Chemistry::File::MidasPattern - Wrapper Chemistry::File class for Midas patterns
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);
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.
0.11
Chemistry::MidasPattern, Chemistry::File, Chemistry::Mol, Chemistry::MacroMol, mok.
The PerlMol website http://www.perlmol.org/
Ivan Tubert <itub@cpan.org>
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.
To install Chemistry::MidasPattern, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Chemistry::MidasPattern
CPAN shell
perl -MCPAN -e shell install Chemistry::MidasPattern
For more information on module installation, please visit the detailed CPAN module installation guide.