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.
- $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.
Chemistry::MacroMol, Chemistry::Mol, Chemistry::Atom, Chemistry::Bond
Ivan Tubert, <itub@cpan.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.