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comment_out_carboxylate_H_v3.0.pl
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comment_out_carboxylate_H_v3.0.pl
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#!/usr/bin/perl
open IN, "<$ARGV[0]";
open OUT, ">temp";
while ($line=<IN>) {
if ($line !~ m/RESIDUE/) { next; }
$resn=substr($line, 10, 3);
%residue_hash=();
%atom_name_hash=();
$key_num=0;
while (1) {
if ($line =~ m/CONECT/) {
$key =$key_num;
$key_num++;
$atom=substr($line, 11, 4);
$residue_hash{$key}=$line;
$atom_name_hash{$atom}=$line;
}
else {
@array=split(" ", $line);
$key = $array[0];
$residue_hash{$key}=$line;
if ($key =~ m/FORMUL/) {
last;
}
}
$line =<IN>;
}
@formula_split=split(" ", $residue_hash{FORMUL});
$contains_carbon=0;
$contains_oxygen=0;
for ($i=0; $i <= scalar(@formula_split); $i++) {
$line_part=$formula_split[$i];
if ($resn eq "ASP") { print $line_part."\n"; }
if ($line_part =~ /^C/ && $line_part !~ /^C[A-Z]/) {
$contains_carbon=1;
}
if ($line_part =~ /^O/ && $line_part !~ /^O[A-Z]/) {
$contains_oxygen=1;
}
}
if ($resn eq "ASP") { print $contains_carbon.$contains_oxygen."\n"; }
if ($contains_oxygen==1 && $contains_carbon==1) {
for ($i=0; $i <= scalar(%residue_hash); $i++) {
$line=$residue_hash{$i};
$conect=substr($line, 0, 11);
$atom=substr($line, 11, 4);
$num_bonded_atoms=substr($line, 15, 5);
$bonded_atom_1=substr($line, 20, 4);
$bonded_atom_2=substr($line, 25, 4);
$bonded_atom_3=substr($line, 30, 4);
$bonded_atom_4=substr($line, 35, 4);
$bonded_atom_5=substr($line, 40, 4);
$bonded_atom_6=substr($line, 45, 4);
$bonded_atom_7=substr($line, 50, 4);
$bonded_atom_8=substr($line, 55, 4);
$bonded_atom_9=substr($line, 60, 4);
$bonded_atom_10=substr($line, 65, 4);
if ($atom =~ /C/ && $bonded_atom_1 && $bonded_atom_2 && $bonded_atom_3 && !($bonded_atom_4)) { # potential sp2 Carbon
$start=substr($atom, 0,2);
$second=substr($atom,1,1);
if ($second eq "C" && !( $start eq "SC" || $start eq "AC" || $start eq "TC" )) { # validate carbon
$start=substr($bonded_atom_1, 0,2);
$second=substr($bonded_atom_1,1,1);
if ($second eq "C" && !( $start eq "SC" || $start eq "AC" || $start eq "TC" )) { # validate first bonded partner as carbon
$start=substr($bonded_atom_2, 0,2);
$second=substr($bonded_atom_2,1,1);
if ($second eq "O" && !( $start eq "CO" || $start eq "MO" || $start eq "PO" )) { # validate second bonded partner as oxygen
$start=substr($bonded_atom_3, 0,2);
$second=substr($bonded_atom_3,1,1);
if ($second eq "O" && !( $start eq "CO" || $start eq "MO" || $start eq "PO" )) { # validate third bonded partner as oxygen
$oxygen_1 = $bonded_atom_2;
$oxygen_2 = $bonded_atom_3;
$oxygen_1_line = $atom_name_hash{$oxygen_1};
$oxygen_2_line = $atom_name_hash{$oxygen_2};
$num_bonded_atoms_1=substr($oxygen_1_line, 15, 5)+0;
$num_bonded_atoms_2=substr($oxygen_2_line, 15, 5)+0;
$num_bonded_atoms=$num_bonded_atoms_1 + $num_bonded_atoms_2;
$bonded_atom_11=substr($oxygen_1_line, 20, 4);
$bonded_atom_12=substr($oxygen_1_line, 25, 4);
$bonded_atom_21=substr($oxygen_2_line, 20, 4);
$bonded_atom_22=substr($oxygen_2_line, 25, 4);
if ( ($num_bonded_atoms == 3 || $num_bonded_atoms == 4) && ($bonded_atom_11 eq $bonded_atom_21 && $bonded_atom_11 eq $atom) && ($bonded_atom_12 || $bonded_atom_22) )
{
if ($bonded_atom_12 && $bonded_atom_22) {
$start=substr($bonded_atom_12, 0,2);
$first=substr($bonded_atom_12, 0,1);
if (($start eq " H") ||
($first eq "H" and resn !~ m/ HG|HG2|HGB|HGC|HGI|MAC|MBO|MMC|PHG|PMB|AAS|AMS|BE7|CMH|EMC|EMT|PHF|HF3|HF5| HO|HO3/))
{
$start=substr($bonded_atom_22, 0,2);
$first=substr($bonded_atom_22, 0,1);
if (($start eq " H") ||
($first eq "H" and resn !~ m/ HG|HG2|HGB|HGC|HGI|MAC|MBO|MMC|PHG|PMB|AAS|AMS|BE7|CMH|EMC|EMT|PHF|HF3|HF5| HO|HO3/))
{
print OUT $resn." ".$bonded_atom_12."\n";
print OUT $resn." ".$bonded_atom_22."\n";
}
}
}
elsif ($bonded_atom_12) {
$start=substr($bonded_atom_12, 0,2);
$first=substr($bonded_atom_12, 0,1);
if (($start eq " H") ||
($first eq "H" and resn !~ m/ HG|HG2|HGB|HGC|HGI|MAC|MBO|MMC|PHG|PMB|AAS|AMS|BE7|CMH|EMC|EMT|PHF|HF3|HF5| HO|HO3/))
{
print OUT $resn." ".$bonded_atom_12."\n";
}
}
else {
$start=substr($bonded_atom_22, 0,2);
$first=substr($bonded_atom_22, 0,1);
if (($start eq " H") ||
($first eq "H" and resn !~ m/ HG|HG2|HGB|HGC|HGI|MAC|MBO|MMC|PHG|PMB|AAS|AMS|BE7|CMH|EMC|EMT|PHF|HF3|HF5| HO|HO3/))
{
print OUT $resn." ".$bonded_atom_22."\n";
}
}
}
}
}
}
}
}
}
}
}
close IN;
close OUT;
open IN, "<temp";
%to_be_commented_hash=();
while ($line=<IN>) {
chomp($line);
$to_be_commented_hash{$line}="bad";
}
close IN;
open DICT, "<$ARGV[0]";
open OUT, ">$ARGV[0]_mod";
while ($line=<DICT>) {
if ($line !~ m/RESIDUE/ && $line !~ m/CONECT/) {
print OUT $line;
next;
}
if ($line =~ m/RESIDUE/) { $resn=substr($line, 10, 3); }
$atom=substr($line, 11, 4);
$key=$resn." ".$atom;
if ($to_be_commented_hash{$key}) {
$line="xx".$line;
}
print OUT $line;
}
close DICT;
close OUT;