Ivan Tubert-Brohman

NAME

Chemistry::Domain - Class for domains in macromolecules

SYNOPSIS

  use Chemistry::Domain;
  my $domain = Chemistry::Domain->new(parent => $bigmol);

DESCRIPTION

A domain is a substructure of a larger molecule. It is typically used to represent aminoacid residues within a protein, or bases within a nucleic acid, but you could use it for any arbitrary substructure such as functional groups and rings. A domain has all the properties of a molecule, plus a "parent". The parent is the larger molecule that contains the domain. In other words, the Chemistry::Domain class inherits from Chemistry::Mol.

METHODS

Note: the methods that are inherited from Chemistry::Mol are not repeated here.

Chemistry::Domain->new(parent => $mol, name => value, ...)

Create a new Domain object with the specified attributes. You can use the same attributes as for Chemistry::Mol->new, plus the parent attribute, which is required.

$domain->parent

Returns the parent of the domain.

$domain->add_atom($atom, ...)

Add one or more Atom objects to the domain. Returns the last atom added. It also automatically adds the atoms to the atom table of the parent molecule.

$domain->add_bond($bond, ...)

Add one or more Bond objects to the domain. Returns the last bond added. It also automatically adds the bond to the bond table of the parent molecule.

VERSION

0.06

SEE ALSO

Chemistry::MacroMol, Chemistry::Mol, Chemistry::Atom, Chemistry::Bond

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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