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3 <title>MayaChemTools:Documentation:InfoAminoAcids.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="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoAminoAcids.pl</strong></td><td width="33%" align="right"><a href="././code/InfoAminoAcids.html" title="View source code">Code</a> | <a href="./../pdf/InfoAminoAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoAminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoAminoAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoAminoAcids.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>InfoAminoAcids.pl - List properties of amino acids</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>InfoAminoAcids.pl AminoAcidIDs...</p>
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26 <p>InfoAminoAcids.pl [<strong>-h, --help</strong>] [<strong>--outdelim</strong> comma | tab | semicolon]
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27 [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> AminoAcidBlock | AminoAcidRows]
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28 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--propertiesmode</strong> Categories | Names | All]
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29 [<strong>-p, --properties</strong> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
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30 [<strong>--propertieslinting</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
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31 [<strong>-w, --workingdir</strong> dirname] AminoAcidIDs...</p>
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32 <p>
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33 </p>
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34 <h2>DESCRIPTION</h2>
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35 <p>List amino acid properties. Amino acids identification supports these three types of IDs: one letter
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36 code, three letter code or name. Amino acid properties data, in addition to basic information about
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37 amino acids - one and three letter codes, name, DNA and RNA codons, molecular weight - include
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38 variety of other properties: polarity, acidity, hydrophobicity, and so on.</p>
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39 <p>
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40 </p>
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41 <h2>PARAMETERS</h2>
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42 <dl>
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43 <dt><strong><strong>AminoAcidIDs</strong> <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em></strong></dt>
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44 <dd>
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45 <p><em>AminoAcidIDs</em> is a space delimited list of values to identify amino acids.</p>
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46 <p>Input value format is: <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em>. Default: <em>Ala</em>.
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47 Examples:</p>
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48 <div class="OptionsBox">
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49 Ala
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50 <br/> Glu A
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51 <br/> Alanine Glu Y "Aspartic acid"</div>
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52 </dd>
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53 </dl>
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54 <p>
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55 </p>
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56 <h2>OPTIONS</h2>
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57 <dl>
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58 <dt><strong><strong>-h, --help</strong></strong></dt>
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59 <dd>
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60 <p>Print this help message.</p>
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61 </dd>
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62 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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63 <dd>
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64 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
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65 Default value: <em>comma</em>.</p>
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66 </dd>
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67 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
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68 <dd>
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69 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
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70 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
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71 </dd>
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72 <dt><strong><strong>--outputstyle</strong> <em>AminoAcidBlock | AminoAcidRows</em></strong></dt>
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73 <dd>
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74 <p>Specify how to list amino acid information: add a new line for each property and present it as a block
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75 for each amino acid; or include all properties in one line and show it as a single line.</p>
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76 <p>Possible values: <em>AminoAcidBlock | AminoAcidRows</em>. Default: <em>AminoAcidBlock</em></p>
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77 <p>An example for <em>AminoAcidBlock</em> output style:</p>
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78 <div class="OptionsBox">
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79 ThreeLetterCode: Ala
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80 <br/> OneLetterCode: A
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81 <br/> AminoAcid: Alanine
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82 <br/> MolecularWeight: 89.0941
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83 <br/> ... ...
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84 <br/> ... ...
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85 <br/> ... ...</div>
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86 <div class="OptionsBox">
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87 ThreeLetterCode: Glu
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88 <br/> OneLetterCode: E
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89 <br/> AminoAcid: Glutamic acid
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90 <br/> MolecularWeight: 147.1308
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91 <br/> ... ...
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92 <br/> ... ...
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93 <br/> ... ...</div>
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94 <p>An example for <em>AminoAcidRows</em> output style:</p>
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95 <div class="OptionsBox">
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96 ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
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97 <br/> Ala,A,Alanine,89.0941..
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98 <br/> Glu,E,Glutamic acid,147.1308..</div>
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99 </dd>
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100 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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101 <dd>
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102 <p>Overwrite existing files.</p>
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103 </dd>
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104 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
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105 <dd>
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106 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
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107 Valid values: positive integers.</p>
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108 </dd>
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109 <dt><strong><strong>--propertiesmode</strong> <em>Categories | Names | All</em></strong></dt>
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110 <dd>
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111 <p>Specify how property names are specified: use category names; explicit list of property names; or
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112 use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p>
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113 <p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of
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114 interest.</p>
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115 </dd>
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116 <dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt>
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117 <dd>
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118 <p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or
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119 property names.</p>
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120 <p>Specify which amino acid properties information to list for the amino acid IDs specified using command:
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121 line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma
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122 separated list of amino acid property names.</p>
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123 <p>Possible values: <em>Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]</em>.
