Bio::Structure::Residue.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   #add synopsis here
 
 

DESCRIPTION

This object stores a Bio::Structure::Residue

FEEDBACK

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Kris Boulez

Email kris.boulez@algonomics.com

APPENDIX

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 usefull untill I get symbolic references to do what I want
  Returns : 
  Args    :
 
 

add_atom()

  Title   : add_atom
  Usage   : 
  Function:  nothing usefull 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    :