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Summary

Bio::Structure::Residue - Bioperl structure Object, describes a Residue

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  #add synopsis here

Description

This object stores a Bio::Structure::Residue

Methods

Methods description

 Title   : DESTROY
 Usage   : 
 Function: destructor ( get rid of circular references )
 Returns : 
 Args    :

 Title   : _grandparent
 Usage   : 
 Function: get/set a symbolic reference to our grandparent
 Returns : 
 Args    :

 Title   : _remove_atoms
 Usage   : 
 Function: Removes the atoms attached to a Residue. Tells the atoms they
 	don't belong to this Residue any more
 Returns : 
 Args    :

 Title   : _remove_chain
 Usage   : 
 Function: Removes the Chain this Residue is atttached to.
 Returns : 
 Args    :

 Title   : add_atom
 Usage   : 
 Function:  nothing usefull untill I get symbolic references to do what I want
 Returns : 
 Args    :

 Title   : atom 
 Usage   : 
 Function:  nothing usefull untill I get symbolic references to do what I want
 Returns : 
 Args    :

 Title   : chain
 Usage   : $chain = $residue->chain($chain)
 Function: Sets the Chain this Residue belongs to
 Returns : Returns the Chain this Residue belongs to
 Args    : reference to a Chain

 Title   : id
 Usage   : $residue->id("TRP-35")
 Function: Gets/sets the ID for this residue
 Returns : the ID
 Args    : the ID

 Title   : new()
 Usage   : $residue = Bio::Structure::Residue->new( 
                                           -id  => 'human_id',
                                           );

 Function: Returns a new Bio::Structure::Residue object from basic 
	constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Residue object

Methods code

sub DESTROY {

	my $self = shift;

	# no specific destruction for now
}


#
# from here on only private methods
#

}

sub _grandparent {

	my($self,$symref) = @_;

	if (ref($symref)) {
		$self->throw("Thou shall only pass strings in here, no references $symref\n");
	}
	if (defined $symref) {
		$self->{'grandparent'} = $symref;
	}
	return $self->{'grandparent'};
}

1;

}

sub _remove_atoms {

	my ($self) = shift;

	$self->throw("no code here\n");

}

sub _remove_chain {

	my ($self) = shift;

	$self->{'chain'} = undef;

}

sub add_atom {

	my($self,$value) = @_;

	$self->throw("nothing here, use a method on an Entry object\n");

}

sub atom {

	my ($self,$value) = @_;

	$self->throw("no code down here, go see an Entry object nearby\n");

}

sub chain {

	my($self, $value) = @_;

	$self->throw("use an Entry based method please\n");

}

sub id {

        my ($self, $value) = @_;;
        if (defined $value) {
	        $self->{'id'} = $value;
        }
        return $self->{'id'};

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id, $atom ) =
        $self->_rearrange([qw(
			      ID
			      ATOM
                              )],
                          @args);

    $id      && $self->id($id);

    $self->{'atom'} = [];

    # the 'smallest' (and only) item that can be added to a residue is an atom 

    $atom && $self->throw("add atoms via an Entry object entry->add_atom(residue,atom)\n");

    return $self;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email kris.boulez@algonomics.com

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _