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1 # $Id: Model.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::Model
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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::Model - Bioperl structure Object, describes a Model
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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::Model;
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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::Chain;
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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 : $struc = Bio::Structure::Model->new(
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72 -id => 'human_id',
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73 );
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74
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75 Function: Returns a new Bio::Structure::Model object from basic
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76 constructors. Probably most called from Bio::Structure::IO.
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77 Returns : a new Bio::Structure::Model object
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78
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79 =cut
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80
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81
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82
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83 sub new {
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84 my ($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, $chain, $residue ) =
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88 $self->_rearrange([qw(
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89 ID
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90 CHAIN
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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 $chain && $self->throw("you have to add chain via an Entry object\n");
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98
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99 $residue && $self->throw("you have to add residues via an Entry object\n");
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100
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101 return $self;
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102 }
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103
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104
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105
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106 =head2 chain()
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107
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108 Title : chain
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109 Usage :
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110 Function: will eventually allow parent/child navigation not via an Entry object
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111 Returns :
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112 Args :
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113
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114 =cut
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115
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116 sub chain {
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117 my ($self,$value) = @_;
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118
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119 $self->throw("go via an Entry object\n");
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120 }
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121
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122
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123 =head2 add_chain()
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124
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125 Title : add_chain
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126 Usage :
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127 Function: will eventually allow parent/child navigation not via an Entry object
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128 Returns :
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129 Args :
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130
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131 =cut
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132
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133 sub add_chain {
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134 my ($self,$value) = @_;
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135
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136 $self->throw("go via an Entry object for now\n");
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137 }
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138
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139 =head2 entry()
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140
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141 Title : entry
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142 Usage :
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143 Function: will eventually allow parent/child navigation not via an Entry object
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144 Returns :
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145 Args :
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146
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147 =cut
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148
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149 sub entry {
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150 my($self) = @_;
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151
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152 $self->throw("Model::entry go via an Entry object please\n");
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153 }
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154
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155
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156 =head2 id()
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157
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158 Title : id
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159 Usage : $model->id("model 5")
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160 Function: Gets/sets the ID for this model
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161 Returns : the ID
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162 Args : the ID
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163
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164 =cut
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165
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166 sub id {
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167 my ($self, $value) = @_;;
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168 if (defined $value) {
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169 $self->{'id'} = $value;
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170 }
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171 return $self->{'id'};
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172 }
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173
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174 =head2 residue()
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175
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176 Title : residue
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177 Usage :
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178 Function: will eventually allow parent/child navigation not via an Entry object
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179 Returns :
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180 Args :
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181
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182 =cut
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183
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184 sub residue {
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185 my ($self, @args) = @_;
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186
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187 $self->throw("need to go via Entry object or learn symbolic refs\n");
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188 }
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189
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190
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191 =head2 add_residue()
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192
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193 Title : add_residue
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194 Usage :
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195 Function: will eventually allow parent/child navigation not via an Entry object
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196 Returns :
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197 Args :
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198
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199 =cut
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200
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201 sub add_residue {
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202 my ($self, @args) = @_;
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203
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204 $self->throw("go via entry->add_residue(chain, residue)\n");
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205 }
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206
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207
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208
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209 sub DESTROY {
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210 my $self = shift;
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211
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212 # no specific DESTROY for now
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213 }
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214
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215 #
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216 # from here on only private methods
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217 #
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218
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219 =head2 _remove_chains()
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220
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221 Title : _remove_chains
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222 Usage :
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223 Function: Removes the chains attached to a Model. Tells the chains they
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224 don't belong to this Model any more
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225 Returns :
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226 Args :
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227
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228 =cut
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229
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230 sub _remove_chains {
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231 my ($self) = shift;
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232
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233 $self->throw("use Entry methods pleae\n");
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234 }
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235
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236
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237 =head2 _remove_entry()
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238
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239 Title : _remove_entry
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240 Usage :
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241 Function: Removes the Entry this Model is atttached to.
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242 Returns :
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243 Args :
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244
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245 =cut
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246
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247 sub _remove_entry {
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248 my ($self) = shift;
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249
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250 $self->throw("use a method based on an Entry object\n");
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251 }
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252
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253
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254 =head2 _create_default_chain()
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255
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256 Title : _create_default_chain
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257 Usage :
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258 Function: Creates a default Chain for this Model. Typical situation
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259 in an X-ray structure where there is only one chain
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260 Returns :
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261 Args :
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262
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263 =cut
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264
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265 sub _create_default_chain {
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266 my ($self) = shift;
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267
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268 my $chain = Bio::Structure::Chain->new(-id => "default");
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269 }
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270
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271
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272 =head2 _grandparent()
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273
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274 Title : _grandparent
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275 Usage :
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276 Function: get/set a symbolic reference to our grandparent
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277 Returns :
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278 Args :
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279
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280 =cut
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281
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282 sub _grandparent {
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283 my($self,$symref) = @_;
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284
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285 if (ref($symref)) {
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286 $self->throw("Thou shall only pass strings in here, no references $symref\n");
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287 }
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288 if (defined $symref) {
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289 $self->{'grandparent'} = $symref;
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290 }
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291 return $self->{'grandparent'};
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292 }
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293
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294 1;
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