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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: InfoPeriodicTableElements.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.28 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use PeriodicTable;
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38
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39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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40
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41 # Autoflush STDOUT
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42 $| = 1;
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43
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44 # Starting message...
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45 $ScriptName = basename($0);
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46 print "\n$ScriptName: Starting...\n\n";
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47 $StartTime = new Benchmark;
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48
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49 # Get the options and setup script...
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50 SetupScriptUsage();
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51 if ($Options{help}) {
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52 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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53 }
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54
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55 print "Processing options...\n";
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56 my(%OptionsInfo);
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57 ProcessOptions();
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58
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59 ListElementProperties();
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60 print "\n$ScriptName:Done...\n\n";
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61
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62 $EndTime = new Benchmark;
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63 $TotalTime = timediff ($EndTime, $StartTime);
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64 print "Total time: ", timestr($TotalTime), "\n";
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65
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66 ###############################################################################
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67
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68 # List atomic properties for elements...
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69 sub ListElementProperties {
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70 my($ElementID, $ElementDataRef, $PropertyName, $PropertyValue, $PropertyUnits, $PropertyUnitsRef, @PropertyLabels, @PropertyValues);
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71
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72 print "Listing information for periodic table element(s)...\n";
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73
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74 if ($OptionsInfo{FileOutput}) {
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75 print "Generating file $OptionsInfo{OutFileName}...\n";
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76 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
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77 }
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78
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79 # Setup property labels...
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80 @PropertyLabels = ();
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81 $PropertyUnitsRef = PeriodicTable::GetElementPropertiesNamesAndUnits();
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82 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
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83 $PropertyUnits = (exists $PropertyUnitsRef->{$PropertyName}) ? $PropertyUnitsRef->{$PropertyName} : '';
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84 if ($PropertyName =~ /^NaturalIsotopeData$/i) {
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85 push @PropertyLabels, qw(MassNumber: RelativeAtomicMass: NaturalAbundance:);
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86 }
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87 else {
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88 push @PropertyLabels, ($PropertyUnits ? "$PropertyName ($PropertyUnits):" : "$PropertyName:");
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89 }
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90 }
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91
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92 if ($OptionsInfo{ElementRowsOutput}) {
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93 ListHeaderRowData(\@PropertyLabels);
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94 }
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95
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96 # Go over specified properties...
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97 for $ElementID (@{$OptionsInfo{SpecifiedElementIDs}}) {
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98 $ElementDataRef = PeriodicTable::GetElementPropertiesData($ElementID);
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99
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100 if (!$OptionsInfo{ElementRowsOutput}) {
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101 if ($OptionsInfo{FileOutput}) {
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102 print OUTFILE "\nListing atomic properties for element $ElementID...\n\n";
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103 }
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104 else {
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105 print "\nListing atomic properties for element $ElementID...\n\n";
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106 }
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107 }
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108
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109 # Collect data..
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110 @PropertyValues = ();
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111 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
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112 if ($PropertyName =~ /^NaturalIsotopeData$/i) {
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113 push @PropertyValues, SetupIsotopeData($ElementID);
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114 }
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115 else {
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116 $PropertyValue = $ElementDataRef->{$PropertyName};
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117 if (IsFloat($PropertyValue)) {
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118 $PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0;
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119 }
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120 push @PropertyValues, $PropertyValue;
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121 }
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122 }
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123 # List data...
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124 ListElementData(\@PropertyLabels, \@PropertyValues);
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125 }
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126 if ($OptionsInfo{FileOutput}) {
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127 close OUTFILE;
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128 }
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129 print "\n";
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130 }
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131
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132 # List data for an element...
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133 sub ListElementData {
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134 my($DataLabelRef, $DataValueRef) = @_;
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135 my($Index, $Line, $Value);
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136
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137 if ($OptionsInfo{ElementRowsOutput}) {
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138 $Line = '';
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139 # Format data...
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140 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) {
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141 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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142 }
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143 else {
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144 # Always quote values containing commas...
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145 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0];
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146 for $Index (1 .. $#{$DataValueRef} ) {
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147 $Value = $DataValueRef->[$Index];
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148 if ($Value =~ /\,/) {
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149 $Value = qq("$Value");
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150 }
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151 $Line .= $OptionsInfo{OutDelim} . $Value;
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152 }
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153 }
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154 if ($OptionsInfo{FileOutput}) {
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155 print OUTFILE "$Line\n";
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156 }
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157 else {
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158 print "$Line\n";
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159 }
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160 }
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161 else {
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162 # Format and list data...
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163 $Line = '';
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164 for $Index (0 .. $#{$DataLabelRef} ) {
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165 $Line = $DataLabelRef->[$Index] . ' ' . $DataValueRef->[$Index];
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166 if ($OptionsInfo{FileOutput}) {
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167 print OUTFILE "$Line\n";
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168 }
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169 else {
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170 print "$Line\n";
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171 }
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172 }
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173 }
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174 }
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175
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176 # List data for an element...
