Ivan Tubert-Brohman > Chemistry-MacroMol-0.06 > Chemistry::MacroMol

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Module Version: 0.06   Source  

NAME ^

Chemistry::MacroMol - Perl module for macromolecules

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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