I need a script that will take a pdb file with discontinuities and will give a pdb file with the same format but with a continuous res number
I'm assuming here that every time the residue name changes, the residue number is incremented. And in fact, that later on, the same residue name may occur again (with some intervening lines with different residue names), but should have a different number.
I would rework your original script to something like this.
#!/usr/bin/env perl
# Read a PDB file and change the residue numbers to be continuous.
use strict;
use warnings;
print "\nEnter the PDB input file: ";
my $inputFile = <STDIN>;
chomp $inputFile;
unless (open(INPUTFILE, "<", $inputFile)) {
die "Cannot read from <$inputFile>, $!";
}
my $output_file = "my2pdb.txt";
open(PDBOUT,">>my2pdb.txt")
or die "Cannot open <$output_file> for writing, $!";
my $last_residue_name = '';
my $last_residue_number = 0;
while (<INPUTFILE>) {
if (m/^ATOM/) {
my @m = split;
# Increment the residue number if the residue name changes
if ($m[3] eq $last_residue_name) {
$m[5] = $last_residue_number;
} else {
$m[5] = ++$last_residue_number;
$last_residue_name = $m[3];
}
printf PDBOUT "%4s %5s %4s %3s %1s %4s %7s %7s %7s %6s %6s
+\n", @m;
}
}
exit;
Here's the input file I used:
ATOM 310 1HH2 ARG A 607 -31.278 29.882 25.723 1.00 99.99
ATOM 311 2HH2 ARG A 607 -32.344 30.932 24.851 1.00 99.99
ATOM 312 N LEU A 608 -36.327 31.914 18.187 1.00 65.62
ATOM 313 CA LEU A 608 -37.435 32.634 17.559 1.00 67.47
ATOM 314 C LEU A 608 -38.434 33.052 18.624 1.00 74.29
ATOM 315 O LEU A 608 -38.982 32.201 19.331 1.00 71.12
ATOM 316 CB LEU A 608 -38.110 31.803 16.459 1.00 64.64
ATOM 317 CG LEU A 608 -39.261 32.481 15.719 1.00 71.07
ATOM 318 CD1 LEU A 608 -38.782 33.704 14.929 1.00 73.68
ATOM 319 CD2 LEU A 608 -39.981 31.498 14.829 1.00 69.63
ATOM 320 H LEU A 608 -36.638 31.041 18.563 1.00 99.99
ATOM 321 N ARG A 565 -38.634 34.587 18.911 1.00 22.27
ATOM 322 CA ARG A 565 -39.655 35.200 19.766 1.00 23.04
ATOM 323 C ARG A 565 -40.963 35.104 19.007 1.00 22.72
ATOM 324 O ARG A 565 -41.046 35.500 17.847 1.00 24.21
ATOM 325 CB ARG A 565 -39.275 36.643 20.105 1.00 99.99
ATOM 326 CG ARG A 565 -38.044 36.770 20.986 1.00 99.99
And here's the output I got (note that column 5 is included, unlike your initial example):
ATOM 310 1HH2 ARG A 1 -31.278 29.882 25.723 1.00 99.99
ATOM 311 2HH2 ARG A 1 -32.344 30.932 24.851 1.00 99.99
ATOM 312 N LEU A 2 -36.327 31.914 18.187 1.00 65.62
ATOM 313 CA LEU A 2 -37.435 32.634 17.559 1.00 67.47
ATOM 314 C LEU A 2 -38.434 33.052 18.624 1.00 74.29
ATOM 315 O LEU A 2 -38.982 32.201 19.331 1.00 71.12
ATOM 316 CB LEU A 2 -38.110 31.803 16.459 1.00 64.64
ATOM 317 CG LEU A 2 -39.261 32.481 15.719 1.00 71.07
ATOM 318 CD1 LEU A 2 -38.782 33.704 14.929 1.00 73.68
ATOM 319 CD2 LEU A 2 -39.981 31.498 14.829 1.00 69.63
ATOM 320 H LEU A 2 -36.638 31.041 18.563 1.00 99.99
ATOM 321 N ARG A 3 -38.634 34.587 18.911 1.00 22.27
ATOM 322 CA ARG A 3 -39.655 35.200 19.766 1.00 23.04
ATOM 323 C ARG A 3 -40.963 35.104 19.007 1.00 22.72
ATOM 324 O ARG A 3 -41.046 35.500 17.847 1.00 24.21
ATOM 325 CB ARG A 3 -39.275 36.643 20.105 1.00 99.99
ATOM 326 CG ARG A 3 -38.044 36.770 20.986 1.00 99.99
(I don't do formats, you'll have to figure that out for yourself.)
Now that still begs the question of whether you wanted the entire input file written to the output, or just the ATOM section.
I'm assuming I've missed several hints about the final output, but this is the basic structure.
-QM
--
Quantum Mechanics: The dreams stuff is made of
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