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177 sub ListHeaderRowData {
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178 my($DataLabelRef) = @_;
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179 my($Line);
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180
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181 # Format data...
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182 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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183 $Line =~ s/\://g;
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184 # List data...
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185 if ($OptionsInfo{FileOutput}) {
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186 print OUTFILE "$Line\n";
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187 }
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188 else {
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189 print "$Line\n";
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190 }
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191 }
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192
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193 # Setup isotope data strings...
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194 sub SetupIsotopeData {
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195 my($ElementID) = @_;
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196 my($MassNumber, $RelativeAtomicMass, $NaturalAbundance, $NaturalIsotopeDataRef, @MassNumbers, @RelativeAtomicMasses, @NaturalAbundances);
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197
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198 # Get natural isotope data: MassNumber, RelativeAtomicMass and NaturalAbundance
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199 @MassNumbers = (); @RelativeAtomicMasses = (); @NaturalAbundances = ();
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200 $NaturalIsotopeDataRef = PeriodicTable::GetElementNaturalIsotopesData($ElementID);
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201 for $MassNumber (sort {$a <=> $b} keys %{$NaturalIsotopeDataRef}) {
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202 $RelativeAtomicMass = $NaturalIsotopeDataRef->{$MassNumber}{RelativeAtomicMass};
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203 $NaturalAbundance = $NaturalIsotopeDataRef->{$MassNumber}{NaturalAbundance};
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204 push @MassNumbers, $MassNumber;
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205 $RelativeAtomicMass = ($RelativeAtomicMass > 0) ? (sprintf("%.$OptionsInfo{Precision}f", $RelativeAtomicMass) + 0) : '';
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206 push @RelativeAtomicMasses, $RelativeAtomicMass;
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207 $NaturalAbundance = ($NaturalAbundance > 0) ? (sprintf("%.$OptionsInfo{Precision}f", $NaturalAbundance) + 0) : '';
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208 push @NaturalAbundances, $NaturalAbundance;
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209 }
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210 $MassNumber = JoinWords(\@MassNumbers, ",", 0);
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211 $RelativeAtomicMass = JoinWords(\@RelativeAtomicMasses, ",", 0);
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212 $NaturalAbundance = JoinWords(\@NaturalAbundances, ",", 0);
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213 return ($MassNumber, $RelativeAtomicMass, $NaturalAbundance);
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214 }
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215
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216 # Get propery names from categories...
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217 sub GetPropertyNamesFromCategories {
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218 my($CategoryName) = @_;
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219 my(@PropertyNames);
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220
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221 @PropertyNames = ();
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222 if ($CategoryName =~ /^Basic$/i) {
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223 @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'AtomicWeight', 'GroundStateConfiguration', 'GroupNumber', 'PeriodNumber', 'FirstIonizationEnergy');
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224 } elsif ($CategoryName =~ /^BasicAndNaturalIsotope$/i) {
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225 # Natural isotope data includes: 'MassNumber', 'RelativeAtomicMass', 'NaturalAbundance'
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226 @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'AtomicWeight', 'GroundStateConfiguration', 'GroupNumber', 'PeriodNumber', 'FirstIonizationEnergy', 'NaturalIsotopeData');
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227 } elsif ($CategoryName =~ /^NaturalIsotope$/i) {
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228 @PropertyNames = ('AtomicNumber', 'ElementSymbol', 'ElementName', 'NaturalIsotopeData');
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229 }
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230
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231 return @PropertyNames;
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232 }
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233
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234 # Process option values...
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235 sub ProcessOptions {
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236 %OptionsInfo = ();
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237
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238 $OptionsInfo{Mode} = $Options{mode};
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239
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240 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
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241 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
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242
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243 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
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244 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
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245
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246 $OptionsInfo{Output} = $Options{output};
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247 $OptionsInfo{OutputStyle} = $Options{outputstyle};
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248
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249 $OptionsInfo{ElementRowsOutput} = ($Options{outputstyle} =~ /^ElementRows$/i) ? 1 : 0;
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250 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
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251
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252 $OptionsInfo{Precision} = $Options{precision};
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253
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254 my($ElementID, @ElementIDs, @GroupElements, @PeriodElements, %GroupNamesMap);
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255
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256 @{$OptionsInfo{SpecifiedElementIDs}} = ();
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257 if (@ARGV >=1 && ($Options{mode} =~ /^All$/i) ) {
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258 warn "Warning: Ignoring comman line element IDs: Not valid for All value of \"-m --mode\" option...\n";
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259 }
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260
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261 # Set up element IDs except for All mode...
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262 @ElementIDs = ();
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263 %GroupNamesMap = ();
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264
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265 if (@ARGV >=1 ) {
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266 if ($Options{mode} !~ /^All$/i) {
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267 push @ElementIDs, @ARGV;
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268 }
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269 }
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270 else {
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271 # Setup mode specified default values...
