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Manual Reference Pages  -  CHEMISTRY::FILE::MIDASPATTERN (3)

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NAME

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

CONTENTS

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);



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 mok. All of the real work is done by Chemistry::MidasPattern.

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

VERSION

0.11

SEE ALSO

Chemistry::MidasPattern, Chemistry::File, Chemistry::Mol, Chemistry::MacroMol, mok.

The PerlMol website <http://www.perlmol.org/>

AUTHOR

Ivan Tubert <itub@cpan.org>

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.
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perl v5.20.3 CHEMISTRY::FILE::MIDASPATTERN (3) 2005-05-16

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