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

	$self->throw("go via an Entry object\n");
}
add_chaindescriptionprevnextTop
sub add_chain {
	my ($self,$value) = @_;

	$self->throw("go via an Entry object for now\n");
}
entrydescriptionprevnextTop
sub entry {
	my($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 $self->{'id'};
}
residuedescriptionprevnextTop
sub residue {
	my ($self, @args) = @_;

	$self->throw("need to go via Entry object or learn symbolic refs\n");
}
add_residuedescriptionprevnextTop
sub add_residue {
	my ($self, @args) = @_;

	$self->throw("go via entry->add_residue(chain, residue)\n");
}
DESTROYdescriptionprevnextTop
sub DESTROY {
	my $self = shift;

	# no specific DESTROY for now
} #
# from here on only private methods
#
}
_remove_chainsdescriptionprevnextTop
sub _remove_chains {
	my ($self) = shift;

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

	$self->throw("use a method based on an Entry object\n");
}
_create_default_chaindescriptionprevnextTop
sub _create_default_chain {
	my ($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;
}
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the web:
  https://redmine.open-bio.org/projects/bioperl/
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 _