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272 my($Nothing);
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273 MODE: {
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274 if ($Options{mode} =~ /^ElementID$/i) { push @ElementIDs, 'H'; last MODE; };
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275 if ($Options{mode} =~ /^AmericanGroupLabel$/i) { push @ElementIDs, 'IA'; last MODE; };
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276 if ($Options{mode} =~ /^EuropeanGroupLabel$/i) { push @ElementIDs, 'IA'; last MODE; };
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277 if ($Options{mode} =~ /^GroupNumber$/i) { push @ElementIDs, '1'; last MODE; };
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278 if ($Options{mode} =~ /^GroupName$/i) { push @ElementIDs, 'AlkaliMetals'; last MODE; };
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279 if ($Options{mode} =~ /^PeriodNumber$/i) { push @ElementIDs, '1'; last MODE; };
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280 $Nothing = 1;
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281 }
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282 }
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283 if ($Options{mode} =~ /^GroupName$/i) {
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284 # Map group names to what's stored in Perioidic table data file...
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285 %GroupNamesMap = ('alkalimetals', 'Alkali metal', 'alkalineearthmetals', 'Alkaline earth metal', 'chalcogens', 'Chalcogen', 'coinagemetals', 'Coinage metal', 'halogens', 'Halogen', 'noblegases', 'Noble gas', 'pnictogens', 'Pnictogen', 'lanthanides', 'Lanthanoid', 'lanthanoids', 'Lanthanoid', 'actinides', 'Actinoid', 'actinoids', 'Actinoid' );
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286 }
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287
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288 # Generate list of elements...
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289 if ($Options{mode} =~ /^All$/i) {
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290 push @{$OptionsInfo{SpecifiedElementIDs}}, PeriodicTable::GetElements();
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291 }
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292 else {
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293 ELEMENTID: for $ElementID (@ElementIDs) {
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294 if ($Options{mode} =~ /^ElementID$/i) {
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295 if (PeriodicTable::IsElement($ElementID)) {
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296 push @{$OptionsInfo{SpecifiedElementIDs}}, $ElementID;
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297 }
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298 else {
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299 warn "Ignoring element ID, $ElementID, specified using command line parameter: Unknown element ID...\n";
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300 next ELEMENTID;
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301 }
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302 }
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303 elsif ($Options{mode} =~ /^AmericanGroupLabel$/i) {
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304 if (@GroupElements = PeriodicTable::GetElementsByAmericanStyleGroupLabel($ElementID)) {
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305 push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
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306 }
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307 else {
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308 warn "Ignoring American style group label, $ElementID, specified using command line parameter: Unknown group label...\n";
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309 next ELEMENTID;
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310 }
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311 }
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312 elsif ($Options{mode} =~ /^EuropeanGroupLabel$/i) {
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313 if (@GroupElements = PeriodicTable::GetElementsByEuropeanStyleGroupLabel($ElementID)) {
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314 push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
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315 }
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316 else {
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317 warn "Ignoring American style group label, $ElementID, specified using command line parameter: Unknown group label...\n";
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318 next ELEMENTID;
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319 }
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320 }
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321 elsif ($Options{mode} =~ /^GroupNumber$/i) {
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322 if (@GroupElements = PeriodicTable::GetElementsByGroupNumber($ElementID)) {
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323 push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
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324 }
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325 else {
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326 warn "Ignoring group number, $ElementID, specified using command line parameter: Unknown group number...\n";
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327 next ELEMENTID;
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328 }
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329 }
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330 elsif ($Options{mode} =~ /^GroupName$/i) {
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331 if (exists $GroupNamesMap{lc($ElementID)}) {
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332 @GroupElements = PeriodicTable::GetElementsByGroupName($GroupNamesMap{lc($ElementID)});
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333 push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
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334 }
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335 else {
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336 warn "Ignoring group name, $ElementID, specified using command line parameter: Unknown group name...\n";
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337 next ELEMENTID;
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338 }
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339 }
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340 elsif ($Options{mode} =~ /^PeriodNumber$/i) {
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341 if (@GroupElements = PeriodicTable::GetElementsByPeriodNumber($ElementID)) {
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342 push @{$OptionsInfo{SpecifiedElementIDs}}, @GroupElements;
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343 }
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344 else {
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345 warn "Ignoring period number, $ElementID, specified using command line parameter: Unknown period number...\n";
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346 next ELEMENTID;
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347 }
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348 }
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349 }
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350 }
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351 SetupSpecifiedProperties();
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352
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353 # Setup output file name...
