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3 <title>MayaChemTools:Documentation:AminoAcids.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./index.html" title="index.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./Atom.html" title="Atom.html">Next</a></td><td width="34%" align="middle"><strong>AminoAcids.pm</strong></td><td width="33%" align="right"><a href="././code/AminoAcids.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/AminoAcids.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/AminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/AminoAcids.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/AminoAcids.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>AminoAcids</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use AminoAcids;</p>
26 <p>use AminoAcids qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>AminoAcids</strong> module provides the following functions:</p>
31 <p> <a href="#getaminoacidpropertiesdata">GetAminoAcidPropertiesData</a>, <a href="#getaminoacidpropertiesnames">GetAminoAcidPropertiesNames</a>, GetAminoAcid&lt;PropertyName&gt;
32 , <a href="#getaminoacids">GetAminoAcids</a>, <a href="#isaminoacid">IsAminoAcid</a>, <a href="#isaminoacidproperty">IsAminoAcidProperty</a>
33 </p><p>
34 </p>
35 <h2>FUNCTIONS</h2>
36 <dl>
37 <dt><strong><a name="getaminoacidpropertiesdata" class="item"><strong>GetAminoAcidPropertiesData</strong></a></strong></dt>
38 <dd>
39 <div class="OptionsBox">
40 $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);</div>
41 <p>Returns a reference to hash containing property names and values for a specified
42 amino acid.</p>
43 </dd>
44 <dt><strong><a name="getaminoacidpropertiesnames" class="item"><strong>GetAminoAcidPropertiesNames</strong></a></strong></dt>
45 <dd>
46 <div class="OptionsBox">
47 @Names = GetAminoAcidPropertiesNames([$Mode]);
48 <br/> $NamesRef = GetAminoAcidPropertiesNames([$Mode]);</div>
49 <p>Returns an array or a reference to an array containing names of amino acids
50 properties. Order of amino acids properties is controlled by optional parameter
51 <em>Mode</em>. Possible values for <em>Mode</em>: <em>Alphabetical or ByGroup</em>; Default: <em>ByGroup</em></p>
52 </dd>
53 <dt><strong><a name="getaminoacidpropertyname" class="item"><strong>GetAminoAcidPropertyName</strong></a></strong></dt>
54 <dd>
55 <div class="OptionsBox">
56 $Value = GetAminoAcid&lt;PropertyName&gt;($AminoAcidID);</div>
57 <p>Returns amino acid property value for a specified amino acid. These functions are
58 not defined in this modules; these are implemented on the fly using Perl's AUTOLOAD
59 funcion. Here is the list of known amino acids <em>property names</em>: DNACodons, RNACodons,
60 AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint,
61 pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O,
62 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume,
63 %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman,
64 AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition,
65 AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
66 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
67 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness,
68 CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4,
69 HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
70 HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers,
71 HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
72 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
73 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin,
74 HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers,
75 HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers,
76 HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
77 HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers,
78 ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
79 RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure,
80 LinearStructureAtpH7.4</p>
81 </dd>
82 <dt><strong><a name="getaminoacids" class="item"><strong>GetAminoAcids</strong></a></strong></dt>
83 <dd>
84 <div class="OptionsBox">
85 $NamesRef = GetAminoAcids([$NameType]);
86 <br/> (@Names) = GetAminoAcids([$NameType]);</div>
87 <p>Returns an array or a reference to an array containing names of amino acids
88 as one letter code, three letter code, or amino acid name controlled by optional
89 parameter $NameType. By default, amino acids names are returned as three
90 letter code. Possible values for <em>NameType</em>: <em>ThreeLetterCode, OneLetterCode, or
91 AminoAcid</em>.</p>
92 </dd>
93 <dt><strong><a name="isaminoacid" class="item"><strong>IsAminoAcid</strong></a></strong></dt>
94 <dd>
95 <div class="OptionsBox">
96 $Status = IsAminoAcid($AminoAcidID);</div>
97 <p>Returns a flag indicating whether or not its a known amino acid ID.</p>
98 </dd>
99 <dt><strong><a name="isaminoacidproperty" class="item"><strong>IsAminoAcidProperty</strong></a></strong></dt>
100 <dd>
101 <div class="OptionsBox">
102 $Status = IsAminoAcid($PropertyName);</div>
103 <p>Returns a flag indicating whether or not its a known amino acid property name.</p>
104 </dd>
105 </dl>
106 <p>
107 </p>
108 <h2>AUTHOR</h2>
109 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
110 <p>
111 </p>
112 <h2>SEE ALSO</h2>
113 <p><a href="./NucleicAcids.html">NucleicAcids.pm</a>,&nbsp<a href="./PeriodicTable.html">PeriodicTable.pm</a>
114 </p>
115 <p>
116 </p>
117 <h2>COPYRIGHT</h2>
118 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
119 <p>This file is part of MayaChemTools.</p>
120 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
121 the terms of the GNU Lesser General Public License as published by the Free
122 Software Foundation; either version 3 of the License, or (at your option)
123 any later version.</p>
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126 <tr align="left" valign="top"><td width="33%" align="left"><a href="./index.html" title="index.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./Atom.html" title="Atom.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AminoAcids.pm</strong></td></tr>
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