lib/SMMIDDb.pm

   1 use strict;
   2
   3 package SMMIDDb;
   4
   5 use Tie::UrlEncoder;
   6
   7 our %urlencode;
   8 our $PARSED;
   9 our %SMMID;
  10
  11 sub new {
  12     my $class = shift;
  13     my $file = shift;
  14     my $smmid = shift;
  15     my $self = bless {}, $class;
  16
  17     $self->set_smmid($smmid);
  18
  19     print STDERR "SMMID FILE = $file\n";
  20     $self->{smmid_file} = $file;
  21
  22     $self->fetch();
  23
  24     return $self;
  25 }
  26
  27 =head2 accessors get_smmid, set_smmid
  28
  29  Usage:
  30  Desc:
  31  Property
  32  Side Effects:
  33  Example:
  34
  35 =cut
  36
  37 sub get_smmid {
  38   my $self = shift;
  39   return $self->{smmid};
  40 }
  41
  42 sub set_smmid {
  43   my $self = shift;
  44   $self->{smmid} = shift;
  45 }
  46
  47 sub fetch {
  48     my $self = shift;
  49
  50     if (!$PARSED) {
  51         open (my $F, "<".$self->{smmid_file}) || die "Can't open the SMMID definition file $self->{smmid_file}.";
  52         my $current = "";
  53         my $section = "";
  54         while (<$F>) {
  55             chomp;
  56             next() if !$_;
  57             if (/^SMMID\:\s*(.*)/) {
  58                 $current = $1;
  59                 $SMMID{$current}->{SMMID}=$current;
  60
  61             }
  62             else {
  63                 my ($key, $value) = split /\s*\:\s*/;
  64                 if ($key=~/^http/) {
  65                     print STDERR "Adding reference to $section: $value.\n";
  66                     push @{$SMMID{$current}->{link_url}->{$section}}, $value;
  67                 }
  68                 elsif ($key=~/^\(/) {
  69                     print STDERR "Adding link to $section: $key\n";
  70                     push @{$SMMID{$current}->{link_text}->{$section}}, $key;
  71                 }
  72                 else {
  73                     $SMMID{$current}->{$key}=$value;
  74                     $section = $key;
  75                 }
  76
  77             }
  78             $PARSED = "TRUE!";
  79         }
  80     }
  81
  82 }
  83
  84 =head2 accessors get_name, set_name
  85
  86  Usage:
  87  Desc:
  88  Property
  89  Side Effects:
  90  Example:
  91
  92 =cut
  93
  94 sub get_name {
  95   my $self = shift;
  96   #if (!exists $SMMID{$self->get_smmid()}) {
  97   #    die "Need to set smmid first with set_smmid()";
  98   #}
  99   my $name =  $SMMID{$self->get_smmid()}->{"CHEMICAL NAME"};
 100   print STDERR "Chemical name is $name\n";
 101   return $name;
 102 }
 103
 104 sub set_name {
 105   my $self = shift;
 106   $SMMID{$self->get_smmid()}->{NAME}=shift;
 107 }
 108
 109 =head2 accessors get_synonyms, set_synonyms
 110
 111  Usage:
 112  Desc:
 113  Property
 114  Side Effects:
 115  Example:
 116
 117 =cut
 118
 119 sub get_synonyms {
 120   my $self = shift;
 121   return $SMMID{$self->get_smmid()}->{SYNONYMS};
 122 }
 123
 124 sub set_synonyms {
 125   my $self = shift;
 126   $SMMID{$self->get_smmid()}->{SYNONYMS}=shift;
 127 }
 128
 129 =head2 accessors get_molecular_formula, set_molecular_formula
 130
 131  Usage:
 132  Desc:
 133  Property
 134  Side Effects:
 135  Example:
 136
 137 =cut
 138
 139 sub get_molecular_formula {
 140   my $self = shift;
 141   return $SMMID{$self->get_smmid()}->{"MOLECULAR FORMULA"};
 142 }
 143
 144 sub set_molecular_formula {
 145   my $self = shift;
 146   $SMMID{$self->get_smmid()}->{"MOLCULAR FORMULA"}=shift;
