#!/usr/bin/perl
# prot_unfold
# Francis Peterson 12/14/02
# unalias 13C shifts in xeasy/dyana shift list (.prot file)
# 13C spectral width (in ppm) of spectrum in which aliased
# chemical shift values were generated is hardcoded below.
#
# syntax: noe_weeder sorted_upl_file noesy_peaklist > output_file 
#  

$file1 = $ARGV[0]; 
$file2 = $ARGV[1];

#  Search sorted upl files for bad sequential NOEs

    open (FILE1, "$file1") || die "Couldn't open file: $!\n";
    while (<FILE1>) {
        @fld = split;        #delimits by whitespace

#        print "$fld[0] $fld[1] $fld[2] $fld[3] $fld[4] $fld[5] $fld[6] $fld[7] $fld[8] $fld[9] \n";
#        print "$fld[3] $fld[0] $fld[5] \n";

# Selects subset of NOE to evaluate for violations
                unless(($fld[5] eq "HN") || ($fld[4] eq "PRO" && ($fld[5] eq "HD2" || $fld[5] eq "HD3" || $fld[5] eq "QD"))){
		   $res_diff=$fld[3]-$fld[0];
#                   print "$res_diff \n";

# Finds violations and stores peak number in an array
			if(($res_diff > 0 ) && ($resk   569
 39 VAL  HB     40 ALA  HN      4.04            #peak   570
 41 ARG+ HN     42 LEU  HN      4.42            #peak   573
 24 LYS+ HN     41 ARG+ HN      4.11            #peak   574
 40 ALA  HA     41 ARG+ HN      2.99            #peak   575
 42 LEU  HN     47 ARG+ HN      4.11            #peak   579
 41 ARG+ HA     42 LEU  HN      2.87            #peak   580
 24 LYS+ HN     43 LYS+ HN      4.14            #peak   586
 42 LEU  HA     43 LYS+ HN      3.21            #peak   587
 23 VAL  HA     43 LYS+ HN      3.76            #peak   588
 23 VAL  HA     42 LEU  HN      5.07            #peak   589
 44 ASN  HA     45 ASN  HN      4.54            #peak   605
 42 LEU  HN     47 ARG+ HN      3.92            #peak   629
 41 ARG+ HA     47 ARG+ HN      4.85            #peak   630
 45 ASN  HB3    47 ARG+ HN      4.26            #peak   632
 47 ARG+ HA     48 GLN  HN      2.74            #peak   637
 47 ARG+ HB2    48 GLN  HN      3.52            #peak   639
 40 ALA  HN     49 VAL  HN      3.70            #peak   649
 48 GLN  HA     49 VAL  HN      2.87            #peak   651
 38 ILE  HN     51 ILE  HN      5.04            #peak   659
 49 VAL  HA     50 CYSS HN      3.61            #peak   660
 49 VAL  HB     50 CYSS HN      3.45            #peak   661
 51 ILE  HN     52 ASP- HN      4.85