File Coverage

blib/lib/Chemistry/File/MidasPattern.pm

Criterion	Covered	Total	%
statement	16	16	100.0
branch			n/a
condition			n/a
subroutine	5	5	100.0
pod	1	1	100.0
total	22	22	100.0

package Chemistry::File::MidasPattern;

$VERSION = '0.11';

=head1 NAME

Chemistry::File::MidasPattern - Wrapper Chemistry::File class for Midas patterns

=head1 SYNOPSIS

    use Chemistry::File::MidasPattern;
    use Chemistry::File::PDB;

    # read a molecule
    my $mol = Chemistry::MacroMol->read("test.pdb");

    # define a pattern matching carbons alpha and beta
    # in all valine residues
    my $str  = ':VAL@CA,CB';
    my $patt = Chemistry::MidasPattern->parse($str, format => 'midas');
    # Chemistry::Mol->parse($str, format => 'midas') also works

    # apply the pattern to the molecule
    $patt->match($mol);

    # extract the results
    for my $atom ($patt->atom_map) {
        printf "%s\t%s\n",  $atom->attr("pdb/residue_name"), $atom->name;
    }
    printf "FOUND %d atoms\n", scalar($patt->atom_map);

=head1 DESCRIPTION

This is a wrapper class for reading Midas Patterns using the standard
Chemistry::Mol I/O interface. This allows Midas patterns to be used
interchangeably with other pattern languages such as SMARTS in the context of
programs such as L. All of the real work is done by
L.

This module register the 'midas' format with Chemistry::Mol.

=cut

use strict;
use warnings;
use base "Chemistry::File";
use Chemistry::MidasPattern;

Chemistry::Mol->register_format(midas => __PACKAGE__);

sub parse_string {
    my ($self, $s, %opts) = @_;
    my $patt = Chemistry::MidasPattern->new($s);
    $patt->options(%opts);
    $patt;
}

1;

=head1 VERSION

0.11

=head1 SEE ALSO

L, L, L,
L, L.

The PerlMol website L

=head1 AUTHOR

Ivan Tubert [e-mail]

=head1 COPYRIGHT

Copyright (c) 2005 Ivan Tubert. All rights reserved. This program is free
software; you can redistribute it and/or modify it under the same terms as
Perl itself.

=cut