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3 <title>MayaChemTools:Documentation:InfoPeriodicTableElements.pl</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoPDBFiles.html" title="InfoPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoSDFiles.html" title="InfoSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoPeriodicTableElements.pl</strong></td><td width="33%" align="right"><a href="././code/InfoPeriodicTableElements.html" title="View source code">Code</a> | <a href="./../pdf/InfoPeriodicTableElements.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoPeriodicTableElements.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoPeriodicTableElements.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoPeriodicTableElements.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>InfoPeriodicTableElements.pl - List atomic properties of elements</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>InfoPeriodicTableElements.pl ElementID(s)...</p>
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26 <p>InfoPeriodicTableElements.pl [<strong>-h, --help</strong>]
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27 [<strong>-m, --mode</strong> ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All]
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28 [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> ElementBlock | ElementRows]
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29 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--propertiesmode</strong> Categories | Names | All]
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30 [<strong>-p, --properties</strong> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
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31 [<strong>--propertieslinting</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
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32 [<strong>-w, --workingdir</strong> dirname] ElementID(s)...</p>
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33 <p>
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34 </p>
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35 <h2>DESCRIPTION</h2>
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36 <p>List atomic properties of elements in the periodic table. A variety of methods are available to
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37 specify elements of interest: atomic numbers, element symbols, American or European style group
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38 labels, IUPAC group numbers, period numbers, and group names.</p>
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39 <p>Atomic properties data, in addition to basic information about the periodic table elements, is
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40 also available for these categories: atomic radii, bulk properties, common valences, electronegativities,
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41 electron affinities, historical data, ionization energies, natural isotopes, oxidation states,
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42 and thermal properties.</p>
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43 <p>Natural isotopes data include mass number, relative atomic mass and percent natural
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44 abundance for each isotope of an element.</p>
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45 <p>
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46 </p>
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47 <h2>PARAMETERS</h2>
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48 <dl>
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49 <dt><strong><strong>ElementIDs</strong> <em>ElementSymbol [AtomicNumber...] | GroupLabel [GroupLabel...] | GroupNumbel [GroupNumber...] | PeriodNumber [PeriodNumbe...]</em></strong></dt>
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50 <dd>
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51 <p>Command line specification of elements is mode specific. In general, it's a space delimited list of values to identify
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52 elements. All element IDs must correspond to a specific mode; mixed specifications is not supported.</p>
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53 <p>For <em>ElementID</em> mode, input value format is: <em>AtomicNumber [ElementSymbol ...]</em>. Default: <em>H</em>.
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54 Examples:</p>
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55 <div class="OptionsBox">
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56 C
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57 <br/> 6
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58 <br/> C N O P S Cl
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59 <br/> 6 7 8 15 16 17
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60 <br/> C 7 8 15 S 17</div>
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61 <p>For <em>AmericanGroupLabel</em> mode, input value format is: <em>GroupLabel [GroupLabel ...]</em>. Default: <em>IA</em>. Possible
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62 group label values are: <em>IA IIA IIIB IVB VB VIB VIIB VIII or VIIIB IB IIB IIIA IVA VA,
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63 VIA, VIIA, VIIA</em>. Examples:</p>
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64 <div class="OptionsBox">
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65 IA
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66 <br/> IA IVA IIB</div>
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67 <p>For <em>EuropeanGroupLabel</em> mode, input value format is: <em>GroupLabel [GroupLabel ...]</em>. Default: <em>IA</em>. Possible
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68 group label values are: <em>IA IIA IIIA IVA VA VIA VIIA VIII or VIIIA IB IIB IIIB IVB VB,
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69 VIB VIIB VIIB</em>. Examples:</p>
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70 <div class="OptionsBox">
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71 IA
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72 <br/> IA IVB IIB</div>
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73 <p>For IUPAC <em>GroupNumber</em> mode, input value format is: <em>GroupNumber [GroupNumber...]</em>. Default: <em>1</em>. Possible
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74 group label values are: <em>1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18</em>. Examples:</p>
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75 <div class="OptionsBox">
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76 1
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77 <br/> 1 14 12</div>
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78 <p>For <em>GroupName</em> mode, input value format is: <em>GroupName [GroupName...]</em>. Default: <em>AlkaliMetals</em>. Possible
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79 group name values are: <em>AlkaliMetals AlkalineEarthMetals Chalcogens CoinageMetals Halogens
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80 NobleGases Pnictogens Lanthanides or Lanthanoids, Actinides or Actinoids</em>. Examples:</p>
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81 <div class="OptionsBox">
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82 AlkaliMetals
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83 <br/> AlkaliMetals Halogens NobleGases</div>
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84 <p>For <em>PeriodNumber</em> mode, input value format is: <em>PeriodNumber [PeriodNumber,...]</em>. Default: <em>1</em>. Possible
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85 group label values are: <em>1 2 3 4 5 6 7</em>. Examples:</p>
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86 <div class="OptionsBox">
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87 1
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88 <br/> 1 2 3</div>
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89 <p>For <em>All</em> mode, no input value is needed and atomic properties information is listed for all the
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90 elements.</p>
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91 </dd>
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92 </dl>
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93 <p>
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94 </p>
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95 <h2>OPTIONS</h2>
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96 <dl>
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97 <dt><strong><strong>-h, --help</strong></strong></dt>
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98 <dd>
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99 <p>Print this help message.</p>
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100 </dd>
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101 <dt><strong><strong>-m, --mode</strong> <em>ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All</em></strong></dt>
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102 <dd>
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103 <p>Specify elements for listing atomic properties using one of these methods: atomic numbers