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124 Default: <em>Basic</em>.</p>
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125 <p><em>Basic</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4</em></p>
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126 <p><em>BasicPlus</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4</em></p>
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127 <p><em>BasicAndHydrophobicity</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers</em></p>
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128 <p><em>BasicAndHydrophobicityPlus</em> includes: <em>(ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers</em></p>
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129 <p>Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume, %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition, AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers, ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4</p>
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130 </dd>
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131 <dt><strong><strong>--propertieslisting</strong> <em>ByGroup | Alphabetical</em></strong></dt>
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132 <dd>
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133 <p>Specify how to list properties for amino acids: group by category or an alphabetical by
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134 property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em>.</p>
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135 </dd>
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136 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
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137 <dd>
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138 <p>Put quotes around column values in output text file. Possible values: <em>yes or
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139 no</em>. Default value: <em>yes</em>.</p>
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140 </dd>
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141 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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142 <dd>
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143 <p>New text file name is generated using the root: <Root>.<Ext>. File name is only
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144 used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
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145 <p>Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv
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146 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p>
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147 </dd>
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148 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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149 <dd>
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150 <p>Location of working directory. Default: current directory.</p>
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151 </dd>
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152 </dl>
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153 <p>
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154 </p>
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155 <h2>EXAMPLES</h2>
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156 <p>To list basic properties information for amino acid Ala, type:</p>
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157 <div class="ExampleBox">
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158 % InfoAminoAcids.pl</div>
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159 <p>To list all available properties information for amino acid Ala, type:</p>
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160 <div class="ExampleBox">
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161 % InfoAminoAcids.pl --propertiesmode all</div>
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162 <p>To list basic properties information for amino acids Ala, Arg, and Asp type:</p>
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163 <div class="ExampleBox">
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164 % InfoAminoAcids.pl Ala Arg Asp
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165 <br/>% InfoAminoAcids.pl A Arg "Aspartic acid"</div>
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166 <p>To list all available properties information for amino acids Ala, Arg, and Asp type:</p>
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167 <div class="ExampleBox">
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168 % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp</div>
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169 <p>To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:</p>
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170 <div class="ExampleBox">
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171 % InfoAminoAcids.pl --propertiesmode Categories
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172 --properties BasicAndHydrophobicity Ala Arg Asp</div>
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173 <p>To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino
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174 acids Ala, Arg, and Asp type:</p>
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175 <div class="ExampleBox">
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176 % InfoAminoAcids.pl --propertiesmode Names
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177 --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
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178 Ala Arg Asp</div>
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179 <p>To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
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180 in rows insetad of amino acid blocks with quotes around the values, type:</p>
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181 <div class="ExampleBox">
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182 % InfoAminoAcids.pl --propertiesmode Categories
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183 --properties BasicAndHydrophobicity --propertieslisting alphabetical
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184 --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp</div>
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185 <p>To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
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186 in rows insetad of amino acid blocks with quotes around the values and write them into a file
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187 AminoAcidProperties.csv, type:</p>
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188 <div class="ExampleBox">
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189 % InfoAminoAcids.pl --propertiesmode Categories
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190 --properties BasicAndHydrophobicity --propertieslisting alphabetical
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191 --outdelim comma --outputstyle AminoAcidRows --quote yes
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192 --output File -r AminoAcidProperties -o Ala Arg Asp</div>
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193 <p>
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194 </p>
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195 <h2>AUTHOR</h2>
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196 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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197 <p>
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198 </p>
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199 <h2>SEE ALSO</h2>
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200 <p><a href="./InfoNucleicAcids.plInfoPeriodicTableElements.html">InfoNucleicAcids.plInfoPeriodicTableElements.pl</a>
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201 </p>
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202 <p>
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203 </p>
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204 <h2>COPYRIGHT</h2>
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205 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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206 <p>This file is part of MayaChemTools.</p>
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207 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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208 the terms of the GNU Lesser General Public License as published by the Free
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209 Software Foundation; either version 3 of the License, or (at your option)
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210 any later version.</p>
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211 <p> </p><p> </p><div class="DocNav">
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212 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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213 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoAminoAcids.pl</strong></td></tr>
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214 </table>
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215 </div>
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216 <br />
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217 <center>
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218 <img src="../../images/h2o2.png">
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219 </center>
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220 </body>
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221 </html>
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