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3 <title>MayaChemTools:Documentation:AminoAcids.pm</title>
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13 <div class="DocNav">
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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="./index.html" title="index.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/AminoAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AminoAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AminoAcids.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>AminoAcids</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>use AminoAcids;</p>
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26 <p>use AminoAcids qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>AminoAcids</strong> module provides the following functions:</p>
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31 <p> <a href="#getaminoacidpropertiesdata">GetAminoAcidPropertiesData</a>, <a href="#getaminoacidpropertiesnames">GetAminoAcidPropertiesNames</a>, GetAminoAcid<PropertyName>
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32 , <a href="#getaminoacids">GetAminoAcids</a>, <a href="#isaminoacid">IsAminoAcid</a>, <a href="#isaminoacidproperty">IsAminoAcidProperty</a>
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33 </p><p>
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34 </p>
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35 <h2>FUNCTIONS</h2>
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36 <dl>
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37 <dt><strong><a name="getaminoacidpropertiesdata" class="item"><strong>GetAminoAcidPropertiesData</strong></a></strong></dt>
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38 <dd>
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39 <div class="OptionsBox">
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40 $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);</div>
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41 <p>Returns a reference to hash containing property names and values for a specified
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42 amino acid.</p>
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43 </dd>
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44 <dt><strong><a name="getaminoacidpropertiesnames" class="item"><strong>GetAminoAcidPropertiesNames</strong></a></strong></dt>
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45 <dd>
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46 <div class="OptionsBox">
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47 @Names = GetAminoAcidPropertiesNames([$Mode]);
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48 <br/> $NamesRef = GetAminoAcidPropertiesNames([$Mode]);</div>
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49 <p>Returns an array or a reference to an array containing names of amino acids
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50 properties. Order of amino acids properties is controlled by optional parameter
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51 <em>Mode</em>. Possible values for <em>Mode</em>: <em>Alphabetical or ByGroup</em>; Default: <em>ByGroup</em></p>
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52 </dd>
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53 <dt><strong><a name="getaminoacidpropertyname" class="item"><strong>GetAminoAcidPropertyName</strong></a></strong></dt>
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54 <dd>
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55 <div class="OptionsBox">
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56 $Value = GetAminoAcid<PropertyName>($AminoAcidID);</div>
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57 <p>Returns amino acid property value for a specified amino acid. These functions are
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58 not defined in this modules; these are implemented on the fly using Perl's AUTOLOAD
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59 funcion. Here is the list of known amino acids <em>property names</em>: DNACodons, RNACodons,
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60 AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint,
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61 pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O,
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62 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume,
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63 %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman,
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64 AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition,
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65 AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
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66 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
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67 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness,
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68 CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4,
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69 HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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70 HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers,
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71 HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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72 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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73 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin,
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74 HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers,
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75 HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers,
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76 HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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77 HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers,
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78 ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
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79 RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure,
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80 LinearStructureAtpH7.4</p>
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81 </dd>
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82 <dt><strong><a name="getaminoacids" class="item"><strong>GetAminoAcids</strong></a></strong></dt>
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83 <dd>
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84 <div class="OptionsBox">
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85 $NamesRef = GetAminoAcids([$NameType]);
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86 <br/> (@Names) = GetAminoAcids([$NameType]);</div>
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87 <p>Returns an array or a reference to an array containing names of amino acids
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88 as one letter code, three letter code, or amino acid name controlled by optional
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89 parameter $NameType. By default, amino acids names are returned as three
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90 letter code. Possible values for <em>NameType</em>: <em>ThreeLetterCode, OneLetterCode, or
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91 AminoAcid</em>.</p>
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92 </dd>
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93 <dt><strong><a name="isaminoacid" class="item"><strong>IsAminoAcid</strong></a></strong></dt>
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94 <dd>
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95 <div class="OptionsBox">
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96 $Status = IsAminoAcid($AminoAcidID);</div>
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97 <p>Returns a flag indicating whether or not its a known amino acid ID.</p>
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98 </dd>
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99 <dt><strong><a name="isaminoacidproperty" class="item"><strong>IsAminoAcidProperty</strong></a></strong></dt>
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100 <dd>
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101 <div class="OptionsBox">
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102 $Status = IsAminoAcid($PropertyName);</div>
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103 <p>Returns a flag indicating whether or not its a known amino acid property name.</p>
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104 </dd>
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105 </dl>
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106 <p>
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107 </p>
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108 <h2>AUTHOR</h2>
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109 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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110 <p>
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111 </p>
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112 <h2>SEE ALSO</h2>
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113 <p><a href="./NucleicAcids.html">NucleicAcids.pm</a>, <a href="./PeriodicTable.html">PeriodicTable.pm</a>
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114 </p>
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115 <p>
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116 </p>
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117 <h2>COPYRIGHT</h2>
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118 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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119 <p>This file is part of MayaChemTools.</p>
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120 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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121 the terms of the GNU Lesser General Public License as published by the Free
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122 Software Foundation; either version 3 of the License, or (at your option)
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123 any later version.</p>
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124 <p> </p><p> </p><div class="DocNav">
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125 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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126 <tr align="left" valign="top"><td width="33%" align="left"><a href="./index.html" title="index.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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127 </table>
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129 <br />
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