#!/usr/bin/perl -w

# gromacs.csh  -force_field 0 -tmp /tmp -nokeeptmp
#	creates a temporary directory, and does a gromacs optimization
#	of the pdb file from stdin in that directory, and returns the
#	optimized pdb file to stdout.

use strict;
use File::Basename;
use English;
use Getopt::Long;
     
# directory with starter files for gromacs
my $gromacs_starter = "/projects/compbio/experiments/protein-predict/casp6/gromacs";
     
my $fixup_script = "/projects/compbio/experiments/protein-predict/casp6/scripts/fix-gromacs";
     
    my  $tmp_root = "/tmp";
    my $force_field = 0;
    my $keep_tmp=0;
    GetOptions(
	      "force_field=n" => \$force_field
	    , "keeptmp!" =>	\$keep_tmp
	    , "tmp=s" =>	\$tmp_root
	);

    # create a name for the temporary directory
    my $user=`/usr/bin/whoami`;
    chomp $user;
    
    my $PROG = basename($0);
    my $rand = int(rand(99999999));
    my $job_dir = "$tmp_root/$PROG-$user-$$-$rand";
    
    mkdir $job_dir, 0775 or die "Error $PROG: could not make directory $job_dir\n";  
    
    print STDERR "$PROG running in $job_dir\n";
    
    # copy the input PDB file to the temporary directory
    open PDBIN, "> $job_dir/tmp.pdb";
    while(<STDIN>)
    {    print PDBIN $_;
    }
    close PDBIN;
    
    # copy the starter files
    foreach my $file ("em.mdp", "full.mdp", "mdout.mdp", "pr.mdp")
    {
        system("cp -pr $gromacs_starter/$file $job_dir")==0
		|| die "Couldn't copy $gromacs_starter/$file to $job_dir\n";
    }
    
    my @commands=(
	  "echo $force_field | pdb2gmx -ignh -f tmp.pdb -p tmp.top -o tmp.gro"
	, "editconf -f tmp -o -d 0.5 -c"
	, "genbox -cp out -cs -p tmp -o tmp.b4em"
	, "grompp -v -f em -c tmp.b4em -o tmp -p tmp"
	, "mdrun -v -s tmp -o tmp -c tmp.after_em -g tmp.emlog"
	, "echo 1 | trjconv -f tmp.after_em.gro -s tmp.tpr -o tmp.raw_gromacs.pdb"
	);
	
    
    foreach my $command (@commands)
    {	print STDERR "Running '$command'\n";
        system("cd $job_dir; $command 2>>gromacs.stderr >> gromacs.stdout");
    } 
    
    system("$fixup_script < $job_dir/tmp.raw_gromacs.pdb")==0
    ||	die "Error: $PROG couldn't copy output from $job_dir/tmp.raw_gromacs.pdb\n";
    


    if (!$keep_tmp)
    {    system("rm -rf $job_dir")==0
    	|| die "Error: $PROG couldn't remove $job_dir\n";
    }

    exit(0);