Summary

Bio::Structure::Chain - Bioperl structure Object, describes a chain

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  #add synopsis here

Description

This object stores a Bio::Structure::Chain

Methods

Methods description

 Title   : new()
 Usage   : $struc = Bio::Structure::Chain->new( 
                                           -id  => 'human_id',
                                           -accession_number => 'AL000012',
                                           );

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

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

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

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

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

 Title   : _remove_residues
 Usage   : 
 Function: 
 Returns : 
 Args    :

 Title   : _remove_model
 Usage   : 
 Function: Removes the Model this Chain is atttached to.
 Returns : 
 Args    :

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

Methods code

sub new {

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

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

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

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

    # the 'smallest' item that can be added to a chain is a residue. 

    $residue && $self->throw("use a method based on an Entry object for now");

    return $self;

}

sub residue {

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

	$self->throw("use a method on an Entry object to do what you want");

}

sub add_residue {

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

	$self->throw("you want entry->add_residue(chain, residue)\n");

}

sub model {

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

	$self->throw("go via a Entry object please\n");

}

sub id {

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

}

sub DESTROY {

	my $self = shift;
	
	# no specific destruction for now

}

sub _remove_residues {

	my ($self) = shift;

	$self->throw("nothing usefull in here, go see Entry\n");

}

sub _remove_model {

	my ($self) = shift;

	$self->throw("go see an Entry object, nothing here\n");

}

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

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
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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 _