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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/InfoPeriodicTableElements.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,287 @@ +<html> +<head> +<title>MayaChemTools:Documentation:InfoPeriodicTableElements.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>InfoPeriodicTableElements.pl - List atomic properties of elements</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>InfoPeriodicTableElements.pl ElementID(s)...</p> +<p>InfoPeriodicTableElements.pl [<strong>-h, --help</strong>] +[<strong>-m, --mode</strong> ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All] +[<strong>--outdelim</strong> comma | tab | semicolon] [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> ElementBlock | ElementRows] +[<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--propertiesmode</strong> Categories | Names | All] +[<strong>-p, --properties</strong> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]] +[<strong>--propertieslinting</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] +[<strong>-w, --workingdir</strong> dirname] ElementID(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>List atomic properties of elements in the periodic table. A variety of methods are available to +specify elements of interest: atomic numbers, element symbols, American or European style group +labels, IUPAC group numbers, period numbers, and group names.</p> +<p>Atomic properties data, in addition to basic information about the periodic table elements, is +also available for these categories: atomic radii, bulk properties, common valences, electronegativities, +electron affinities, historical data, ionization energies, natural isotopes, oxidation states, +and thermal properties.</p> +<p>Natural isotopes data include mass number, relative atomic mass and percent natural +abundance for each isotope of an element.</p> +<p> +</p> +<h2>PARAMETERS</h2> +<dl> +<dt><strong><strong>ElementIDs</strong> <em>ElementSymbol [AtomicNumber...] | GroupLabel [GroupLabel...] | GroupNumbel [GroupNumber...] | PeriodNumber [PeriodNumbe...]</em></strong></dt> +<dd> +<p>Command line specification of elements is mode specific. In general, it's a space delimited list of values to identify +elements. All element IDs must correspond to a specific mode; mixed specifications is not supported.</p> +<p>For <em>ElementID</em> mode, input value format is: <em>AtomicNumber [ElementSymbol ...]</em>. Default: <em>H</em>. +Examples:</p> +<div class="OptionsBox"> + C +<br/> 6 +<br/> C N O P S Cl +<br/> 6 7 8 15 16 17 +<br/> C 7 8 15 S 17</div> +<p>For <em>AmericanGroupLabel</em> mode, input value format is: <em>GroupLabel [GroupLabel ...]</em>. Default: <em>IA</em>. Possible +group label values are: <em>IA IIA IIIB IVB VB VIB VIIB VIII or VIIIB IB IIB IIIA IVA VA, +VIA, VIIA, VIIA</em>. Examples:</p> +<div class="OptionsBox"> + IA +<br/> IA IVA IIB</div> +<p>For <em>EuropeanGroupLabel</em> mode, input value format is: <em>GroupLabel [GroupLabel ...]</em>. Default: <em>IA</em>. Possible +group label values are: <em>IA IIA IIIA IVA VA VIA VIIA VIII or VIIIA IB IIB IIIB IVB VB, +VIB VIIB VIIB</em>. Examples:</p> +<div class="OptionsBox"> + IA +<br/> IA IVB IIB</div> +<p>For IUPAC <em>GroupNumber</em> mode, input value format is: <em>GroupNumber [GroupNumber...]</em>. Default: <em>1</em>. Possible +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> +<div class="OptionsBox"> + 1 +<br/> 1 14 12</div> +<p>For <em>GroupName</em> mode, input value format is: <em>GroupName [GroupName...]</em>. Default: <em>AlkaliMetals</em>. Possible +group name values are: <em>AlkaliMetals AlkalineEarthMetals Chalcogens CoinageMetals Halogens +NobleGases Pnictogens Lanthanides or Lanthanoids, Actinides or Actinoids</em>. Examples:</p> +<div class="OptionsBox"> + AlkaliMetals +<br/> AlkaliMetals Halogens NobleGases</div> +<p>For <em>PeriodNumber</em> mode, input value format is: <em>PeriodNumber [PeriodNumber,...]</em>. Default: <em>1</em>. Possible +group label values are: <em>1 2 3 4 5 6 7</em>. Examples:</p> +<div class="OptionsBox"> + 1 +<br/> 1 2 3</div> +<p>For <em>All</em> mode, no input value is needed and atomic properties information is listed for all the +elements.</p> +</dd> +</dl> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>ElementID | AmericanGroupLabel | EuropeanGroupLabel | GroupNumber | GroupName | PeriodNumber | All</em></strong></dt> +<dd> +<p>Specify elements for listing atomic properties using one of these methods: atomic numbers +and/or element symbols list, American style group labels, European style group labels, IUPAC +group number, group names, period numbers, or all elements.</p> +<p>Possible values: <em>ElementID, AmericanGroupLabel, EuropeanGroupLabel, GroupNumber, +GroupName, PeriodNumber, All</em>. Default: <em>ElementID</em>.</p> +</dd> +<dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt> +<dd> +<p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default: +<em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p> +</dd> +<dt><strong><strong>--outputstyle</strong> <em>ElementBlock | ElementRows</em></strong></dt> +<dd> +<p>Specify how to list element information: add a new line for each property and present it as a block +for each element; or include all properties in one line and show it as a single line.</p> +<p>Possible values: <em>ElementBlock | ElementRows</em>. Default: <em>ElementBlock</em></p> +<p>An example for <em>ElementBlock</em> output style:</p> +<div class="OptionsBox"> + Atomic number: 1 +<br/> Element symbol: H +<br/> Element name: Hydrogen +<br/> Atomic weight: 1.00794 +<br/> ... ... +<br/> ... ...</div> +<div class="OptionsBox"> + Atomic number: 6 +<br/> Element symbol: C +<br/> Element name: Carbon +<br/> Atomic weight: 12.0107 +<br/> ... ... +<br/> ... ...</div> +<p>An example for <em>ElementRows</em> output style:</p> +<div class="OptionsBox"> + Atomic number, Element symbol, Elemenet name, Atomic weight, ... +<br/> 1,H,Hydrogen,1.00794,.. +<br/> 6,C,Carbon,12.0107,..