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354 $OptionsInfo{OutFileName} = '';
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355 if ($OptionsInfo{FileOutput}) {
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356 my($OutFileRoot, $OutFileExt);
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357
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358 $OutFileRoot = '';
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359 $OutFileExt = "csv";
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360 if ($Options{outdelim} =~ /^tab$/i) {
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361 $OutFileExt = "tsv";
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362 }
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363 if ($Options{root}) {
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364 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
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365 if ($RootFileName && $RootFileExt) {
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366 $OutFileRoot = $RootFileName;
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367 }
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368 else {
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369 $OutFileRoot = $Options{root};
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370 }
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371 }
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372 else {
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373 $OutFileRoot = 'PeriodicTableElementsInfo' . $Options{mode};
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374 }
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375 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt;
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376 if (!$Options{overwrite}) {
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377 if (-e $OptionsInfo{OutFileName}) {
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378 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n";
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|
|
379 }
|
|
|
380 }
|
|
|
381 }
|
|
|
382 }
|
|
|
383
|
|
|
384 # Setup properties to list...
|
|
|
385 sub SetupSpecifiedProperties {
|
|
|
386 $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef;
|
|
|
387
|
|
|
388 $OptionsInfo{PropertiesMode} = $Options{propertiesmode};
|
|
|
389 $OptionsInfo{PropertiesListing} = $Options{propertieslisting};
|
|
|
390
|
|
|
391 # Make sure atomic appropriate properties/category names are specified...
|
|
|
392 @{$OptionsInfo{SpecifiedProperies}} = ();
|
|
|
393 if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) {
|
|
|
394 warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n";
|
|
|
395 }
|
|
|
396 if ($Options{propertiesmode} =~ /^All$/i) {
|
|
|
397 if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
|
|
|
398 push @{$OptionsInfo{SpecifiedProperies}}, PeriodicTable::GetElementPropertiesNames('Alphabetical');
|
|
|
399 }
|
|
|
400 else {
|
|
|
401 push @{$OptionsInfo{SpecifiedProperies}}, PeriodicTable::GetElementPropertiesNames();
|
|
|
402 }
|
|
|
403 push @{$OptionsInfo{SpecifiedProperies}}, 'NaturalIsotopeData';
|
|
|
404 }
|
|
|
405 else {
|
|
|
406 if ($Options{properties}) {
|
|
|
407 if ($Options{propertiesmode} =~ /^Categories$/i) {
|
|
|
408 # Check category name...
|
|
|
409 if ($Options{properties} !~ /^(Basic|BasicAndNaturalIsotope|NaturalIsotope)$/i) {
|
|
|
410 die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicAndNaturalIsotope, NaturalIsotope\n";
|
|
|
411 }
|
|
|
412 # Set propertynames...
|
|
|
413 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties});
|
|
|
414 }
|
|
|
415 else {
|
|
|
416 # Check property names..
|
|
|
417 my($Name, $PropertyName, @Names);
|
|
|
418 @Names = split /\,/, $Options{properties};
|
|
|
419 NAME: for $Name (@Names) {
|
|
|
420 $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name);
|
|
|
421 if ($PropertyName =~ /^NaturalIsotopeData$/i) {
|
|
|
422 push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
|
|
|
423 next NAME;
|
|
|
424 }
|
|
|
425 if (PeriodicTable::IsElementProperty($PropertyName)) {
|
|
|
426 push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
|
|
|
427 }
|
|
|
428 else {
|
|
|
429 warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n";
|
|
|
430 }
|
|
|
431 }
|
|
|
432 if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
|
|
|
433 # AtomicNumber, ElementSymbol and ElementName are always listed first and
|
|
|
434 # NaturalIsotopeData in the end...
|
|
|
435 my($AtomicNumberPresent, $ElementSymbolPresent, $ElementNamePresent, $NaturalIsotopeDataPresent, @AlphabeticalProperties, %PropertiesMap);
|
|
|
436 %PropertiesMap = ();
|
|
|
437 @AlphabeticalProperties = ();
|
|
|
438 $AtomicNumberPresent = 0; $ElementSymbolPresent = 0; $ElementNamePresent = 0; $NaturalIsotopeDataPresent = 0;
|
|
|
439 NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) {
|
|
|
440 if ($Name =~ /^AtomicNumber$/i) {
|
|
|
441 $AtomicNumberPresent = 1;
|
|
|
442 next NAME;
|
|
|
443 }
|
|
|
444 if ($Name =~ /^ElementSymbol$/i) {
|
|
|
445 $ElementSymbolPresent = 1;
|
|
|
446 next NAME;
|
|
|
447 }
|
|
|
448 if ($Name =~ /^ElementName$/i) {
|
|
|
449 $ElementNamePresent = 1;
|
|
|
450 next NAME;
|
|
|
451 }
|
|
|
452 if ($Name =~ /^NaturalIsotopeData$/i) {
|
|
|
453 $NaturalIsotopeDataPresent = 1;
|
|
|
454 next NAME;
|
|
|
455 }
|
|
|
456 $PropertiesMap{$Name} = $Name;
|
|
|
457 }
|
|
|
458 # Setup the alphabetical list...
