Chemistry::Domain - Class for domains in macromolecules
use Chemistry::Domain; my $domain = Chemistry::Domain->new(parent => $bigmol);
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.
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.
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.
Ivan Tubert, <firstname.lastname@example.org>
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.