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1 # $Id: Chain.pm,v 1.6 2002/10/22 07:38:44 lapp Exp $
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2 #
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3 # bioperl module for Bio::Structure::Chain
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4 #
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5 # Cared for by Kris Boulez <kris.boulez@algonomics.com>
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6 #
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7 # Copyright Kris Boulez
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Structure::Chain - Bioperl structure Object, describes a chain
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16
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17 =head1 SYNOPSIS
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18
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19 #add synopsis here
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20
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21 =head1 DESCRIPTION
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22
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23 This object stores a Bio::Structure::Chain
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to one
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31 of the Bioperl mailing lists. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bio.perl.org/MailList.html - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 the bugs and their resolution. Bug reports can be submitted via email
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40 or the web:
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41
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42 bioperl-bugs@bio.perl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Kris Boulez
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46
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47 Email kris.boulez@algonomics.com
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48
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49 =head1 APPENDIX
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50
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51 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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52
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53 =cut
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54
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55
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56 # Let the code begin...
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57
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58 package Bio::Structure::Chain;
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59 use vars qw(@ISA);
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60 use strict;
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61
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62 use Bio::Root::Root;
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63 use Bio::Structure::Entry;
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64 use Bio::Structure::Model;
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65 @ISA = qw(Bio::Root::Root);
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66
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67
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68 =head2 new()
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69
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70 Title : new()
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71 Usage : $struc = Bio::Structure::Chain->new(
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72 -id => 'human_id',
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73 -accession_number => 'AL000012',
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74 );
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75
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76 Function: Returns a new Bio::Structure::Chain object from basic
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77 constructors. Probably most called from Bio::Structure::IO.
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78 Returns : a new Bio::Structure::Chain object
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79
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80 =cut
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81
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82
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83
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84 sub new {
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85 my ($class, @args) = @_;
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86 my $self = $class->SUPER::new(@args);
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87
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88 my($id, $residue ) =
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89 $self->_rearrange([qw(
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90 ID
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91 RESIDUE
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92 )],
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93 @args);
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94
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95 $id && $self->id($id);
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96
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97 $self->{'residue'} = [];
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98
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99 # the 'smallest' item that can be added to a chain is a residue.
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100
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101 $residue && $self->throw("use a method based on an Entry object for now");
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102
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103 return $self;
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104 }
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105
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106
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107
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108 =head2 residue()
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109
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110 Title : residue
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111 Usage :
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112 Function: nothing usefull untill I get symbolic references to do what I want
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113 Returns :
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114 Args :
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115
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116 =cut
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117
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118 sub residue {
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119 my ($self,$value) = @_;
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120
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121 $self->throw("use a method on an Entry object to do what you want");
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122 }
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123
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124
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125 =head2 add_residue()
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126
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127 Title : add_residue
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128 Usage :
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129 Function: nothing usefull untill I get symbolic references to do what I want
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130 Returns :
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131 Args :
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132
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133 =cut
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134
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135 sub add_residue {
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136 my($self,$value) = @_;
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137
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138 $self->throw("you want entry->add_residue(chain, residue)\n");
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139 }
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140
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141 =head2 model()
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142
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143 Title : model
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144 Usage :
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145 Function: nothing usefull untill I get symbolic references to do what I want
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146 Returns :
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147 Args :
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148
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149 =cut
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150
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151 sub model {
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152 my($self, $value) = @_;
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153
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154 $self->throw("go via a Entry object please\n");
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155 }
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156
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157
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158 =head2 id()
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159
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160 Title : id
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161 Usage : $chain->id("chain B")
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162 Function: Gets/sets the ID for this chain
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163 Returns : the ID
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164 Args : the ID
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165
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166 =cut
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167
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168 sub id {
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169 my ($self, $value) = @_;;
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170 if (defined $value) {
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171 $self->{'id'} = $value;
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172 }
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173 return $self->{'id'};
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174 }
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175
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176
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177 sub DESTROY {
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178 my $self = shift;
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179
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180 # no specific destruction for now
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181 }
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182
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183
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184 #
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185 # from here on only private methods
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186 #
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187
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188 =head2 _remove_residues()
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189
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190 Title : _remove_residues
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191 Usage :
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192 Function:
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193 Returns :
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194 Args :
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195
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196 =cut
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197
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198 sub _remove_residues {
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199 my ($self) = shift;
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200
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201 $self->throw("nothing usefull in here, go see Entry\n");
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202 }
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203
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204
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205 =head2 _remove_model()
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206
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207 Title : _remove_model
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208 Usage :
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209 Function: Removes the Model this Chain is atttached to.
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210 Returns :
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211 Args :
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212
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213 =cut
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214
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215 sub _remove_model {
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216 my ($self) = shift;
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217
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218 $self->throw("go see an Entry object, nothing here\n");
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219 }
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220
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221
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222 =head2 _grandparent()
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223
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224 Title : _grandparent
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225 Usage :
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226 Function: get/set a symbolic reference to our grandparent
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227 Returns :
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228 Args :
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229
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230 =cut
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231
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232 sub _grandparent {
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233 my($self,$symref) = @_;
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234
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235 if (ref($symref)) {
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236 $self->throw("Thou shall only pass strings in here, no references $symref\n");
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237 }
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238 if (defined $symref) {
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239 $self->{'grandparent'} = $symref;
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240 }
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241 return $self->{'grandparent'};
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242 }
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243
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244
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245 1;
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