|
|
|
459 if ($AtomicNumberPresent) {
|
|
|
460 push @AlphabeticalProperties, 'AtomicNumber';
|
|
|
461 }
|
|
|
462 if ($ElementSymbolPresent) {
|
|
|
463 push @AlphabeticalProperties, 'ElementSymbol';
|
|
|
464 }
|
|
|
465 if ($ElementNamePresent) {
|
|
|
466 push @AlphabeticalProperties, 'ElementName';
|
|
|
467 }
|
|
|
468 for $Name (sort keys %PropertiesMap) {
|
|
|
469 push @AlphabeticalProperties, $Name;
|
|
|
470 }
|
|
|
471 if ($NaturalIsotopeDataPresent) {
|
|
|
472 push @AlphabeticalProperties, 'NaturalIsotopeData';
|
|
|
473 }
|
|
|
474 @{$OptionsInfo{SpecifiedProperies}} = ();
|
|
|
475 push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties;
|
|
|
476 }
|
|
|
477 }
|
|
|
478 }
|
|
|
479 else {
|
|
|
480 # Set default value...
|
|
|
481 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic');
|
|
|
482 }
|
|
|
483 }
|
|
|
484 }
|
|
|
485
|
|
|
486 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
487 sub SetupScriptUsage {
|
|
|
488
|
|
|
489 # Retrieve all the options...
|
|
|
490 %Options = ();
|
|
|
491 $Options{mode} = "ElementID";
|
|
|
492 $Options{outdelim} = "comma";
|
|
|
493 $Options{output} = "STDOUT";
|
|
|
494 $Options{outputstyle} = "ElementBlock";
|
|
|
495 $Options{precision} = 4;
|
|
|
496 $Options{propertiesmode} = "Categories";
|
|
|
497 $Options{propertieslisting} = "ByGroup";
|
|
|
498 $Options{quote} = "yes";
|
|
|
499
|
|
|
500 if (!GetOptions(\%Options, "help|h", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) {
|
|
|
501 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
502 }
|
|
|
503 if ($Options{workingdir}) {
|
|
|
504 if (! -d $Options{workingdir}) {
|
|
|
505 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
506 }
|
|
|
507 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
508 }
|
|
|
509 if ($Options{mode} !~ /^(ElementID|AmericanGroupLabel|EuropeanGroupLabel|GroupNumber|GroupName|PeriodNumber|All)$/i) {
|
|
|
510 die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber, GroupName, PeriodNumber, or All\n";
|
|
|
511 }
|
|
|
512 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
513 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
514 }
|
|
|
515 if ($Options{output} !~ /^(STDOUT|File)$/i) {
|
|
|
516 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n";
|
|
|
517 }
|
|
|
518 if ($Options{outputstyle} !~ /^(ElementBlock|ElementRows)$/i) {
|
|
|
519 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: ElementBlock or ElementRows\n";
|
|
|
520 }
|
|
|
521 if (!IsPositiveInteger($Options{precision})) {
|
|
|
522 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
|
|
|
523 }
|
|
|
524 if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) {
|
|
|
525 die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n";
|
|
|
526 }
|
|
|
527 if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) {
|
|
|
528 die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n";
|
|
|
529 }
|
|
|
530 if ($Options{quote} !~ /^(yes|no)$/i) {
|
|
|
531 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
|
|
|
532 }
|
|
|
533 }
|
|
|
534
|
|
|
535 __END__
|
|
|
536
|
|
|
537 =head1 NAME
|
|
|
538
|
|
|
539 InfoPeriodicTableElements.pl - List atomic properties of elements
|
|
|
540
|
|
|
541 =head1 SYNOPSIS
|
|
|
542
|
|
|
543 InfoPeriodicTableElements.pl ElementID(s)...
|
|
|
544
|
|
|
545 InfoPeriodicTableElements.pl [B<-h, --help>]
|
|
|
546 [B<-m, --mode> ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All]
|
|
|
547 [B<--outdelim> comma | tab | semicolon] [B<--output> STDOUT | File] [B<--outputstyle> ElementBlock | ElementRows]
|
|
|
548 [B<-o, --overwrite>] [B<--precision> number] [B<--propertiesmode> Categories | Names | All]
|
|
|
549 [B<-p, --properties> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
|
|
|
550 [B<--propertieslinting> ByGroup | Alphabetical] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
|
|
|
551 [B<-w, --workingdir> dirname] ElementID(s)...
|
|
|
552
|
|
|
553 =head1 DESCRIPTION
|
|
|
554
|
|
|
555 List atomic properties of elements in the periodic table. A variety of methods are available to
|
|
|
556 specify elements of interest: atomic numbers, element symbols, American or European style group
|
|
|
557 labels, IUPAC group numbers, period numbers, and group names.
|
|
|
558
|
|
|
559 Atomic properties data, in addition to basic information about the periodic table elements, is
|
|
|
560 also available for these categories: atomic radii, bulk properties, common valences, electronegativities,
|
|
|
561 electron affinities, historical data, ionization energies, natural isotopes, oxidation states,
|
|
|
562 and thermal properties.
|
|
|
563
|
|
|
564 Natural isotopes data include mass number, relative atomic mass and percent natural
|
|
|
565 abundance for each isotope of an element.
