Residue documentation.

 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

atom()

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

add_atom()

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

chain()

 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

id()

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

DESTROY()

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

_remove_atoms()

 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    :

_remove_chain()

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

_grandparent()

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

Methods code

new

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;

}

atom

sub atom {

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

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

}

add_atom

sub add_atom {

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

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

}

chain

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'};

}

DESTROY

sub DESTROY {

	my $self = shift;

	# no specific destruction for now

}

_remove_atoms

sub _remove_atoms {

	my ($self) = shift;

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

}

_remove_chain

sub _remove_chain {

	my ($self) = shift;

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

}

_grandparent

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'};

}

General documentation

FEEDBACK

Mailing Lists

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

Reporting Bugs

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://bio.perl.org/bioperl-bugs/

AUTHOR - Kris Boulez

Email kris.boulez@algonomics.com

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