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| Chemistry::File::MidasPattern(3) | User Contributed Perl Documentation | Chemistry::File::MidasPattern(3) |
NAME
Chemistry::File::MidasPattern - Wrapper Chemistry::File class for Midas patternsSYNOPSIS
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
0.11SEE 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.| 2005-05-16 | perl v5.32.1 |
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