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104 and/or element symbols list, American style group labels, European style group labels, IUPAC
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105 group number, group names, period numbers, or all elements.</p>
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106 <p>Possible values: <em>ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber,
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107 GroupName, PeriodNumber, All</em>. Default: <em>ElementID</em>.</p>
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108 </dd>
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109 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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110 <dd>
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111 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
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112 Default value: <em>comma</em>.</p>
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113 </dd>
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114 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
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115 <dd>
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116 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
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117 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
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118 </dd>
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119 <dt><strong><strong>--outputstyle</strong> <em>ElementBlock | ElementRows</em></strong></dt>
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120 <dd>
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121 <p>Specify how to list element information: add a new line for each property and present it as a block
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122 for each element; or include all properties in one line and show it as a single line.</p>
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123 <p>Possible values: <em>ElementBlock | ElementRows</em>. Default: <em>ElementBlock</em></p>
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124 <p>An example for <em>ElementBlock</em> output style:</p>
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125 <div class="OptionsBox">
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126 Atomic number: 1
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127 <br/> Element symbol: H
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128 <br/> Element name: Hydrogen
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129 <br/> Atomic weight: 1.00794
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130 <br/> ... ...
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131 <br/> ... ...</div>
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132 <div class="OptionsBox">
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133 Atomic number: 6
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134 <br/> Element symbol: C
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135 <br/> Element name: Carbon
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136 <br/> Atomic weight: 12.0107
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137 <br/> ... ...
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138 <br/> ... ...</div>
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139 <p>An example for <em>ElementRows</em> output style:</p>
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140 <div class="OptionsBox">
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141 Atomic number, Element symbol, Elemenet name, Atomic weight, ...
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142 <br/> 1,H,Hydrogen,1.00794,..
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143 <br/> 6,C,Carbon,12.0107,..</div>
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144 </dd>
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145 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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146 <dd>
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147 <p>Overwrite existing files.</p>
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148 </dd>
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149 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
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150 <dd>
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151 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
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152 Valid values: positive integers.</p>
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153 </dd>
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154 <dt><strong><strong>--propertiesmode</strong> <em>Categories | Names | All</em></strong></dt>
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155 <dd>
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156 <p>Specify how property names are specified: use category names; explicit list of property names; or
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157 use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p>
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158 <p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of
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159 interest.</p>
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160 </dd>
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161 <dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt>
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162 <dd>
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163 <p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or
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164 property names.</p>
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165 <p>Specify which atomic properties information to list for the elements specified using command line
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166 parameters: list basic and/or isotope information; list all available information; or specify a comma
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167 separated list of atomic property names.</p>
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168 <p>Possible values: <em>Basic| BasicAndNaturalIsotope | NaturalIsotope | PropertyName,[PropertyName,...]</em>.
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169 Default: <em>Basic</em>.</p>
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170 <p><em>Basic</em> includes: <em>AtomicNumber, ElementSymbol, ElementName, AtomicWeight, GroundStateConfiguration,
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171 GroupNumber, PeriodNumber, FirstIonizationEnergy</em>.</p>
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172 <p><em>NaturalIsotope</em> includes: <em>AtomicNumber, ElementSymbol, ElementName, MassNumber,
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173 RelativeAtomicMass, NaturalAbundance</em>.</p>
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174 <p>Here is a complete list of available properties: AllenElectronegativity, AllredRochowElectronegativity, AtomicNumber,
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175 AtomicRadiusCalculated, AtomicRadiusEmpirical, AtomicWeight, Block, BoilingPoint, BondLength,
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176 BrinellHardness, BulkModulus, Classification, CoefficientOfLinearExpansion, Color,
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177 CommonValences, LowestCommonValence, HighestCommonValence,
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178 CommonOxidationNumbers, LowestCommonOxidationNumber, HighestCommonOxidationNumber,
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179 CovalentRadiusEmpirical, CriticalTemperature, DensityOfSolid, DiscoveredAt, DiscoveredBy,
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180 DiscoveredWhen, ElectricalResistivity, ElectronAffinity, ElementName, ElementSymbol, EnthalpyOfAtmization,
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181 EnthalpyOfFusion, EnthalpyOfVaporization, FirstIonizationEnergy, GroundStateConfiguration, GroundStateLevel,
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182 GroupName, GroupNumber, NaturalIsotopeData, MeltingPoint, MineralHardness, MolarVolume,
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183 MullikenJaffeElectronegativity, OriginOfName, PaulingElectronegativity, PeriodNumber, PoissonsRatio,
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184 Reflectivity, RefractiveIndex, RigidityModulus, SandersonElectronegativity, StandardState,
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185 SuperconductionTemperature, ThermalConductivity, VanderWaalsRadius, VelocityOfSound, VickersHardness,
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186 YoungsModulus.</p>
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187 </dd>
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188 <dt><strong><strong>--propertieslisting</strong> <em>ByGroup | Alphabetical</em></strong></dt>
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189 <dd>
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190 <p>Specify how to list properties for elements: group by category or an alphabetical by
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191 property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em>.
