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1 # $Id: Residue.pm,v 1.7 2002/10/22 07:38:44 lapp Exp $
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2 #
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3 # bioperl module for Bio::Structure::Residue
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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::Residue - Bioperl structure Object, describes a Residue
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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::Residue
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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
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59 package Bio::Structure::Residue;
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60 use vars qw(@ISA);
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61 use strict;
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62
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63 use Bio::Root::Root;
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64 use Bio::Structure::Chain;
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65 use Bio::Structure::Atom;
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66 @ISA = qw(Bio::Root::Root);
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67
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68
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69 =head2 new()
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70
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71 Title : new()
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72 Usage : $residue = Bio::Structure::Residue->new(
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73 -id => 'human_id',
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74 );
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75
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76 Function: Returns a new Bio::Structure::Residue object from basic
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77 constructors. Probably most called from Bio::Structure::IO.
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78 Returns : a new Bio::Structure::Residue object
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79
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80 =cut
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81
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82
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83 sub new {
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84 my ($class, @args) = @_;
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85 my $self = $class->SUPER::new(@args);
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86
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87 my($id, $atom ) =
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88 $self->_rearrange([qw(
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89 ID
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90 ATOM
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91 )],
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92 @args);
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93
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94 $id && $self->id($id);
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95
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96 $self->{'atom'} = [];
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97
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98 # the 'smallest' (and only) item that can be added to a residue is an atom
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99
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100 $atom && $self->throw("add atoms via an Entry object entry->add_atom(residue,atom)\n");
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101
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102 return $self;
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103 }
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104
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105
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106
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107 =head2 atom()
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108
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109 Title : atom
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110 Usage :
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111 Function: nothing usefull untill I get symbolic references to do what I want
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112 Returns :
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113 Args :
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114
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115 =cut
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116
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117 sub atom {
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118 my ($self,$value) = @_;
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119
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120 $self->throw("no code down here, go see an Entry object nearby\n");
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121 }
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122
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123
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124 =head2 add_atom()
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125
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126 Title : add_atom
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127 Usage :
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128 Function: nothing usefull untill I get symbolic references to do what I want
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129 Returns :
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130 Args :
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131
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132 =cut
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133
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134 sub add_atom {
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135 my($self,$value) = @_;
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136
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137 $self->throw("nothing here, use a method on an Entry object\n");
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138 }
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139
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140
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141 =head2 chain()
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142
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143 Title : chain
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144 Usage : $chain = $residue->chain($chain)
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145 Function: Sets the Chain this Residue belongs to
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146 Returns : Returns the Chain this Residue belongs to
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147 Args : reference to a Chain
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148
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149 =cut
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150
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151 sub chain {
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152 my($self, $value) = @_;
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153
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154 $self->throw("use an Entry based method 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 : $residue->id("TRP-35")
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162 Function: Gets/sets the ID for this residue
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163 Returns : the ID
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164 Args : the ID
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165
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166 =cut
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167
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168 sub id {
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169 my ($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 =head2 DESTROY()
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178
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179 Title : DESTROY
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180 Usage :
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181 Function: destructor ( get rid of circular references )
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182 Returns :
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183 Args :
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184
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185 =cut
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186
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187 sub DESTROY {
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188 my $self = shift;
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189
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190 # no specific destruction for now
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191 }
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192
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193
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194 #
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195 # from here on only private methods
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196 #
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197
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198 =head2 _remove_atoms()
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199
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200 Title : _remove_atoms
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201 Usage :
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202 Function: Removes the atoms attached to a Residue. Tells the atoms they
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203 don't belong to this Residue any more
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204 Returns :
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205 Args :
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206
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207 =cut
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208
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209 sub _remove_atoms {
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210 my ($self) = shift;
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211
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212 $self->throw("no code here\n");
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213 }
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214
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215
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216 =head2 _remove_chain()
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217
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218 Title : _remove_chain
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219 Usage :
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220 Function: Removes the Chain this Residue is atttached to.
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221 Returns :
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222 Args :
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223
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224 =cut
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225
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226 sub _remove_chain {
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227 my ($self) = shift;
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228
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229 $self->{'chain'} = undef;
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230 }
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231
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232
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233 =head2 _grandparent()
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234
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235 Title : _grandparent
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236 Usage :
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237 Function: get/set a symbolic reference to our grandparent
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238 Returns :
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239 Args :
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240
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241 =cut
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242
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243 sub _grandparent {
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244 my($self,$symref) = @_;
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245
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246 if (ref($symref)) {
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247 $self->throw("Thou shall only pass strings in here, no references $symref\n");
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248 }
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249 if (defined $symref) {
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250 $self->{'grandparent'} = $symref;
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251 }
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252 return $self->{'grandparent'};
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253 }
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254
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255 1;
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