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=head2 Step 1: create a class that does ProteaseI.

    package My::Protease;
    use Moose;
    with 'Bio::ProteaseI';

    1;

Simply create a new Moose class, and consume the L<Bio::ProteaseI>
role.

=head2 Step 2: Implement a _cuts() method.

The C<_cuts> method will be used by the methods C<digest>, C<cut>,
C<cleavage_sites> and C<is_substrate>. It will B<always> be passed a
string of 8 characters; if the method returns true, then the peptide
bond between the 4th and 5th residues will be marked as siscile, and the
appropiate action will be performed depending on which method was
called.

Your specificity logic should only be concerned in deciding whether the
8-residue long peptide passed to it as an argument should be cut between
the 4th and 5th residues. This is done in the private C<_cuts> method,
like so:

    sub _cuts {
        my ( $self, $peptide ) = @_;

        # some code that decides
        # if $peptide should be cut or not

        if ( $peptide_should_be_cut ) { return 1 }
        else                          { return   }
    };

And that's it. Your class will be composed with all the methods
mentioned above, and will work according to the specificity logic that
you define in your C<_cuts()> method.

=head2 Example: a ridiculously specific protease

Suppose you want to model a protease that only cleaves the sequence
C<MAEL^VIKP>. Your Protease class would be like this:

    package My::Ridiculously::Specific::Protease;
    use Moose;
    with 'Bio::ProteaseI';

    sub _cuts {
        my ( $self, $substrate ) = @_;

        if ( $substrate eq 'MAELVIKP' ) { return 1 }
        else                            { return   }
    };

    1;

Then you can use your class easily in your application:

    #!/usr/bin/env perl
    use Modern::Perl;

    use My::Ridiculously::Specific::Protease;

    my $protease = My::Ridiculously::Specific::Protease->new;
    my @products = $protease->digest( 'AAAAMAELVIKPYYYYYYY' );

    say for @products; # ["AAAAMAEL", "VIKPYYYYYYY"]

Of course, this specificity model is too simple to deserve a new class,
as it could be perfectly defined by a regex and passed to the
C<specificity> attribute of L<Bio::Protease>. It's only used here as an
example.

=head1 AUTHOR

Bruno Vecchi <vecchi.b gmail.com>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Bruno Vecchi.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut