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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

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::Chain->new( 
                           -id  => 'human_id',
                           -accession_number => 'AL000012',
                                           );

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

residue()

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

add_residue()

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

model()

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

id()

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

_remove_residues()

 Title   : _remove_residues
 Usage   : 
 Function: 
 Returns : 
 Args    :

_remove_model()

 Title   : _remove_model
 Usage   : 
 Function: Removes the Model this Chain is atttached to.
 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::Chain
#
# 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::Chain;
use strict;

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



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
}


#
# from here on only private methods
#


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'};
}

1;