#!/bin/perl5

if($#ARGV != 5)
{
   $prgName = $0;
   $prgName = `basename $prgName`;
   chomp($prgName);
   die <<EODIE;
This program reads a dd.mtx file output from discom along with a sequence
file that specifies the residue number and name for each dd.mtx line. It
then builds an MSI NMR restraint list.

minimum distance:
Distances whose absolute values are greater than or equal to this number
are printed.

dd.mtx:
  1 ALA CA          0.00   -0.04
  2 ALA CA         -0.04    0.00

Sequence:
3 SER
4 PRO

Steps for use:
1) Read PDB file into InsightII.
2) From within InsightII, choose the NMR_Refine module.
3) NMR_DB->Files
4) Unselect Peaks
5) Put in a project name. Just make something up.
6) Select the molecule for NMR_Molecule_Name.
7) Select the .rstrnt file for Restraint_File.
8) Execute.
9) Display restraints using Distance, Dihedral, etc.

Usage: $prgName -r [minimum distance] -m dd.mtx -s sequence [> out.rstrnt]
EODIE
}

require "ctime.pl";
require "getopt.pl";

&Getopt('rms');
$minDis = $opt_r;
$matrix = $opt_m;
$sequence = $opt_s;

# Parse the sequence file. Store residue numbers and names in arrays.
open(SEQFILE, $sequence) || die("Can't open $sequence: $!\n");
while(<SEQFILE>)
{
   chomp;
   ($resNum, $resName) = split;
   push @resNum, $resNum;
   push @resName, $resName;
}
close(SEQFILE);

#Need this to start the .rstrnt file.
print "!BIOSYM restraint 1\n";
#Some comments.
print "!Converted from the $matrix discom matrix.\n";
$date = &ctime(time);
print "!$date";
print "#distance\n";

# First run through the ddm matrix to grab the atom names.
open(DDMFILE, $matrix) || die("Can't open $matrix: $!\n");
while(<DDMFILE>)
{
   @words = split;
   push @atomNames, $words[2];
}
close(DDMFILE);

# Second run through the ddm matrix to generate the restraints.
# $countLine keeps track of what matrix line we are on.
$countLine = 0;
open(DDMFILE, $matrix) || die("Can't open $matrix: $!\n");
while(<DDMFILE>)
{
# Melanie tells me that sometimes negative numbers bump, so add a space.
   s/-/ -/g;
# Grab the numbers from a matrix line.
   @nums = split;
# Build the first atom.
   $atom1  = "1:$resName[$countLine]_$resNum[$countLine]";
   $atom1 .= ":$atomNames[$countLine]";
# Get rid of the junk residue number, residue name and atom name. Just the
# numbers, please.
   shift(@nums); shift(@nums); shift(@nums);
# $countNum keeps track of the number for residue numbering.
   $countNum = 0;
# Run through the numbers.
   foreach $num (@nums)
   {
# Build the second atom.
      $atom2  = "1:$resName[$countNum]_$resNum[$countNum]";
      $atom2 .= ":$atomNames[$countNum]";

# Print the rstrnt, unless it is to itself or has already been printed,
# even in reverse.
      printf("%-15s %-15s %8.3f %8.3f 1.00 1.00 1000.000\n",
            $atom1, $atom2, $nums[$countNum], $nums[$countNum])
      unless($atom1 eq $atom2
          || $printed{"$atom1 $atom2"}
          || $printed{"$atom2 $atom1"}
          || abs($nums[$countNum]) < $minDis);
      ++$printed{"$atom1 $atom2"};
      ++$printed{"$atom2 $atom1"};

      ++$countNum;
   }
   ++$countLine;
}
close(DDMFILE);