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1 NAME
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2 InfoAminoAcids.pl - List properties of amino acids
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3
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4 SYNOPSIS
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5 InfoAminoAcids.pl AminoAcidIDs...
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6
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7 InfoAminoAcids.pl [-h, --help] [--outdelim comma | tab | semicolon]
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8 [--output STDOUT | File] [--outputstyle AminoAcidBlock | AminoAcidRows]
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9 [-o, --overwrite] [--precision number] [--propertiesmode Categories |
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10 Names | All] [-p, --properties CategoryName,[CategoryName,...] |
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11 PropertyName,[PropertyName,...]] [--propertieslinting ByGroup |
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12 Alphabetical] [-q, --quote yes | no] [-r, --root rootname] [-w,
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13 --workingdir dirname] AminoAcidIDs...
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14
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15 DESCRIPTION
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16 List amino acid properties. Amino acids identification supports these
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17 three types of IDs: one letter code, three letter code or name. Amino
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18 acid properties data, in addition to basic information about amino acids
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19 - one and three letter codes, name, DNA and RNA codons, molecular weight
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20 - include variety of other properties: polarity, acidity,
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21 hydrophobicity, and so on.
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22
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23 PARAMETERS
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24 AminoAcidIDs *ThreeLetterCode [OneLetterCode AminoAcidName...]*
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25 *AminoAcidIDs* is a space delimited list of values to identify amino
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26 acids.
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27
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28 Input value format is: *ThreeLetterCode [OneLetterCode
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29 AminoAcidName...]*. Default: *Ala*. Examples:
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30
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31 Ala
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32 Glu A
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33 Alanine Glu Y "Aspartic acid"
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34
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35 OPTIONS
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36 -h, --help
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37 Print this help message.
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38
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39 --outdelim *comma | tab | semicolon*
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40 Output text file delimiter. Possible values: *comma, tab, or
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41 semicolon* Default value: *comma*.
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42
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43 --output *STDOUT | File*
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44 List information at STDOUT or write it to a file. Possible values:
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45 *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to
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46 generate output file name.
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47
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48 --outputstyle *AminoAcidBlock | AminoAcidRows*
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49 Specify how to list amino acid information: add a new line for each
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50 property and present it as a block for each amino acid; or include
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51 all properties in one line and show it as a single line.
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52
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53 Possible values: *AminoAcidBlock | AminoAcidRows*. Default:
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54 *AminoAcidBlock*
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55
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56 An example for *AminoAcidBlock* output style:
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57
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58 ThreeLetterCode: Ala
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59 OneLetterCode: A
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60 AminoAcid: Alanine
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61 MolecularWeight: 89.0941
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62 ... ...
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63 ... ...
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64 ... ...
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65
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66 ThreeLetterCode: Glu
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67 OneLetterCode: E
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68 AminoAcid: Glutamic acid
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69 MolecularWeight: 147.1308
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70 ... ...
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71 ... ...
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72 ... ...
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73
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74 An example for *AminoAcidRows* output style:
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75
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76 ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
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77 Ala,A,Alanine,89.0941..
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78 Glu,E,Glutamic acid,147.1308..
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79
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80 -o, --overwrite
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81 Overwrite existing files.
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82
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83 --precision *number*
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84 Precision for listing numerical values. Default: up to *4* decimal
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85 places. Valid values: positive integers.
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86
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87 --propertiesmode *Categories | Names | All*
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88 Specify how property names are specified: use category names;
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89 explicit list of property names; or use all available properties.
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90 Possible values: *Categories, Names, or All*. Default: *Categories*.
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91
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92 This option is used in conjunction with -p, --properties option to
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93 specify properties of interest.
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94
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95 -p, --properties *CategoryName,[CategoryName,...] |
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96 PropertyName,[PropertyName,...]*
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97 This option is --propertiesmode specific. In general, it's a list of
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98 comma separated category or property names.
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99
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100 Specify which amino acid properties information to list for the
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101 amino acid IDs specified using command: line parameters: list basic
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102 and/or hydrophobicity information; list all available information;
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103 or specify a comma separated list of amino acid property names.
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104
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105 Possible values: *Basic | BasicPlus | BasicAndHydrophobicity |
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106 BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]*.
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107 Default: *Basic*.