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192 During <em>Alphabetical</em> listing, element identification data - <em>AtomicNumber, ElementSymbol,
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193 ElementName</em> - is show first, and natural isotope data - <em>MassNumber, RelativeAtomicMass,
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194 NaturalAbundance</em> - is listed in the end.</p>
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195 </dd>
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196 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
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197 <dd>
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198 <p>Put quotes around column values in output text file. Possible values: <em>yes or
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199 no</em>. Default value: <em>yes</em>.</p>
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200 </dd>
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201 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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202 <dd>
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203 <p>New text file name is generated using the root: <Root>.<Ext>. File name is only
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204 used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
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205 <p>Default file name: PeriodicTableElementsInfo<mode>.<Ext>. The csv, and tsv
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206 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p>
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207 </dd>
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208 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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209 <dd>
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210 <p>Location of working directory. Default: current directory.</p>
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211 </dd>
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212 </dl>
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213 <p>
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214 </p>
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215 <h2>EXAMPLES</h2>
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216 <p>To list basic atomic properties information for element H, type:</p>
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217 <div class="ExampleBox">
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218 % InfoPeriodicTableElements.pl</div>
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219 <p>To list basic atomic properties information for elements C,N,O and F, type:</p>
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220 <div class="ExampleBox">
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221 % InfoPeriodicTableElements.pl C N O F</div>
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222 <p>To list all available atomic properties information for elements C,N,O and F, type:</p>
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223 <div class="ExampleBox">
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224 % InfoPeriodicTableElements.pl --propertiesmode all 6 N O 9</div>
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225 <p>To list basic and natural isotope information for elements C,N,O and F, type:</p>
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226 <div class="ExampleBox">
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227 % InfoPeriodicTableElements.pl --propertiesmode Categories
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228 --properties BasicAndNaturalIsotope C N O F</div>
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229 <p>To list AtomicNumber, ElementName, AtomicWeight and CommonValences information
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230 for elements C,N,O and F, type:</p>
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231 <div class="ExampleBox">
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232 % InfoPeriodicTableElements.pl --propertiesmode Names
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233 --properties AtomicNumber,ElementName,AtomicWeight,CommonValences
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234 C N O F</div>
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235 <p>To alphabetically list basic and natural isotope information for elements C,N,O and F in rows instead of
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236 element blocks with quotes around the values, type:</p>
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237 <div class="ExampleBox">
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238 % InfoPeriodicTableElements.pl --propertiesmode Categories
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239 --properties BasicAndNaturalIsotope --propertieslisting alphabetical
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240 --outdelim comma --outputstyle ElementRows --quote yes C N O F</div>
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241 <p>To alphabetically list all available atomic information for elements C,N,O and F in rows instead of
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242 element blocks with quotes around the values and write them into a file ElementProperties.csv, type:</p>
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243 <div class="ExampleBox">
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244 % InfoPeriodicTableElements.pl --propertiesmode Categories
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245 --properties BasicAndNaturalIsotope --propertieslisting alphabetical
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246 --outdelim comma --outputstyle ElementRows --quote yes
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247 --output File -r ElementsProperties -o -m All</div>
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248 <p>To list basic atomic properties information for elements in groups IA and VIA using American
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249 style group labels, type:</p>
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250 <div class="ExampleBox">
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251 % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VIA</div>
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252 <p>To list basic atomic properties information for elements in groups IA and VB using European
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253 style group labels, type:</p>
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254 <div class="ExampleBox">
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255 % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VB</div>
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256 <p>To list basic atomic properties information for elements in groups Halogens and NobleGases, type:</p>
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257 <div class="ExampleBox">
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258 % InfoPeriodicTableElements.pl -m GroupName Halogens NobleGases</div>
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259 <p>
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260 </p>
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261 <h2>AUTHOR</h2>
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262 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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263 <p>
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264 </p>
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265 <h2>SEE ALSO</h2>
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266 <p><a href="./InfoAminoAcids.plInfoNucleicAcids.html">InfoAminoAcids.plInfoNucleicAcids.pl</a>
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267 </p>
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268 <p>
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269 </p>
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270 <h2>COPYRIGHT</h2>
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271 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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272 <p>This file is part of MayaChemTools.</p>
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273 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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274 the terms of the GNU Lesser General Public License as published by the Free
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275 Software Foundation; either version 3 of the License, or (at your option)
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276 any later version.</p>
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277 <p> </p><p> </p><div class="DocNav">
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278 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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279 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoPDBFiles.html" title="InfoPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoSDFiles.html" title="InfoSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoPeriodicTableElements.pl</strong></td></tr>
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280 </table>
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281 </div>
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282 <br />
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283 <center>
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284 <img src="../../images/h2o2.png">
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285 </center>
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286 </body>
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287 </html>
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