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

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Module Version: 0.06   Source  

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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