Raw content of Bio::Structure::Model
<![CDATA[# $Id: Model.pm,v 1.6 2002/10/22 07:38:44 lapp Exp $
#
# bioperl module for Bio::Structure::Model
#
# Cared for by Kris Boulez <kris.boulez@algonomics.com>
#
# Copyright Kris Boulez
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Structure::Model - Bioperl structure Object, describes a Model
=head1 SYNOPSIS
#add synopsis here
=head1 DESCRIPTION
This object stores a Bio::Structure::Chain
=head1 FEEDBACK
=head2 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
=head2 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://bugzilla.bioperl.org/
=head1 AUTHOR - Kris Boulez
Email kris.boulez@algonomics.com
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Structure::Model;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Structure::Entry;
use Bio::Structure::Chain;
@ISA = qw(Bio::Root::Root);
=head2 new()
Title : new()
Usage : $struc = Bio::Structure::Model->new(
-id => 'human_id',
);
Function: Returns a new Bio::Structure::Model object from basic
constructors. Probably most called from Bio::Structure::IO.
Returns : a new Bio::Structure::Model object
=cut
sub new {
my ($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 $self;
}
=head2 chain()
Title : chain
Usage :
Function: will eventually allow parent/child navigation not via an Entry object
Returns :
Args :
=cut
sub chain {
my ($self,$value) = @_;
$self->throw("go via an Entry object\n");
}
=head2 add_chain()
Title : add_chain
Usage :
Function: will eventually allow parent/child navigation not via an Entry object
Returns :
Args :
=cut
sub add_chain {
my ($self,$value) = @_;
$self->throw("go via an Entry object for now\n");
}
=head2 entry()
Title : entry
Usage :
Function: will eventually allow parent/child navigation not via an Entry object
Returns :
Args :
=cut
sub entry {
my($self) = @_;
$self->throw("Model::entry go via an Entry object please\n");
}
=head2 id()
Title : id
Usage : $model->id("model 5")
Function: Gets/sets the ID for this model
Returns : the ID
Args : the ID
=cut
sub id {
my ($self, $value) = @_;;
if (defined $value) {
$self->{'id'} = $value;
}
return $self->{'id'};
}
=head2 residue()
Title : residue
Usage :
Function: will eventually allow parent/child navigation not via an Entry object
Returns :
Args :
=cut
sub residue {
my ($self, @args) = @_;
$self->throw("need to go via Entry object or learn symbolic refs\n");
}
=head2 add_residue()
Title : add_residue
Usage :
Function: will eventually allow parent/child navigation not via an Entry object
Returns :
Args :
=cut
sub add_residue {
my ($self, @args) = @_;
$self->throw("go via entry->add_residue(chain, residue)\n");
}
sub DESTROY {
my $self = shift;
# no specific DESTROY for now
}
#
# from here on only private methods
#
=head2 _remove_chains()
Title : _remove_chains
Usage :
Function: Removes the chains attached to a Model. Tells the chains they
don't belong to this Model any more
Returns :
Args :
=cut
sub _remove_chains {
my ($self) = shift;
$self->throw("use Entry methods pleae\n");
}
=head2 _remove_entry()
Title : _remove_entry
Usage :
Function: Removes the Entry this Model is atttached to.
Returns :
Args :
=cut
sub _remove_entry {
my ($self) = shift;
$self->throw("use a method based on an Entry object\n");
}
=head2 _create_default_chain()
Title : _create_default_chain
Usage :
Function: Creates a default Chain for this Model. Typical situation
in an X-ray structure where there is only one chain
Returns :
Args :
=cut
sub _create_default_chain {
my ($self) = shift;
my $chain = Bio::Structure::Chain->new(-id => "default");
}
=head2 _grandparent()
Title : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
=cut
sub _grandparent {
my($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;
]]>