Bio::Structure::Model - Bioperl structure Object, describes a Model

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Structure::Model - Bioperl structure Object, describes a Model

SYNOPSIS

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  #add synopsis here

DESCRIPTION

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This object stores a Bio::Structure::Chain

FEEDBACK

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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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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 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 the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Kris Boulez

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Email kris.boulez@algonomics.com

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

chain()

 Title   : chain
 Usage   : 
 Function: will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :

add_chain()

 Title   : add_chain
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :

entry()

 Title   : entry
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :

id()

 Title   : id
 Usage   : $model->id("model 5")
 Function: Gets/sets the ID for this model
 Returns : the ID
 Args    : the ID

residue()

 Title   : residue
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :

add_residue()

 Title   : add_residue
 Usage   : 
 Function:  will eventually allow parent/child navigation not via an Entry object
 Returns : 
 Args    :

_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    :

_remove_entry()

 Title   : _remove_entry
 Usage   : 
 Function: Removes the Entry this Model is atttached to.
 Returns : 
 Args    :

_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    :

_grandparent()

 Title   : _grandparent
 Usage   : 
 Function: get/set a symbolic reference to our grandparent
 Returns : 
 Args    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# bioperl module for Bio::Structure::Model
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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



# Let the code begin...

package Bio::Structure::Model;
use strict;

use Bio::Structure::Entry;
use Bio::Structure::Chain;
use base qw(Bio::Root::Root);





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;
}




sub chain {
	my ($self,$value) = @_;

	$self->throw("go via an Entry object\n");
}



sub add_chain {
	my ($self,$value) = @_;

	$self->throw("go via an Entry object for now\n");
}


sub entry {
	my($self) = @_;

	$self->throw("Model::entry go via an Entry object please\n");
}



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


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

	$self->throw("need to go via Entry object or learn symbolic refs\n");
}



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
#


sub _remove_chains {
	my ($self) = shift;

	$self->throw("use Entry methods pleae\n");
}



sub _remove_entry {
	my ($self) = shift;

	$self->throw("use a method based on an Entry object\n");
}



sub _create_default_chain {
	my ($self) = shift;

	my $chain = Bio::Structure::Chain->new(-id => "default");
}



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;