|
|
|
566
|
|
|
567 =head1 PARAMETERS
|
|
|
568
|
|
|
569 =over 4
|
|
|
570
|
|
|
571 =item B<ElementIDs> I<ElementSymbol [AtomicNumber...] | GroupLabel [GroupLabel...] | GroupNumbel [GroupNumber...] | PeriodNumber [PeriodNumbe...]>
|
|
|
572
|
|
|
573 Command line specification of elements is mode specific. In general, it's a space delimited list of values to identify
|
|
|
574 elements. All element IDs must correspond to a specific mode; mixed specifications is not supported.
|
|
|
575
|
|
|
576 For I<ElementID> mode, input value format is: I<AtomicNumber [ElementSymbol ...]>. Default: I<H>.
|
|
|
577 Examples:
|
|
|
578
|
|
|
579 C
|
|
|
580 6
|
|
|
581 C N O P S Cl
|
|
|
582 6 7 8 15 16 17
|
|
|
583 C 7 8 15 S 17
|
|
|
584
|
|
|
585 For I<AmericanGroupLabel> mode, input value format is: I<GroupLabel [GroupLabel ...]>. Default: I<IA>. Possible
|
|
|
586 group label values are: I<IA IIA IIIB IVB VB VIB VIIB VIII or VIIIB IB IIB IIIA IVA VA,
|
|
|
587 VIA, VIIA, VIIA>. Examples:
|
|
|
588
|
|
|
589 IA
|
|
|
590 IA IVA IIB
|
|
|
591
|
|
|
592 For I<EuropeanGroupLabel> mode, input value format is: I<GroupLabel [GroupLabel ...]>. Default: I<IA>. Possible
|
|
|
593 group label values are: I<IA IIA IIIA IVA VA VIA VIIA VIII or VIIIA IB IIB IIIB IVB VB,
|
|
|
594 VIB VIIB VIIB>. Examples:
|
|
|
595
|
|
|
596 IA
|
|
|
597 IA IVB IIB
|
|
|
598
|
|
|
599 For IUPAC I<GroupNumber> mode, input value format is: I<GroupNumber [GroupNumber...]>. Default: I<1>. Possible
|
|
|
600 group label values are: I<1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18>. Examples:
|
|
|
601
|
|
|
602 1
|
|
|
603 1 14 12
|
|
|
604
|
|
|
605 For I<GroupName> mode, input value format is: I<GroupName [GroupName...]>. Default: I<AlkaliMetals>. Possible
|
|
|
606 group name values are: I<AlkaliMetals AlkalineEarthMetals Chalcogens CoinageMetals Halogens
|
|
|
607 NobleGases Pnictogens Lanthanides or Lanthanoids, Actinides or Actinoids>. Examples:
|
|
|
608
|
|
|
609 AlkaliMetals
|
|
|
610 AlkaliMetals Halogens NobleGases
|
|
|
611
|
|
|
612 For I<PeriodNumber> mode, input value format is: I<PeriodNumber [PeriodNumber,...]>. Default: I<1>. Possible
|
|
|
613 group label values are: I<1 2 3 4 5 6 7>. Examples:
|
|
|
614
|
|
|
615 1
|
|
|
616 1 2 3
|
|
|
617
|
|
|
618 For I<All> mode, no input value is needed and atomic properties information is listed for all the
|
|
|
619 elements.
|
|
|
620
|
|
|
621 =back
|
|
|
622
|
|
|
623 =head1 OPTIONS
|
|
|
624
|
|
|
625 =over 4
|
|
|
626
|
|
|
627 =item B<-h, --help>
|
|
|
628
|
|
|
629 Print this help message.
|
|
|
630
|
|
|
631 =item B<-m, --mode> I<ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All>
|
|
|
632
|
|
|
633 Specify elements for listing atomic properties using one of these methods: atomic numbers
|
|
|
634 and/or element symbols list, American style group labels, European style group labels, IUPAC
|
|
|
635 group number, group names, period numbers, or all elements.
|
|
|
636
|
|
|
637 Possible values: I<ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber,
|
|
|
638 GroupName, PeriodNumber, All>. Default: I<ElementID>.
|
|
|
639
|
|
|
640 =item B<--outdelim> I<comma | tab | semicolon>
|
|
|
641
|
|
|
642 Output text file delimiter. Possible values: I<comma, tab, or semicolon>
|
|
|
643 Default value: I<comma>.
|
|
|
644
|
|
|
645 =item B<--output> I<STDOUT | File>
|
|
|
646
|
|
|
647 List information at STDOUT or write it to a file. Possible values: I<STDOUT or File>. Default:
|
|
|
648 I<STDOUT>. B<-r, --root> option is used to generate output file name.
|
|
|
649
|
|
|
650 =item B<--outputstyle> I<ElementBlock | ElementRows>
|
|
|
651
|
|
|
652 Specify how to list element information: add a new line for each property and present it as a block
|
|
|
653 for each element; or include all properties in one line and show it as a single line.
