Bio::Structure Model
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Summary
Bio::Structure::Model - Bioperl structure Object, describes a Model
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Structure::Chain
Bio::Structure::Entry
Inherit
Bio::Root::Root
Synopsis
  #add synopsis here
Description
This object stores a Bio::Structure::Chain
Methods
DESTROY
No description
Code
_create_default_chainDescriptionCode
_grandparentDescriptionCode
_remove_chainsDescriptionCode
_remove_entryDescriptionCode
add_chainDescriptionCode
add_residueDescriptionCode
chainDescriptionCode
entryDescriptionCode
idDescriptionCode
newDescriptionCode
residueDescriptionCode
Methods description
_create_default_chain()code    nextTop
 Title   : _create_default_chain
 Usage   : 
 Function: Creates a default Chain for this Model. Typical situation
 	in an X-ray structure where there is only one chain
 Returns : 
 Args    :
_grandparent()codeprevnextTop
 Title   : _grandparent
 Usage   : 
 Function: get/set a symbolic reference to our grandparent
 Returns : 
 Args    :
_remove_chains()codeprevnextTop
 Title   : _remove_chains
 Usage   : 
 Function: Removes the chains attached to a Model. Tells the chains they
 	don't belong to this Model any more
 Returns : 
 Args    :
_remove_entry()codeprevnextTop
 Title   : _remove_entry
 Usage   : 
 Function: Removes the Entry this Model is atttached to.
 Returns : 
 Args    :
add_chain()codeprevnextTop
 Title   : add_chain
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :
add_residue()codeprevnextTop
 Title   : add_residue
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :
chain()codeprevnextTop
 Title   : chain
 Usage   : 
 Function: will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :
entry()codeprevnextTop
 Title   : entry
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :
id()codeprevnextTop
 Title   : id
 Usage   : $model->id("model 5")
 Function: Gets/sets the ID for this model
 Returns : the ID
 Args    : the ID
new()codeprevnextTop
 Title   : new()
 Usage   : $struc = Bio::Structure::Model->new( 
                                           -id  => 'human_id',
                                           );

 Function: Returns a new Bio::Structure::Model object from basic 
	constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Model object
residue()codeprevnextTop
 Title   : residue
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :
Methods code
DESTROYdescriptionprevnextTop
sub DESTROY {
	my $self = shift;

	# no specific DESTROY for now
}

#
# from here on only private methods
#
}
_create_default_chaindescriptionprevnextTop
sub _create_default_chain {
	my ($self) = shift;

	my $chain = Bio::Structure::Chain->new(-id => "default");
}
_grandparentdescriptionprevnextTop
sub _grandparent {
	my($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;
}
_remove_chainsdescriptionprevnextTop
sub _remove_chains {
	my ($self) = shift;

	$self->throw("use Entry methods pleae\n");
}
_remove_entrydescriptionprevnextTop
sub _remove_entry {
	my ($self) = shift;

	$self->throw("use a method based on an Entry object\n");
}
add_chaindescriptionprevnextTop
sub add_chain {
	my ($self,$value) = @_;

	$self->throw("go via an Entry object for now\n");
}
add_residuedescriptionprevnextTop
sub add_residue {
	my ($self, @args) = @_;

	$self->throw("go via entry->add_residue(chain, residue)\n");
}
chaindescriptionprevnextTop
sub chain {
	my ($self,$value) = @_;

	$self->throw("go via an Entry object\n");
}
entrydescriptionprevnextTop
sub entry {
	my($self) = @_;

	$self->throw("Model::entry go via an Entry object please\n");
}
iddescriptionprevnextTop
sub id {
	my ($self, $value) = @_;;
	if (defined $value) {
		$self->{'id'} = $value;
	}
	return $self->{'id'};
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

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

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

    $chain && $self->throw("you have to add chain via an Entry object\n");

    $residue && $self->throw("you have to add residues via an Entry object\n");

    return $self;
}
residuedescriptionprevnextTop
sub residue {
	my ($self, @args) = @_;

	$self->throw("need to go via Entry object or learn symbolic refs\n");
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 BugsTop
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/
AUTHOR - Kris BoulezTop
Email kris.boulez@algonomics.com
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _