Permalink
Find file
Fetching contributors…
Cannot retrieve contributors at this time
executable file 184 lines (137 sloc) 4.54 KB
#!/usr/bin/perl
use strict;
# This program will read in an NMR derived PDB file containing
# multiple conformers, and will allow the user to extract either
# one or all of the models to separate files.
#
# Although the program will run interactively, the command line
# usage is "nmrsplit [input.file] [number of model to extract]"
#
#
#
# Written 13/12/00 by Simon Andrews (simon.andrews@bbsrc.ac.uk)
# Submitted to bioperl script project 2001/08/06
# Description: Script which reads an NMR-derived multiple structure
# PDB file, and will either extract a single structure from it, or
# will extract all of the structures into single files. This is
# useful when you want to work with a single representative structure
# from an NMR ensemble - especially in conjunction with the OLDERADO
# database (http://neon.chem.le.ac.uk/olderado/) which finds the
# most representative structure from an ensemble.
my $Input = $ARGV[0]; # File to be read
my $Pullout = $ARGV[1]; # Specific model to extract
my @Pdbfile; # Array for whole PDB file
my $Header = ""; # String to hold the PDB header
my $Model = ""; # String to hold individual models
my $Output; # Prefix for output files
my $Modno = 1; # Number of the model being processed
while () {
if ($Input) {
if (-r $Input) {
last;
}else{
print "\"$Input\" does not exist, or could not be read\n";
}
}
print "\nEnter name of multiple PDB file: ";
$Input = <STDIN>;
chomp $Input;
$Input =~ s/^\s*//;
$Input =~ s/\s*$//;
next;
}
while () {
if ($Pullout) {
if ($Pullout =~ /^\d+$/){
if ($Pullout == int $Pullout) {
last;
}else {
print "\"$Pullout\" should be an integer\n";
}
}else {
print "\"$Pullout\" should be a number\n";
}
}
print "\nEnter number of specific model to extract (Return for none): ";
$Pullout = <STDIN>;
chomp $Pullout;
$Pullout =~ s/^\s*//;
$Pullout =~ s/\s*$//;
last unless ($Pullout);
next;
}
($Output = $Input) =~ s/\.\w*$//; # Take off everything after the last . to use as prefix
open (PDB,$Input) || die "Can't open $Input because $!";
########## Read the header information ####################
while (<PDB>) {
if (/^MODEL\b/){last;}
$Header = $Header . $_;
}
######### Read the separate models #######################
while () {
model();
if ($Model) { # Check if we're past the last model
if ($Pullout) { # Check if we're writing one or all
last if ($Modno > $Pullout);# No point continuing if we've got the one we want
readout();
}else {
writeout();
}
$Model = "";
++$Modno;
}else {
last;
}
}
--$Modno; # Correct last increment which didn't find a model
if (($Pullout) & ($Modno < $Pullout)) {
print "\nCannot find model $Pullout : Only $Modno models in this file\n";
}
#################### subroutines start here ##########################
sub model {
while (<PDB>) {
if (/^(MODEL\b|END\b|MASTER\b)/){next;}
# Stops you getting MODEL... at the top of the output
# and makes sure there isn't a file containing just END or MASTER
if (/^ENDMDL\b/){last;} # Check for the end of the model
$Model = $Model . $_; # Append the line to $Model
}
}
sub writeout { # Used when all files are being written out
if (-e "$Output\_$Modno.pdb"){ # Check whether we're overwriting anything
print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? ";
my $Question = <STDIN>;
unless ($Question =~ /^y/i) {
print "\nSkipping $Output\_$Modno.pdb";
return;
}
}
open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!";
print "\nWriting $Output\_$Modno.pdb ...";
print OUT $Header;
print OUT $Model;
print OUT "END\n"; # Adds and END statement to the PDB file
close OUT || die "Couldn't close $Output\_$Modno.pdb because $!";
}
sub readout {
if ($Modno == $Pullout) {
if (-e "$Output\_$Modno.pdb") { # Check whether we're overwriting anything
print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? ";
my $Question = <STDIN>;
unless ($Question =~ /^y/i) {
print "\nModel not extracted\n";
$Model = "";
return;
}
}
open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!";
print "\nWriting $Output\_$Modno.pdb ...\n";
print OUT $Header;
print OUT $Model;
print OUT "END\n"; # Adds and END statement to the PDB file
close OUT || die "Couldn't close $Output\_$Modno.pdb because $!";
$Model = ""; # Stops the reading after this model
}else {
print "\nReading Model $Modno ...";
}
}