));
  $symfile = $args{s} || $path."1JJ2_sym.pdb";
  $namfile = $args{p} || $path."1JJ2_nam.pdb";
  if($args{r}) {
    my $root = $args{r};
    $symfile = $path."sym/".$root."_nam.pdb.sym";
    $namfile = $path."nam/".$root."_nam.pdb";
  }
  $outfile = $args{o} || $path."getVolume.out";
  $atomdef = $args{a} || $path."atom-defs.dat";
  $residef = $path."resi-defs.dat";
  $stdvol = $path."stdvol173.dat";
  foreach my $file ($atomdef,$residef,$stdvol,$symfile,$namfile) {
    if(!stat($stdvol)) { die "\n$file not found\n\n"; }
  }
  return ($atomdef,$residef,$stdvol,$symfile,$namfile,$outfile);
};