Chemistry-File-PDB
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# http://module-build.sourceforge.net/META-spec.html
#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#
name: Chemistry-File-PDB
version: 0.23
version_from: PDB.pm
installdirs: site
requires:
Chemistry::MacroMol: 0.05
Chemistry::Mol: 0.30
distribution_type: module
generated_by: ExtUtils::MakeMaker version 6.30
Makefile.PL view on Meta::CPAN
use 5.006;
use ExtUtils::MakeMaker;
WriteMakefile(
'NAME' => 'Chemistry::File::PDB',
'VERSION_FROM' => 'PDB.pm',
'PREREQ_PM' => {
'Chemistry::MacroMol' => 0.05,
'Chemistry::Mol' => '0.30',
},
);
package Chemistry::File::PDB;
our $VERSION = '0.23';
# $Id: PDB.pm,v 1.13 2009/05/10 21:57:32 itubert Exp $
use base qw(Chemistry::File);
use Chemistry::MacroMol;
use Chemistry::Domain;
use Scalar::Util qw(weaken);
use Carp;
use strict;
use warnings;
=head1 NAME
Chemistry::File::PDB - Protein Data Bank file format reader/writer
=head1 SYNOPSIS
use Chemistry::File::PDB;
# read a PDB file
my $macro_mol = Chemistry::MacroMol->read("myfile.pdb");
# write a PDB file
$macro_mol->write("out.pdb");
# read all models in a multi-model file
my @mols = Chemistry::MacroMol->read("models.pdb");
# read one model at a time
my $file = Chemistry::MacroMol->file("models.pdb");
$file->open;
while (my $mol = $file->read_mol($file->fh)) {
# do something with $mol
}
=cut
=head1 DESCRIPTION
This module reads and writes PDB files. The PDB file format is commonly used to
ATOM
HETATM
ENDMDL
END
This module automatically registers the 'pdb' format with Chemistry::Mol,
so that PDB files may be identified and read by Chemistry::Mol->read(). For
autodetection purpuses, it assumes that files ending in .pdb or having
a line matching /^(ATOM |HETATM)/ are PDB files.
The PDB reader and writer is designed for dealing with Chemistry::MacroMol
objects, but it can also create and use Chemistry::Mol objects by throwing some
information away.
=head2 Properties
When reading and writing files, this module stores or gets some of the
information in the following places:
=over
=cut
Chemistry::Mol->register_format(pdb => __PACKAGE__);
sub read_mol {
my ($self, $fh, %options) = @_;
return if $fh->eof;
my $domain;
my $mol_class = $options{mol_class} || "Chemistry::MacroMol";
my $mol = $mol_class->new;
my $is_macro = $mol->isa('Chemistry::MacroMol');
$domain = $mol unless $is_macro;
local $_;
my $curr_residue = 0;
while (<$fh>) {
if (/^TER/) {
# TODO read separated molecules?
} elsif (/^(?:HETATM|ATOM)/) {
my ($atom_n, $symbol, $suff, $res_name, $chain_id,
$seq_n, $ins_code, $x, $y, $z
}
return 0;
}
sub write_string {
my ($class, $mol, %opts) = @_;
my $ret = '';
$ret .= 'TITLE ' . $mol->name . "\n" if defined $mol->name;
$ret .= 'REMARK Generated by ' . __PACKAGE__ . " version $VERSION\n";
if ($mol->isa("Chemistry::MacroMol")) {
my $i = 1;
my $j = 1;
for my $res ($mol->domains) {
my $seq_n = $res->attr("pdb/sequence_number");
$seq_n = $j++ unless defined $seq_n;
my $res_name = substr($res->name, 0, 3) || "UNK";
for my $atom ($res->atoms) {
my $serial_n = $res->attr("pdb/serial_number");
my $ins_code = $res->attr("pdb/insertion_code");
}
1;
=head1 VERSION
0.23
=head1 SEE ALSO
L<Chemistry::MacroMol>, L<Chemistry::Mol>, L<Chemistry::File>,
L<http://www.perlmol.org/>.
The PDB format description at
L<http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html>
There is another PDB reader in Perl, as part of the BioPerl project:
L<Bio::Structure::IO::pdb>.
=head1 AUTHOR
This module reads and writes PDB files. The PDB file format is commonly used to
describe proteins, particularly those stored in the Protein Data Bank
(L<http://www.rcsb.org/pdb/>). The current version of this module only uses the
ATOM and HETATM records, ignoring everything else.
This module automatically registers the 'pdb' format with Chemistry::Mol,
so that PDB files may be identified and read by Chemistry::Mol->read(). For
autodetection purpuses, it assumes that files ending in .pdb or having
a line matching /^(ATOM |HETATM)/ are PDB files.
The PDB reader and writer is designed for dealing with Chemistry::MacroMol
objects, but it can also create and use Chemistry::Mol objects by throwing some
information away.
CHANGES SINCE VERSION 0.21
- Add unique ID to atom names when generating from a $mol object.
- Also treat END as a molecule separator in multi-molecule files.
- Fixed insertion code bug (thanks to kparkes).
- Fixed memory leak.
- Fixed a couple of atom symbol bugs.
- Add a title on output.
perl Makefile.PL
make
make test
make install
DEPENDENCIES
This module requires these other modules and libraries:
Chemistry::MacroMol 0.05
Chemistry::Mol 0.24
COPYRIGHT AND LICENSE
Copyright (C) 2009 Ivan Tubert-Brohman
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
use Test::More;
use Chemistry::File::PDB;
my $mol = Chemistry::Mol->read("test.pdb");
my $macromol = Chemistry::MacroMol->read("test.pdb");
plan tests => 9;
is(scalar($mol->atoms), 139, '$mol->atoms');
is(scalar($macromol->atoms), 139, '$macromol->atoms');
is(scalar($macromol->domains), 10, '$macromol->domains');
is($macromol->domains(4)->type, 'VAL', '$macromol->domains(4)->name');
is($macromol->domains(4)->name, 'VAL4', '$macromol->domains(4)->name');
is($mol->atoms(48)->name, 'CG1', '$mol->atoms(44)->name');
is($mol->atoms(48)->symbol, 'C', '$mol->atoms(44)->name');
#!/home/ivan/bin/perl
use strict;
use warnings;
use Test::More tests => 1;
use Chemistry::File::PDB;
my $mol = Chemistry::MacroMol->read("test.pdb");
$mol->write("out.pdb");
my ($got, $expected);
{
local $/;
open F, "<test.pdb" or die "couldn't open test.pdb: $!\n";
$expected = <F>;
open F, "<out.pdb" or die "couldn't open test.pdb: $!\n";
$got = <F>;
}
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