|
|
|
654
|
|
|
655 Possible values: I<ElementBlock | ElementRows>. Default: I<ElementBlock>
|
|
|
656
|
|
|
657 An example for I<ElementBlock> output style:
|
|
|
658
|
|
|
659 Atomic number: 1
|
|
|
660 Element symbol: H
|
|
|
661 Element name: Hydrogen
|
|
|
662 Atomic weight: 1.00794
|
|
|
663 ... ...
|
|
|
664 ... ...
|
|
|
665
|
|
|
666 Atomic number: 6
|
|
|
667 Element symbol: C
|
|
|
668 Element name: Carbon
|
|
|
669 Atomic weight: 12.0107
|
|
|
670 ... ...
|
|
|
671 ... ...
|
|
|
672
|
|
|
673 An example for I<ElementRows> output style:
|
|
|
674
|
|
|
675 Atomic number, Element symbol, Elemenet name, Atomic weight, ...
|
|
|
676 1,H,Hydrogen,1.00794,..
|
|
|
677 6,C,Carbon,12.0107,..
|
|
|
678
|
|
|
679 =item B<-o, --overwrite>
|
|
|
680
|
|
|
681 Overwrite existing files.
|
|
|
682
|
|
|
683 =item B<--precision> I<number>
|
|
|
684
|
|
|
685 Precision for listing numerical values. Default: up to I<4> decimal places.
|
|
|
686 Valid values: positive integers.
|
|
|
687
|
|
|
688 =item B<--propertiesmode> I<Categories | Names | All>
|
|
|
689
|
|
|
690 Specify how property names are specified: use category names; explicit list of property names; or
|
|
|
691 use all available properties. Possible values: I<Categories, Names, or All>. Default: I<Categories>.
|
|
|
692
|
|
|
693 This option is used in conjunction with B<-p, --properties> option to specify properties of
|
|
|
694 interest.
|
|
|
695
|
|
|
696 =item B<-p, --properties> I<CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]>
|
|
|
697
|
|
|
698 This option is B<--propertiesmode> specific. In general, it's a list of comma separated category or
|
|
|
699 property names.
|
|
|
700
|
|
|
701 Specify which atomic properties information to list for the elements specified using command line
|
|
|
702 parameters: list basic and/or isotope information; list all available information; or specify a comma
|
|
|
703 separated list of atomic property names.
|
|
|
704
|
|
|
705 Possible values: I<Basic| BasicAndNaturalIsotope | NaturalIsotope | PropertyName,[PropertyName,...]>.
|
|
|
706 Default: I<Basic>.
|
|
|
707
|
|
|
708 I<Basic> includes: I<AtomicNumber, ElementSymbol, ElementName, AtomicWeight, GroundStateConfiguration,
|
|
|
709 GroupNumber, PeriodNumber, FirstIonizationEnergy>.
|
|
|
710
|
|
|
711 I<NaturalIsotope> includes: I<AtomicNumber, ElementSymbol, ElementName, MassNumber,
|
|
|
712 RelativeAtomicMass, NaturalAbundance>.
|
|
|
713
|
|
|
714 Here is a complete list of available properties: AllenElectronegativity, AllredRochowElectronegativity, AtomicNumber,
|
|
|
715 AtomicRadiusCalculated, AtomicRadiusEmpirical, AtomicWeight, Block, BoilingPoint, BondLength,
|
|
|
716 BrinellHardness, BulkModulus, Classification, CoefficientOfLinearExpansion, Color,
|
|
|
717 CommonValences, LowestCommonValence, HighestCommonValence,
|
|
|
718 CommonOxidationNumbers, LowestCommonOxidationNumber, HighestCommonOxidationNumber,
|
|
|
719 CovalentRadiusEmpirical, CriticalTemperature, DensityOfSolid, DiscoveredAt, DiscoveredBy,
|
|
|
720 DiscoveredWhen, ElectricalResistivity, ElectronAffinity, ElementName, ElementSymbol, EnthalpyOfAtmization,
|
|
|
721 EnthalpyOfFusion, EnthalpyOfVaporization, FirstIonizationEnergy, GroundStateConfiguration, GroundStateLevel,
|
|
|
722 GroupName, GroupNumber, NaturalIsotopeData, MeltingPoint, MineralHardness, MolarVolume,
|
|
|
723 MullikenJaffeElectronegativity, OriginOfName, PaulingElectronegativity, PeriodNumber, PoissonsRatio,
|
|
|
724 Reflectivity, RefractiveIndex, RigidityModulus, SandersonElectronegativity, StandardState,
|
|
|
725 SuperconductionTemperature, ThermalConductivity, VanderWaalsRadius, VelocityOfSound, VickersHardness,
|
|
|
726 YoungsModulus.
|
|
|
727
|
|
|
728 =item B<--propertieslisting> I<ByGroup | Alphabetical>
|
|
|
729
|
|
|
730 Specify how to list properties for elements: group by category or an alphabetical by
|
|
|
731 property names. Possible values: I<ByGroup or Alphabetical>. Default: I<ByGroup>.
