#!/usr/bin/perl

# --------------------------------------------------------------
# Convert a CHARMM card file into PDB file for use with MOLMOL
#
#                                                 March 4 2003
#                                    Modified December 10 2004
# --------------------------------------------------------------
#
# Usage :   crd2pdb.prl    file1.crd file2.crd file3.crd ...
#



foreach $file (@ARGV) {

  ($output_name=$file) =~ s/\.crd/\.pdb/g;

  open(IN,"$file");
  @line=<IN>;
  $end=@line-1;
  close(IN);

  open(OUT,">$output_name");


  # Gets title from crd file and writes it as REMARK

  for $i (0..$end) {
    if ($line[$i] !~ /\*/) {
      $begin=$i+1;
      last;
    }
    $l = "REMARK ".substr($line[$i],1,80);
    print OUT "$l";
  }
  # $begin : number of first line containing an atom
  # $end   : number of last  line containing an atom



  # Prevents writing a "TER" before the first segment

  $firstseg=1;
  $preseg="";



  # Main loop

  for $i ($begin..$end) {
    $num=substr($line[$i],0,5);
    $resid=substr($line[$i],5,5);
    $resname=substr($line[$i],11,4);
    $atomname=substr($line[$i],16,4);
    $x=substr($line[$i],20,10);
    $y=substr($line[$i],30,10);
    $z=substr($line[$i],40,10);
    $segname=substr($line[$i],51,4);
    $resnum=substr($line[$i],56,5);
    $w=substr($line[$i],61,9);
    # Writes a "TER" between segments
    if ( ($segname ne $preseg) and ($firstseg==1) ) {
      $firstseg=0;
      $preseg=$segname;
    } elsif ( $segname ne $preseg ) {
      print OUT "TER \n";
      $preseg=$segname;
    }
    # Writes an ATOM line in PDB format, with "weight" in B-factor column
    printf OUT ("ATOM%7d %-5s%4s%5d    %8.3f%8.3f%8.3f  1.00%6.2f      %4s \n",
	   $num,$atomname,$resname,$resnum,$x,$y,$z,$w,$segname);
  }
  print OUT "TER\n";

  close(OUT);

}