diff variant_effect_predictor/Bio/Structure/Residue.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Structure/Residue.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,255 @@
+# $Id: Residue.pm,v 1.7 2002/10/22 07:38:44 lapp Exp $
+#
+# bioperl module for Bio::Structure::Residue
+#
+# Cared for by Kris Boulez <[e-mail]>
+#
+# 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::Residue - Bioperl structure Object, describes a Residue
+
+=head1 SYNOPSIS
+
+  #add synopsis here
+
+=head1 DESCRIPTION
+
+This object stores a Bio::Structure::Residue
+
+=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.
+
+  [e-mail]             - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Kris Boulez
+
+Email [e-mail]
+
+=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::Residue;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Structure::Chain;
+use Bio::Structure::Atom;
+@ISA = qw(Bio::Root::Root);
+
+
+=head2 new()
+
+ Title   : new()
+ Usage   : $residue = Bio::Structure::Residue->new( 
+                                           -id  => 'human_id',
+                                           );
+
+ Function: Returns a new Bio::Structure::Residue object from basic 
+	constructors. Probably most called from Bio::Structure::IO.
+ Returns : a new Bio::Structure::Residue object
+
+=cut
+
+
+sub new {
+    my ($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 $self;
+}
+
+
+
+=head2 atom()
+
+ Title   : atom 
+ Usage   : 
+ Function:  nothing usefull untill I get symbolic references to do what I want
+ Returns : 
+ Args    : 
+
+=cut
+
+sub atom {
+	my ($self,$value) = @_;
+
+	$self->throw("no code down here, go see an Entry object nearby\n");
+}
+
+
+=head2 add_atom()
+
+ Title   : add_atom
+ Usage   : 
+ Function:  nothing usefull untill I get symbolic references to do what I want
+ Returns : 
+ Args    : 
+
+=cut
+
+sub add_atom {
+	my($self,$value) = @_;
+
+	$self->throw("nothing here, use a method on an Entry object\n");
+}
+
+
+=head2 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
+
+=cut
+
+sub chain {
+	my($self, $value) = @_;
+
+	$self->throw("use an Entry based method please\n");
+}
+
+
+=head2 id()
+
+ Title   : id
+ Usage   : $residue->id("TRP-35")
+ Function: Gets/sets the ID for this residue
+ Returns : the ID
+ Args    : the ID
+
+=cut
+
+sub id {
+        my ($self, $value) = @_;;
+        if (defined $value) {
+	        $self->{'id'} = $value;
+        }
+        return $self->{'id'};
+}
+
+
+=head2 DESTROY()
+
+ Title   : DESTROY
+ Usage   : 
+ Function: destructor ( get rid of circular references )
+ Returns : 
+ Args    : 
+
+=cut
+
+sub DESTROY {
+	my $self = shift;
+
+	# no specific destruction for now
+}
+
+
+#
+# from here on only private methods
+#
+
+=head2 _remove_atoms()
+
+ Title   : _remove_atoms
+ Usage   : 
+ Function: Removes the atoms attached to a Residue. Tells the atoms they
+ 	don't belong to this Residue any more
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _remove_atoms {
+	my ($self) = shift;
+
+	$self->throw("no code here\n");
+}
+
+
+=head2 _remove_chain()
+
+ Title   : _remove_chain
+ Usage   : 
+ Function: Removes the Chain this Residue is atttached to.
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _remove_chain {
+	my ($self) = shift;
+
+	$self->{'chain'} = undef;
+}
+
+
+=head2 _grandparent()
+
+ Title   : _grandparent
+ Usage   : 
+ Function: get/set a symbolic reference to our grandparent
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _grandparent {
+	my($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;