Bio/Structure/Chain.pm

   1 #
   2 # bioperl module for Bio::Structure::Chain
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Kris Boulez <kris.boulez@algonomics.com>
   7 #
   8 # Copyright Kris Boulez
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Structure::Chain - Bioperl structure Object, describes a chain
  17
  18 =head1 SYNOPSIS
  19
  20   #add synopsis here
  21
  22 =head1 DESCRIPTION
  23
  24 This object stores a Bio::Structure::Chain
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to one
  32 of the Bioperl mailing lists.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 I<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 the bugs and their resolution.  Bug reports can be submitted via the web:
  52
  53   https://github.com/bioperl/bioperl-live/issues
  54
  55 =head1 AUTHOR - Kris Boulez
  56
  57 Email kris.boulez@algonomics.com
  58
  59 =head1 APPENDIX
  60
  61 The rest of the documentation details each of the object methods.
  62 Internal methods are usually preceded with a _
  63
  64 =cut
  65
  66
  67 # Let the code begin...
  68
  69 package Bio::Structure::Chain;
  70 use strict;
  71
  72 use Bio::Structure::Entry;
  73 use Bio::Structure::Model;
  74 use base qw(Bio::Root::Root);
  75
  76
  77 =head2 new()
  78
  79  Title   : new()
  80  Usage   : $struc = Bio::Structure::Chain->new(
  81                            -id  => 'human_id',
  82                            -accession_number => 'AL000012',
  83                                            );
  84
  85  Function: Returns a new Bio::Structure::Chain object from basic
  86                 constructors. Usually called from Bio::Structure::IO.
  87  Returns : a new Bio::Structure::Chain object
  88
  89 =cut
  90
  91 sub new {
  92     my ($class, @args) = @_;
  93     my $self = $class->SUPER::new(@args);
  94
  95     my($id, $residue ) =
  96         $self->_rearrange([qw(
  97                               ID
  98                               RESIDUE
  99                               )],
 100                           @args);
 101
 102     $id      && $self->id($id);
 103     $self->{'residue'} = [];
 104     # the 'smallest' item that can be added to a chain is a residue.
 105     $residue && $self->throw("use a method based on an Entry object for now");
 106     return $self;
 107 }
 108
 109
 110
 111 =head2 residue()
 112
 113  Title   : residue
 114  Usage   :
 115  Function:  nothing useful until I get symbolic references to do what I want
 116  Returns :
 117  Args    :
 118
 119 =cut
 120
 121 sub residue {
 122         my ($self,$value) = @_;
 123
 124         $self->throw("use a method on an Entry object to do what you want");
 125 }
 126
 127
 128 =head2 add_residue()
 129
 130  Title   : add_residue
 131  Usage   :
 132  Function: nothing useful until I get symbolic references to do what I want
 133  Returns :
 134  Args    :
 135
 136 =cut
 137
 138 sub add_residue {
 139         my($self,$value) = @_;
 140
 141         $self->throw("you want entry->add_residue(chain, residue)\n");
 142 }
 143
 144 =head2 model()
 145
 146  Title   : model
 147  Usage   :
 148  Function: nothing useful until I get symbolic references to do what I want
 149  Returns :
 150  Args    :
 151
 152 =cut
 153
 154 sub model {
 155         my($self, $value) = @_;
 156
 157         $self->throw("go via a Entry object please\n");
 158 }
 159
 160
 161 =head2 id()
 162
 163  Title   : id
 164  Usage   : $chain->id("chain B")
 165  Function: Gets/sets the ID for this chain
 166  Returns : the ID
 167  Args    : the ID
 168
 169 =cut
 170
 171 sub id {
 172         my ($self, $value) = @_;;
 173         if (defined $value) {
 174                 $self->{'id'} = $value;
 175         }
 176         return $self->{'id'};
 177 }
 178
 179
 180 sub DESTROY {
 181         my $self = shift;
 182
 183         # no specific destruction for now
 184 }
 185
 186
 187 #
 188 # from here on only private methods
 189 #
 190
 191 =head2 _remove_residues()
 192
 193  Title   : _remove_residues
 194  Usage   :
 195  Function:
 196  Returns :
 197  Args    :
 198
 199 =cut
 200
 201 sub _remove_residues {
 202         my ($self) = shift;
 203
 204         $self->throw("nothing usefull in here, go see Entry\n");
 205 }
 206
 207
 208 =head2 _remove_model()
 209
 210  Title   : _remove_model
 211  Usage   :
 212  Function: Removes the Model this Chain is atttached to.
 213  Returns :
 214  Args    :
 215
 216 =cut
 217
 218 sub _remove_model {
 219         my ($self) = shift;
 220
 221         $self->throw("go see an Entry object, nothing here\n");
 222 }
 223
 224
 225 =head2 _grandparent()
 226
 227  Title   : _grandparent
 228  Usage   :
 229  Function: get/set a symbolic reference to our grandparent
 230  Returns :
 231  Args    :
 232
 233 =cut
 234
 235 sub _grandparent {
 236         my($self,$symref) = @_;
 237
 238         if (ref($symref)) {
 239                 $self->throw("Thou shall only pass strings in here, no references $symref\n");
 240         }
 241         if (defined $symref) {
 242                 $self->{'grandparent'} = $symref;
 243         }
 244         return $self->{'grandparent'};
 245 }
 246
 247 1;