 147 }
 148
 149
 150 =head2 accessors get_molecular_weight, set_molecular_weight
 151
 152  Usage:
 153  Desc:
 154  Property
 155  Side Effects:
 156  Example:
 157
 158 =cut
 159
 160 sub get_molecular_weight {
 161   my $self = shift;
 162   return $SMMID{$self->get_smmid()}->{"MOLECULAR WEIGHT"};
 163 }
 164
 165 sub set_molecular_weight {
 166   my $self = shift;
 167   $SMMID{$self->get_smmid()}->{"MOLECULAR WEIGHT"}=shift;
 168 }
 169
 170 =head2 get_structure_file
 171
 172  Usage:
 173  Desc:
 174  Ret:
 175  Args:
 176  Side Effects:
 177  Example:
 178
 179 =cut
 180
 181 sub get_structure_file {
 182     my $self = shift;
 183     my $file = $self->get_smmid();
 184     $file =~ s/\#/\%23/g;
 185     return $file;
 186
 187 }
 188
 189 =head2 get_smmid_for_link
 190
 191  Usage:
 192  Desc:
 193  Ret:
 194  Args:
 195  Side Effects:
 196  Example:
 197
 198 =cut
 199
 200 sub get_smmid_for_link {
 201     my $self = shift;
 202     return $urlencode{$self->get_smmid()};
 203
 204 }
 205
 206 =head2 get_links
 207
 208  Usage:
 209  Desc:
 210  Ret:
 211  Args:
 212  Side Effects:
 213  Example:
 214
 215 =cut
 216
 217 sub get_links {
 218     my $self =shift;
 219     my $section = shift;
 220     print STDERR "getting links for section $section\n";
 221     my @links = ();
 222     if (!defined($SMMID{$self->get_smmid()}->{link_text}->{$section})) { return; }
 223     print STDERR scalar(@{$SMMID{$self->get_smmid()}->{link_text}->{$section}})." entries\n";
 224     for (my $i=0; $i<@{$SMMID{$self->get_smmid()}->{link_text}->{$section}}; $i++) {
 225         push @links, [ ${$SMMID{$self->get_smmid()}->{link_text}->{$section}}[$i], ${$SMMID{$self->get_smmid()}->{link_url}->{$section}}[$i] ];
 226     }
 227     return @links;
 228
 229 }
 230
 231
 232 =head2 get_cas
 233
 234  Usage:
 235  Desc:
 236  Ret:
 237  Args:
 238  Side Effects:
 239  Example:
 240
 241 =cut
 242
 243 sub get_cas {
 244     my $self = shift;
 245     return $SMMID{$self->get_smmid()}->{CAS};
 246 }
 247
 248 =head2 get_concise_summary
 249
 250  Usage:
 251  Desc:
 252  Ret:
 253  Args:
 254  Side Effects:
 255  Example:
 256
 257 =cut
 258
 259 sub get_concise_summary {
 260     my $self = shift;
 261     return $SMMID{$self->get_smmid()}->{"CONCISE SUMMARY"};
 262 }
 263
 264 =head2 get_biosynthesis
 265
 266  Usage:
 267  Desc:
 268  Ret:
 269  Args:
 270  Side Effects:
 271  Example:
 272
 273 =cut
 274
 275 sub get_biosynthesis {
 276     my $self = shift;
 277     return $SMMID{$self->get_smmid()}->{BIOSYNTHESIS};
 278 }
 279
 280 =head2 get_receptors
 281
 282  Usage:
 283  Desc:
 284  Ret:
 285  Args:
 286  Side Effects:
 287  Example:
 288
 289 =cut
 290
 291 sub get_receptors {
 292     my $self = shift;
 293     return $SMMID{$self->get_smmid()}->{RECEPTORS};
 294 }
 295
 296
 297
 298
 299
 300
 301 =head2 all_smmids
 302
 303  Usage:
 304  Desc:
 305  Ret:
 306  Args:
 307  Side Effects:
 308  Example:
 309
 310 =cut
 311
 312 sub all_smmids {
 313     my $class = shift;
 314     my $path = shift;
 315
 316     my $self = $class->new($path);
 317
 318     $self->fetch();
 319
 320     my @all_smmids = ();
 321
 322     foreach my $s (sort keys(%SMMID)) {
 323         my $smmid = SMMIDDb->new($path, $s);
 324
 325         push @all_smmids, $smmid;
 326     }
 327     return @all_smmids;
 328
 329 }
 330
 331
 332
 333
 334
 335 return 1;