replaceTBL.pl

#!/usr/bin/env perl
#===============================================================================
#  Li Xue
#  Sep. 16, 2015
#
#  DESCRIPTION: replace the tbl data in the haddock parameter file with a new tbl file
#
#  Unambiguous restraints in the parameter file:
#  unambigtbldata = "assign (name ca and segid A and resi 64) (name ca and segid B and resi 177) 8.319 1.006 1.171\nassi...... 1.168\n",
#
#  Ambiguous restraints in the parameter file:
#  tbldata = "assign ( ...",
#
#===============================================================================

use strict;
use warnings;
use utf8;
use File::Copy;

my $haddockparamFL = shift @ARGV;
my $tblFL          = shift @ARGV;
my $restraint_type = shift @ARGV;

if ( !defined $restraint_type  ) {
    die("\nUSAGE: replaceTBL.pl original_haddock_paramFL new.tbl restraint_type (ambig or unambig)\n\n");
}

if ($restraint_type !~/^ambig$/ && $restraint_type !~/^unambig$/){
    print ("\nrestraint type has to be: ambig or unambig\n\n");
    die("USAGE: replaceTBL.pl original_haddock_paramFL new.tbl restraint_type (ambig or unambig)\n\n");
}

#-- read the new tbl file
open( INPUT, "<$tblFL" ) or die("Cannot open $tblFL:$!");
my @a = <INPUT>;
map {s/[\n\r]//g} @a;
close INPUT;

if ( !@a ) {
    die("Nothing read from $tblFL:$!");
}
my $newTbl = join( '\n', @a );

# -- add the new tbl content to haddock param file

my $flag = 0;
copy( $haddockparamFL, "$haddockparamFL.ori" )
  or die("Cannot copy $haddockparamFL to $haddockparamFL.ori:$!");
my $haddockparamFL_tmp = "$haddockparamFL.tmp";
unlink $haddockparamFL_tmp if ( -e $haddockparamFL_tmp );

open( OUTPUT, ">>$haddockparamFL_tmp" )
  or die("Cannot open $haddockparamFL_tmp:$!");
open( INPUT, "<$haddockparamFL" ) or die("Cannot open $haddockparamFL:$!");
while (<INPUT>) {
    s/[\n\r]//mg;

    if ($restraint_type eq 'unambig' && $_=~/^(\s*\"unambigtblfile\s*\":\s*)['"]{1}/) {
        # "unambigtblfile": "assign (segid A and resi 23 and ....)",
        $_    = "$1\"$newTbl\",";
        $flag = 1;
    }

    if ($restraint_type eq 'ambig' && $_ =~/^(\s*\"tblfile\"\s*:\s*)['"]{1}/) {
       # tbldata = '! generated by ...',
       #
        $_    = "$1\"$newTbl\",";
        $flag = 1;
    }

    print OUTPUT "$_\n";
}
close INPUT;
close OUTPUT;

if ( $flag == 0 ) {
    print "\nWARNING: nothing changed!!!\n";
    unlink $haddockparamFL_tmp;
    unlink "$haddockparamFL.ori";
}
else {

    move( $haddockparamFL_tmp, $haddockparamFL )
      or die("Cannot rename $haddockparamFL_tmp as $haddockparamFL:$!");
    print "unambig tbl data updated in $haddockparamFL.\n";
}