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#!/usr/bin/perl
# set up abundances first
open ABUNDANCE, "abundances.txt";
while (<ABUNDANCE>) {
chomp;
my @line = split; # let's just save the line items
my $symbol = shift @line;
next if ($symbol eq "#");
my $isotope = shift @line;
my $percent = shift @line;
$abundance{$symbol}{$isotope} = $percent;
}
close ABUNDANCE;
#set up spin
open SPIN, "spin.txt";
while (<SPIN>) {
chomp;
my @line = split; #let's just save the line items
my $symbol = shift @line;
next if ($symbol eq "#");
my $isotope = shift @line;
my $spinparity = shift @line;
$spin{$symbol}{$isotope} = $spinparity;
}
close SPIN;
#set up magnetic moment
open MAGMOMENT, "magmoment.txt";
while (<MAGMOMENT>) {
chomp;
my @line = split; #let's just save the line items
my $symbol = shift @line;
next if ($symbol eq "#");
my $isotope = shift @line;
my $moment = shift @line;
$magmoment{$symbol}{$isotope} = $moment;
}
close HALFLIFE;
#set up halflife
open HALFLIFE, "halflife.txt";
while (<HALFLIFE>) {
chomp;
my @line = split; #let's just save the line items
my $symbol = shift @line;
next if ($symbol eq "#");
my $isotope = shift @line;
my $halflifeformat = shift @line;
if ($halflifeformat eq "years"){
$halflifeformat = "units:y"; }
else {
$halflifeformat = "siUnits:s";
}
my $halflife = shift @line;
$hlformat{$symbol}{$isotope} = $halflifeformat;
$hl{$symbol}{$isotope} = $halflife
}
close HALFLIFE;
#set up decay
open DECAY, "decay.txt";
while (<DECAY>) {
chomp;
my @line = split "\t",$_; #let's just save the line items
my $symbol = shift @line;
next if ($symbol =~/^#/); # only lines starting with # are to be removed
my $isotope = (shift @line) + (shift @line);
foreach my $pre (('alpha', 'betaplus', 'betaminus', 'ec')){ # the array to be created and filled
foreach my $sur (('perc', 'dec')){
${$pre.$sur}{$symbol}{$isotope} = shift @line || undef; # if empty field is in @line, set to undef
}
}
}
close DECAY;
# now read isotopes
open ISOTOPES, "isotopes.txt";
print "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n";
print "<cml xmlns=\"http://www.xml-cml.org/schema\" convention=\"bodr:isotopes\"\n";
print " xmlns:xml=\"http://www.w3.org/XML/1998/namespace\" \n";
print " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" \n";
print " xmlns:bo=\"http://www.blueobelisk.org/dict/terminology\" \n";
print " xmlns:boUnits=\"http://www.blueobelisk.org/dict/units\" \n";
print " xmlns:units=\"http://www.xml-cml.org/units/units\" \n";
print " xmlns:isUnits=\"http://www.xml-cml.org/units/siUnits\" \n";
print " xmlns:bibx=\"http://bibtexml.sf.net/\" \n\n";
print " xsi:schemaLocation=\"http://www.xml-cml.org/schema ../schemas/cml25.xsd\n";
print " http://bibtexml.sf.net/ ../schemas/bibtexml.xsd\"\n";
print " id=\"isotopes\" \n";
print " title=\"properties of the isotopes\">\n\n";
print " <metadataList>\n";
print " <!-- manually updated -->\n\n";
print " <metadata name=\"dc:title\" content=\"Blue Obelisk Element Repository\" />\n";
print " <metadata name=\"dc:creator\" content=\"The Blue Obelisk Movement\" />\n";
print " <metadata name=\"dc:license\" content=\"The MIT License\" />\n";
print " <metadata name=\"dc:contributor\" content=\"Geoffrey R. Hutchison\" />\n";
print " <metadata name=\"dc:contributor\" content=\"Carsten Niehaus\" />\n";
print " <metadata name=\"dc:contributor\" content=\"Egon Willighagen\" />\n";
print " <metadata name=\"dc:contributor\" content=\"Jörg Buchwald\" />\n";
print " <metadata name=\"dc:contributor\" content=\"Martin Pfeiffer\" />\n";
print " <metadata name=\"dc:description\" content=\"Database of isotopes and isotopic properties (names, symbols, exact masses, spin, abundances, magnetic dipole moment, decay energy, etc)\" />\n";
print " </metadataList>\n\n";
while (<ISOTOPES>) {
chomp;
my @line = split; # let's just save the line items
my $symbol = shift @line;
next if ($symbol eq "#");
next if ($symbol eq "Xx");
my $atomicNum = shift @line;
print "<isotopeList id=\"$symbol\">\n";
while ($isotope = shift @line) {
$exactMass = shift @line;
$error = shift @line;
print "\t<isotope id=\"$symbol$isotope\" number=\"$isotope\" elementType=\"$symbol\">\n";
if (exists $abundance{$symbol} && $abundance{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:relativeAbundance\">$abundance{$symbol}{$isotope}</scalar>\n";
}
print "\t\t<scalar dictRef=\"bo:exactMass\" errorValue=\"$error\">$exactMass</scalar>\n";
if (exists $spin{$symbol} && $spin{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:spin\">$spin{$symbol}{$isotope}</scalar>\n";
}
if (exists $magmoment{$symbol} && $magmoment{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:magneticMoment\">$magmoment{$symbol}{$isotope}</scalar>\n";
}
if (exists $hl{$symbol} && $hl{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:halfLife\" units=\"$hlformat{$symbol}{$isotope}\">$hl{$symbol}{$isotope}</scalar>\n";
}
if (exists $alphaperc{$symbol} && $alphaperc{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:alphaDecay\">$alphadec{$symbol}{$isotope}</scalar>\n";
print "\t\t<scalar dictRef=\"bo:alphaDecayLikeliness\" units=\"bo:percentage\">$alphaperc{$symbol}{$isotope}</scalar>\n";
}
if (exists $betaplusperc{$symbol} && $betaplusperc{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:betaplusDecay\">$betaplusdec{$symbol}{$isotope}</scalar>\n";
print "\t\t<scalar dictRef=\"bo:betaplusDecayLikeliness\" units=\"bo:percentage\">$betaplusperc{$symbol}{$isotope}</scalar>\n";
}
if (exists $betaminusperc{$symbol} && $betaminusperc{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:betaminusDecay\">$betaminusdec{$symbol}{$isotope}</scalar>\n";
print "\t\t<scalar dictRef=\"bo:betaminusDecayLikeliness\" units=\"bo:percentage\">$betaminusperc{$symbol}{$isotope}</scalar>\n";
}
if (exists $ecperc{$symbol} && $ecperc{$symbol}{$isotope}) {
print "\t\t<scalar dictRef=\"bo:ecDecay\">$ecdec{$symbol}{$isotope}</scalar>\n";
print "\t\t<scalar dictRef=\"bo:ecDecayLikeliness\" units=\"bo:percentage\">$ecperc{$symbol}{$isotope}</scalar>\n";
}
print "\t\t<scalar dictRef=\"bo:atomicNumber\">$atomicNum</scalar>\n";
print "\t</isotope>\n";
}
print "</isotopeList>\n";
}
close ISOTOPES;
print "</cml>\n";
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