script/calculate_molecular_weights.pl

   1
   2 use strict;
   3
   4 use SMIDDB;
   5
   6 my $schema = SMIDDB->connect('dbi:Pg:dbname=smid_db;host=localhost;user=postgres;password=DebianBox**');
   7
   8 my $compounds = $schema->resultset("SMIDDB::Result::Compound")->search( {} );
   9
  10 while (my $compound = $compounds->next()) {
  11     my $molecular_weight = molecular_weight($compound->formula());
  12
  13     $compound->update( { molecular_weight => $molecular_weight });
  14
  15
  16 }
  17
  18
  19
  20 sub molecular_weight {
  21   #...
  22   #The default variable will be used as the chemical Formula
  23   $_ = shift(@_);
  24
  25   my %elements = (
  26   "H" => 1.00794,
  27   "D" => 2.014101,
  28   "T" => 3.016049,
  29   "He" => 4.002602,
  30   "Li" => 6.941,
  31   "Be" => 9.012182,
  32   "B" => 10.811,
  33   "C" => 12.0107,
  34   "N" => 14.00674,
  35   "O" => 15.9994,
  36   "F" => 18.9984032,
  37   "Ne" => 20.1797,
  38   "Na" => 22.989770,
  39   "Mg" => 24.3050,
  40   "Al" => 26.981538,
  41   "Si" => 28.0855,
  42   "P" => 30.973761,
  43   "S" => 32.066,
  44   "Cl" => 35.4527,
  45   "Ar" => 39.948,
  46   "K" => 39.0983,
  47   "Ca" => 40.078,
  48   "Sc" => 44.955910,
  49   "Ti" => 47.867,
  50   "V" => 50.9415,
  51   "Cr" => 51.9961,
  52   "Mn" => 54.938049,
  53   "Fe" => 55.845,
  54   "Co" => 58.933200,
  55   "Ni" => 58.6934,
  56   "Cu" => 63.546,
  57   "Zn" => 65.39,
  58   "Ga" => 69.723,
  59   "Ge" => 72.61,
  60   "As" => 74.92160,
  61   "Se" => 78.96,
  62   "Br" => 79.904,
  63   "Kr" => 83.80,
  64   "Rb" => 85.4678,
  65   "Sr" => 87.62,
  66   "Y" => 88.90585,
  67   "Zr" => 91.224,
  68   "Nb" => 92.90638,
  69   "Mo" => 95.94,
  70   "Tc" => 98,
  71   "Ru" => 101.07,
  72   "Rh" => 102.90550,
  73   "Pd" => 106.42,
  74   "Ag" => 107.8682,
  75   "Cd" => 112.411,
  76   "In" => 114.818,
  77   "Sn" => 118.710,
  78   "Sb" => 121.760,
  79   "Te" => 127.60,
  80   "I" => 126.90447,
  81   "Xe" => 131.29,
  82   "Cs" => 132.90545,
  83   "Ba" => 137.327,
  84   "La" => 138.9055,
  85   "Ce" => 140.116,
  86   "Pr" => 140.90765,
  87   "Nd" => 144.24,
  88   "Pm" => 145,
  89   "Sm" => 150.36,
  90   "Eu" => 151.964,
  91   "Gd" => 157.25,
  92   "Tb" => 158.92534,
  93   "Dy" => 162.50,
  94   "Ho" => 164.93032,
  95   "Er" => 167.26,
  96   "Tm" => 168.93421,
  97   "Yb" => 173.04,
  98   "Lu" => 174.967,
  99   "Hf" => 178.49,
 100   "Ta" => 180.9479,
 101   "W" => 183.84,
 102   "Re" => 186.207,
 103   "Os" => 190.23,
 104   "Ir" => 192.217,
 105   "Pt" => 195.078,
 106   "Au" => 196.96655,
 107   "Hg" => 200.59,
 108   "Tl" => 204.3833,
 109   "Pb" => 207.2,
 110   "Bi" => 208.98038,
 111   "Po" => 209,
 112   "At" => 210,
 113   "Rn" => 222,
 114   "Fr" => 223,
 115   "Ra" => 226,
 116   "Ac" => 227,
 117   "Th" => 232.038,
 118   "Pa" => 231.03588,
 119   "U" => 238.0289,
 120   "Np" => 237,
 121   "Pu" => 244,
 122   "Am" => 243,
 123   "Cm" => 247,
 124   "Bk" => 247,
 125   "Cf" => 251,
 126   "Es" => 252,
 127   "Fm" => 257,
 128   "Md" => 258,
 129   "No" => 259,
 130   "Lr" => 262,
 131   "Rf" => 261,
 132   "Db" => 262,
 133   "Sg" => 266,
 134   "Bh" => 264,
 135   "Hs" => 269,
 136   "Mt" => 268,
 137   "Uun" => 271,
 138   "Uuu" => 272
 139   );
 140   my $weight = 0;
 141
 142   my @pairs = /([CHONPS][0-9]*)/g;
 143   foreach my $pair (@pairs){
 144     if (length($pair)==1){
 145       $weight += $elements{substr($pair, 0, 1)};
 146     }else{
 147       $weight += $elements{substr($pair, 0, 1)}*substr($pair, 1);
 148     }
 149   }
 150   return $weight;
 151 }