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108
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109 *Basic* includes: *ThreeLetterCode, OneLetterCode, AminoAcid,
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110 DNACodons, RNACodons, ChemicalFormula, MolecularWeight,
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111 LinearStructure, LinearStructureAtpH7.4*
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112
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113 *BasicPlus* includes: *ThreeLetterCode, OneLetterCode, AminoAcid,
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114 DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic,
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115 HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+,
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116 ChemicalFormula, MolecularWeight, ExactMass,
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117 ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524),
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118 ExactMassMinusH2O(18.01056), LinearStructure,
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119 LinearStructureAtpH7.4*
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120
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121 *BasicAndHydrophobicity* includes: *ThreeLetterCode, OneLetterCode,
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122 AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight,
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123 LinearStructure, LinearStructureAtpH7.4,
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124 HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods,
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125 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
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126 HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers*
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127
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128 *BasicAndHydrophobicityPlus* includes: *(ThreeLetterCode,
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129 OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula,
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130 MolecularWeight, LinearStructure, LinearStructureAtpH7.4,
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131 HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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132 HydrophobicityBullAndBreese, HydrophobicityChothia,
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133 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers,
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134 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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135 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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136 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods,
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137 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
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138 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers,
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139 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos,
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140 HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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141 HydrophobicityRoseman, HydrophobicityWellingAndOthers,
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142 HydrophobicityWolfendenAndOthers*
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143
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144 Here is a complete list of available properties: ThreeLetterCode,
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145 OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic,
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146 PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic,
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147 IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight,
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148 ExactMass, ChemicalFormulaMinusH2O,
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149 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056),
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150 vanderWaalsVolume, %AccessibleResidues, %BuriedResidues,
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151 AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt,
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152 AminoAcidsComposition, AminoAcidsCompositionInSwissProt,
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153 AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
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154 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
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155 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt,
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156 Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention,
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157 HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention,
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158 HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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159 HydrophobicityBullAndBreese, HydrophobicityChothia,
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160 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers,
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161 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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162 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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163 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods,
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164 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
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165 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers,
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166 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos,
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167 HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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168 HydrophobicityRoseman, HydrophobicityWellingAndOthers,
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169 HydrophobicityWolfendenAndOthers, ParallelBetaStrand,
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170 PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
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171 RecognitionFactors, Refractivity, RelativeMutability,
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172 TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4
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173
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174 --propertieslisting *ByGroup | Alphabetical*
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175 Specify how to list properties for amino acids: group by category or
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176 an alphabetical by property names. Possible values: *ByGroup or
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177 Alphabetical*. Default: *ByGroup*.
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178
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179 -q, --quote *yes | no*
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180 Put quotes around column values in output text file. Possible
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181 values: *yes or no*. Default value: *yes*.
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182
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183 -r, --root *rootname*
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184 New text file name is generated using the root: <Root>.<Ext>. File
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185 name is only used during *File* value of -o, --output option.
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186
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187 Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv <Ext>
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188 values are used for comma/semicolon, and tab delimited text files
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189 respectively.
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190
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191 -w, --workingdir *dirname*
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192 Location of working directory. Default: current directory.
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193
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194 EXAMPLES
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195 To list basic properties information for amino acid Ala, type:
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196
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197 % InfoAminoAcids.pl
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198
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199 To list all available properties information for amino acid Ala, type:
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200
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201 % InfoAminoAcids.pl --propertiesmode all
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202
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203 To list basic properties information for amino acids Ala, Arg, and Asp
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204 type:
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205
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206 % InfoAminoAcids.pl Ala Arg Asp
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207 % InfoAminoAcids.pl A Arg "Aspartic acid"
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208
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209 To list all available properties information for amino acids Ala, Arg,
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210 and Asp type:
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211
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212 % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp
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213
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214 To list basic and hydrophobicty properties information for amino acids
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215 Ala, Arg, and Asp type:
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216
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217 % InfoAminoAcids.pl --propertiesmode Categories
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218 --properties BasicAndHydrophobicity Ala Arg Asp
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219
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220 To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight
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221 for amino acids Ala, Arg, and Asp type:
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222
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223 % InfoAminoAcids.pl --propertiesmode Names
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224 --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
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225 Ala Arg Asp
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226
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227 To alphabetically list basic and hydrophobicty properties information
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228 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks
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229 with quotes around the values, type:
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230
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231 % InfoAminoAcids.pl --propertiesmode Categories
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232 --properties BasicAndHydrophobicity --propertieslisting alphabetical
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233 --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp
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234
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235 To alphabetically list basic and hydrophobicty properties information
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236 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks
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237 with quotes around the values and write them into a file
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238 AminoAcidProperties.csv, type:
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239
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240 % InfoAminoAcids.pl --propertiesmode Categories
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241 --properties BasicAndHydrophobicity --propertieslisting alphabetical
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242 --outdelim comma --outputstyle AminoAcidRows --quote yes
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243 --output File -r AminoAcidProperties -o Ala Arg Asp
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244
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245 AUTHOR
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246 Manish Sud <msud@san.rr.com>
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247
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248 SEE ALSO
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249 InfoNucleicAcids.pl InfoPeriodicTableElements.pl
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250
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251 COPYRIGHT
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252 Copyright (C) 2015 Manish Sud. All rights reserved.
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253
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254 This file is part of MayaChemTools.
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255
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256 MayaChemTools is free software; you can redistribute it and/or modify it
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257 under the terms of the GNU Lesser General Public License as published by
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258 the Free Software Foundation; either version 3 of the License, or (at
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259 your option) any later version.
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260
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