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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  #add synopsis here

DESCRIPTION

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This object stores a Bio::Structure::Residue

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   : $residue = Bio::Structure::Residue->new( 
                                           -id  => 'human_id',
                                           );

 Function: Returns a new Bio::Structure::Residue object from basic 
	constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Residue object

atom()

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

add_atom()

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

chain()

 Title   : chain
 Usage   : $chain = $residue->chain($chain)
 Function: Sets the Chain this Residue belongs to
 Returns : Returns the Chain this Residue belongs to
 Args    : reference to a Chain

id()

 Title   : id
 Usage   : $residue->id("TRP-35")
 Function: Gets/sets the ID for this residue
 Returns : the ID
 Args    : the ID

DESTROY()

 Title   : DESTROY
 Usage   : 
 Function: destructor ( get rid of circular references )
 Returns : 
 Args    :

_remove_atoms()

 Title   : _remove_atoms
 Usage   : 
 Function: Removes the atoms attached to a Residue. Tells the atoms they
 	don't belong to this Residue any more
 Returns : 
 Args    :

_remove_chain()

 Title   : _remove_chain
 Usage   : 
 Function: Removes the Chain this Residue 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::Residue
#
# 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::Residue;
use strict;

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




sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id, $atom ) =
        $self->_rearrange([qw(
			      ID
			      ATOM
                              )],
                          @args);

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

    $self->{'atom'} = [];

    # the 'smallest' (and only) item that can be added to a residue is an atom 

    $atom && $self->throw("add atoms via an Entry object entry->add_atom(residue,atom)\n");

    return $self;
}




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

	$self->throw("no code down here, go see an Entry object nearby\n");
}



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

	$self->throw("nothing here, use a method on an Entry object\n");
}



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

	$self->throw("use an Entry based method 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_atoms {
	my ($self) = shift;

	$self->throw("no code here\n");
}



sub _remove_chain {
	my ($self) = shift;

	$self->{'chain'} = undef;
}



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;