|
|
|
732 During I<Alphabetical> listing, element identification data - I<AtomicNumber, ElementSymbol,
|
|
|
733 ElementName> - is show first, and natural isotope data - I<MassNumber, RelativeAtomicMass,
|
|
|
734 NaturalAbundance> - is listed in the end.
|
|
|
735
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|
|
736 =item B<-q, --quote> I<yes | no>
|
|
|
737
|
|
|
738 Put quotes around column values in output text file. Possible values: I<yes or
|
|
|
739 no>. Default value: I<yes>.
|
|
|
740
|
|
|
741 =item B<-r, --root> I<rootname>
|
|
|
742
|
|
|
743 New text file name is generated using the root: <Root>.<Ext>. File name is only
|
|
|
744 used during I<File> value of B<-o, --output> option.
|
|
|
745
|
|
|
746 Default file name: PeriodicTableElementsInfo<mode>.<Ext>. The csv, and tsv
|
|
|
747 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
|
|
|
748
|
|
|
749 =item B<-w, --workingdir> I<dirname>
|
|
|
750
|
|
|
751 Location of working directory. Default: current directory.
|
|
|
752
|
|
|
753 =back
|
|
|
754
|
|
|
755 =head1 EXAMPLES
|
|
|
756
|
|
|
757 To list basic atomic properties information for element H, type:
|
|
|
758
|
|
|
759 % InfoPeriodicTableElements.pl
|
|
|
760
|
|
|
761 To list basic atomic properties information for elements C,N,O and F, type:
|
|
|
762
|
|
|
763 % InfoPeriodicTableElements.pl C N O F
|
|
|
764
|
|
|
765 To list all available atomic properties information for elements C,N,O and F, type:
|
|
|
766
|
|
|
767 % InfoPeriodicTableElements.pl --propertiesmode all 6 N O 9
|
|
|
768
|
|
|
769 To list basic and natural isotope information for elements C,N,O and F, type:
|
|
|
770
|
|
|
771 % InfoPeriodicTableElements.pl --propertiesmode Categories
|
|
|
772 --properties BasicAndNaturalIsotope C N O F
|
|
|
773
|
|
|
774 To list AtomicNumber, ElementName, AtomicWeight and CommonValences information
|
|
|
775 for elements C,N,O and F, type:
|
|
|
776
|
|
|
777 % InfoPeriodicTableElements.pl --propertiesmode Names
|
|
|
778 --properties AtomicNumber,ElementName,AtomicWeight,CommonValences
|
|
|
779 C N O F
|
|
|
780
|
|
|
781 To alphabetically list basic and natural isotope information for elements C,N,O and F in rows instead of
|
|
|
782 element blocks with quotes around the values, type:
|
|
|
783
|
|
|
784 % InfoPeriodicTableElements.pl --propertiesmode Categories
|
|
|
785 --properties BasicAndNaturalIsotope --propertieslisting alphabetical
|
|
|
786 --outdelim comma --outputstyle ElementRows --quote yes C N O F
|
|
|
787
|
|
|
788 To alphabetically list all available atomic information for elements C,N,O and F in rows instead of
|
|
|
789 element blocks with quotes around the values and write them into a file ElementProperties.csv, type:
|
|
|
790
|
|
|
791 % InfoPeriodicTableElements.pl --propertiesmode Categories
|
|
|
792 --properties BasicAndNaturalIsotope --propertieslisting alphabetical
|
|
|
793 --outdelim comma --outputstyle ElementRows --quote yes
|
|
|
794 --output File -r ElementsProperties -o -m All
|
|
|
795
|
|
|
796 To list basic atomic properties information for elements in groups IA and VIA using American
|
|
|
797 style group labels, type:
|
|
|
798
|
|
|
799 % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VIA
|
|
|
800
|
|
|
801 To list basic atomic properties information for elements in groups IA and VB using European
|
|
|
802 style group labels, type:
|
|
|
803
|
|
|
804 % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VB
|
|
|
805
|
|
|
806 To list basic atomic properties information for elements in groups Halogens and NobleGases, type:
|
|
|
807
|
|
|
808 % InfoPeriodicTableElements.pl -m GroupName Halogens NobleGases
|
|
|
809
|
|
|
810 =head1 AUTHOR
|
|
|
811
|
|
|
812 Manish Sud <msud@san.rr.com>
|
|
|
813
|
|
|
814 =head1 SEE ALSO
|
|
|
815
|
|
|
816 InfoAminoAcids.pl InfoNucleicAcids.pl
|
|
|
817
|
|
|
818 =head1 COPYRIGHT
|
|
|
819
|
|
|
820 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
821
|
|
|
822 This file is part of MayaChemTools.
|
|
|
823
|
|
|
824 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
825 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
826 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
827 any later version.
|
|
|
828
|
|
|
829 =cut
|