</div> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>--precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision for listing numerical values. Default: up to <em>4</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>--propertiesmode</strong> <em>Categories | Names | All</em></strong></dt> +<dd> +<p>Specify how property names are specified: use category names; explicit list of property names; or +use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p> +<p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of +interest.</p> +</dd> +<dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt> +<dd> +<p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or +property names.</p> +<p>Specify which atomic properties information to list for the elements specified using command line +parameters: list basic and/or isotope information; list all available information; or specify a comma +separated list of atomic property names.</p> +<p>Possible values: <em>Basic| BasicAndNaturalIsotope | NaturalIsotope | PropertyName,[PropertyName,...]</em>. +Default: <em>Basic</em>.</p> +<p><em>Basic</em> includes: <em>AtomicNumber, ElementSymbol, ElementName, AtomicWeight, GroundStateConfiguration, +GroupNumber, PeriodNumber, FirstIonizationEnergy</em>.</p> +<p><em>NaturalIsotope</em> includes: <em>AtomicNumber, ElementSymbol, ElementName, MassNumber, +RelativeAtomicMass, NaturalAbundance</em>.</p> +<p>Here is a complete list of available properties: AllenElectronegativity, AllredRochowElectronegativity, AtomicNumber, +AtomicRadiusCalculated, AtomicRadiusEmpirical, AtomicWeight, Block, BoilingPoint, BondLength, +BrinellHardness, BulkModulus, Classification, CoefficientOfLinearExpansion, Color, +CommonValences, LowestCommonValence, HighestCommonValence, +CommonOxidationNumbers, LowestCommonOxidationNumber, HighestCommonOxidationNumber, +CovalentRadiusEmpirical, CriticalTemperature, DensityOfSolid, DiscoveredAt, DiscoveredBy, +DiscoveredWhen, ElectricalResistivity, ElectronAffinity, ElementName, ElementSymbol, EnthalpyOfAtmization, +EnthalpyOfFusion, EnthalpyOfVaporization, FirstIonizationEnergy, GroundStateConfiguration, GroundStateLevel, +GroupName, GroupNumber, NaturalIsotopeData, MeltingPoint, MineralHardness, MolarVolume, +MullikenJaffeElectronegativity, OriginOfName, PaulingElectronegativity, PeriodNumber, PoissonsRatio, +Reflectivity, RefractiveIndex, RigidityModulus, SandersonElectronegativity, StandardState, +SuperconductionTemperature, ThermalConductivity, VanderWaalsRadius, VelocityOfSound, VickersHardness, +YoungsModulus.</p> +</dd> +<dt><strong><strong>--propertieslisting</strong> <em>ByGroup | Alphabetical</em></strong></dt> +<dd> +<p>Specify how to list properties for elements: group by category or an alphabetical by +property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em>. +During <em>Alphabetical</em> listing, element identification data - <em>AtomicNumber, ElementSymbol, +ElementName</em> - is show first, and natural isotope data - <em>MassNumber, RelativeAtomicMass, +NaturalAbundance</em> - is listed in the end.</p> +</dd> +<dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Put quotes around column values in output text file. Possible values: <em>yes or +no</em>. Default value: <em>yes</em>.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New text file name is generated using the root: <Root>.<Ext>. File name is only +used during <em>File</em> value of <strong>-o, --output</strong> option.</p> +<p>Default file name: PeriodicTableElementsInfo<mode>.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p> +</dd> +<dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To list basic atomic properties information for element H, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl</div> +<p>To list basic atomic properties information for elements C,N,O and F, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl C N O F</div> +<p>To list all available atomic properties information for elements C,N,O and F, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl --propertiesmode all 6 N O 9</div> +<p>To list basic and natural isotope information for elements C,N,O and F, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl --propertiesmode Categories + --properties BasicAndNaturalIsotope C N O F</div> +<p>To list AtomicNumber, ElementName, AtomicWeight and CommonValences information +for elements C,N,O and F, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl --propertiesmode Names + --properties AtomicNumber,ElementName,AtomicWeight,CommonValences + C N O F</div> +<p>To alphabetically list basic and natural isotope information for elements C,N,O and F in rows instead of +element blocks with quotes around the values, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl --propertiesmode Categories + --properties BasicAndNaturalIsotope --propertieslisting alphabetical + --outdelim comma --outputstyle ElementRows --quote yes C N O F</div> +<p>To alphabetically list all available atomic information for elements C,N,O and F in rows instead of +element blocks with quotes around the values and write them into a file ElementProperties.csv, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl --propertiesmode Categories + --properties BasicAndNaturalIsotope --propertieslisting alphabetical + --outdelim comma --outputstyle ElementRows --quote yes + --output File -r ElementsProperties -o -m All</div> +<p>To list basic atomic properties information for elements in groups IA and VIA using American +style group labels, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VIA</div> +<p>To list basic atomic properties information for elements in groups IA and VB using European +style group labels, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl -m AmericanGroupLabel IA VB</div> +<p>To list basic atomic properties information for elements in groups Halogens and NobleGases, type:</p> +<div class="ExampleBox"> + % InfoPeriodicTableElements.pl -m GroupName Halogens NobleGases</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./InfoAminoAcids.plInfoNucleicAcids.html">InfoAminoAcids.plInfoNucleicAcids.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>