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