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Manual Reference Pages  -  CHEMISTRY::MACROMOL (3)

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NAME

Chemistry::MacroMol - Perl module for macromolecules

CONTENTS

SYNOPSIS



    use Chemistry::MacroMol;

    my $mol = Chemistry::MacroMol->new(name => my big molecule);
    $mol->new_domain(name => "ASP"); # see Chemistry::Domain for details
    my @domains = $mol->domains;



DESCRIPTION

For the purposes of this module, a macromolecule is just a molecule that consists of several domains. For example, a protein consists of aminoacid residues, or a nucleic acid consists of bases. Therefore Chemistry::MacroMol is derived from Chemistry::Mol, with additional methods to handle the domains.

The way things are currently structured, an atom in a macromolecule belong both to the MacroMol object and to a Domain object. This way you can get all the atoms in $protein via $protein->atoms, or to the atoms in residue 123 via $protein->domain(123)->atoms.

METHODS

Remember that this class inherits all the methods from Chemistry::Mol. They won’t be repeated here.
Chemistry::MacroMol->new(name => value, ...) Create a new MacroMol object with the specified attributes. You can use the same attributes as for Chemistry::Mol->new.
$mol->add_domain($domain, ...) Add one or more Domain objects to the molecule. Returns the last domain added.
$mol->domain_class Returns the domain class that a macromolecule class expects to use by default. Chemistry::MacroMol objects return Chemistry::Domain, but subclasses will likely override this method.
$mol->new_domain(name => value, ...) Shorthand for $mol->add_domain($mol->domain_class->new(parent => $mol, name => value, ...));
$mol->domains($n1, ...) Returns the domains with the given indices, or all by default. NOTE: the indices start from one (1), not from zero.

VERSION

0.06

SEE ALSO

Chemistry::Domain, Chemistry::Mol

AUTHOR

Ivan Tubert, <itub@cpan.org>

COPYRIGHT AND LICENSE

Copyright 2004 by Ivan Tubert

This library 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 MACROMOL (3) 2004-07-03

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