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    print $atom->attr("pdb/residue_name"); # prints "ALA123"

=head1 Molecule subclasses

You can do lots of interesting thing with plain molecules. However, for some
applications you may want to extend the features of the main Chemistry::Mol
class. There are several subclasses of Chemistry::Mol available already:

=over

=item L<Chemistry::MacroMol>

Used for macromolecules.

=item L<Chemistry::Pattern>

Used for substructure matching.

=item L<Chemistry::Ring>

Used for representing rings (cycles) in molecules.

=item L<Chemistry::Reaction>

Used for representing and applying chemical transformations.

=back

As an example we'll discuss macromolecules. Future versions of this tutorial
may also include a discussion about patterns and rings.

=head1 Macromolecules

So far we have assumed that we are dealing with molecules of the
L<Chemistry::Mol> class.  However, one of the interesting things about
object-oriented programming is that classes can be extended. For dealing with
macromolecules, we have the MacroMol class, which extends the L<Chemistry::Mol>
class. This means that in practice you can use a L<Chemistry::MacroMol> object
exactly as you would use a L<Chemistry::Mol> object, but with some added
functionality. In fact, the PDB reader can return L<Chemistry::MacroMol>
instead of L<Chemistry::Mol> objects just by changing the first example like
this:

    use Chemistry::MacroMol;
    use Chemistry::File::PDB;
    my $macromol = Chemistry::MacroMol->read("test.pdb");

Now the question is, what is the "added functionality" that MacroMol objects
have on top of the original Chemistry::Mol object?

=head2 The MacroMol object

For the purposes of this module, a macromolecule is considered to be a big
molecule where atoms are divided in I<Domains>. A domain is just a subset of
the atoms in the molecule; in a protein, a domain would be just a residue.

You can select domains in a molecule in a way similar to that used for atoms
and bonds, in this case through the C<domains> method:

    my @all_domains = $macromol->domains;
    my $domain      = $macromol->domains(57);

Tutorial.pod  view on Meta::CPAN

0.38

=head1 SOURCE CODE REPOSITORY

L<https://github.com/perlmol/Chemistry-Mol>

=head1 SEE ALSO

L<Chemistry::Mol>, L<Chemistry::Atom>, L<Chemistry::Bond>, L<Chemistry::File>,
L<Chemistry::MacroMol>, L<Chemistry::Domain>.

=head1 AUTHOR

Ivan Tubert-Brohman E<lt>itub@cpan.orgE<gt>

=head1 COPYRIGHT

Copyright (c) 2005 Ivan Tubert-Brohman. All rights reserved. This program is
free software; you can redistribute it and/or modify it under the same terms as
Perl itself.