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124 .\" ========================================================================
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125 .\"
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126 .IX Title "AMINOACIDS 1"
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127 .TH AMINOACIDS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 AminoAcids
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use AminoAcids;
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137 .PP
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138 use AminoAcids qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBAminoAcids\fR module provides the following functions:
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142 .PP
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143 GetAminoAcidPropertiesData, GetAminoAcidPropertiesNames, GetAminoAcid<PropertyName>,
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144 GetAminoAcids, IsAminoAcid, IsAminoAcidProperty
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145 .SH "FUNCTIONS"
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146 .IX Header "FUNCTIONS"
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147 .IP "\fBGetAminoAcidPropertiesData\fR" 4
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148 .IX Item "GetAminoAcidPropertiesData"
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149 .Vb 1
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150 \& $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);
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151 .Ve
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152 .Sp
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153 Returns a reference to hash containing property names and values for a specified
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154 amino acid.
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155 .IP "\fBGetAminoAcidPropertiesNames\fR" 4
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156 .IX Item "GetAminoAcidPropertiesNames"
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157 .Vb 2
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158 \& @Names = GetAminoAcidPropertiesNames([$Mode]);
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159 \& $NamesRef = GetAminoAcidPropertiesNames([$Mode]);
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160 .Ve
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161 .Sp
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162 Returns an array or a reference to an array containing names of amino acids
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163 properties. Order of amino acids properties is controlled by optional parameter
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164 \&\fIMode\fR. Possible values for \fIMode\fR: \fIAlphabetical or ByGroup\fR; Default: \fIByGroup\fR
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165 .IP "\fBGetAminoAcidPropertyName\fR" 4
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166 .IX Item "GetAminoAcidPropertyName"
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167 .Vb 1
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168 \& $Value = GetAminoAcid<PropertyName>($AminoAcidID);
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169 .Ve
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170 .Sp
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171 Returns amino acid property value for a specified amino acid. These functions are
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172 not defined in this modules; these are implemented on the fly using Perl's \s-1AUTOLOAD\s0
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173 funcion. Here is the list of known amino acids \fIproperty names\fR: DNACodons, RNACodons,
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174 AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint,
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175 pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O,
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176 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume,
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177 \&\f(CW%AccessibleResidues\fR, \f(CW%BuriedResidues\fR, AlphaHelixChouAndFasman,
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178 AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition,
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179 AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
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180 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
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181 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness,
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182 CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4,
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183 HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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184 HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers,
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185 HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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186 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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187 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin,
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188 HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers,
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189 HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers,
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190 HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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191 HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers,
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192 ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
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193 RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure,
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194 LinearStructureAtpH7.4
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195 .IP "\fBGetAminoAcids\fR" 4
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196 .IX Item "GetAminoAcids"
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197 .Vb 2
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198 \& $NamesRef = GetAminoAcids([$NameType]);
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199 \& (@Names) = GetAminoAcids([$NameType]);
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200 .Ve
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201 .Sp
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202 Returns an array or a reference to an array containing names of amino acids
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203 as one letter code, three letter code, or amino acid name controlled by optional
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204 parameter \f(CW$NameType\fR. By default, amino acids names are returned as three
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205 letter code. Possible values for \fINameType\fR: \fIThreeLetterCode, OneLetterCode, or
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206 AminoAcid\fR.
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207 .IP "\fBIsAminoAcid\fR" 4
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208 .IX Item "IsAminoAcid"
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209 .Vb 1
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210 \& $Status = IsAminoAcid($AminoAcidID);
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211 .Ve
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212 .Sp
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213 Returns a flag indicating whether or not its a known amino acid \s-1ID\s0.
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214 .IP "\fBIsAminoAcidProperty\fR" 4
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215 .IX Item "IsAminoAcidProperty"
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216 .Vb 1
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217 \& $Status = IsAminoAcid($PropertyName);
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218 .Ve
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219 .Sp
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220 Returns a flag indicating whether or not its a known amino acid property name.
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221 .SH "AUTHOR"
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222 .IX Header "AUTHOR"
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223 Manish Sud <msud@san.rr.com>
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224 .SH "SEE ALSO"
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225 .IX Header "SEE ALSO"
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226 NucleicAcids.pm, PeriodicTable.pm
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227 .SH "COPYRIGHT"
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228 .IX Header "COPYRIGHT"
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229 Copyright (C) 2015 Manish Sud. All rights reserved.
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230 .PP
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231 This file is part of MayaChemTools.
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232 .PP
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233 MayaChemTools is free software; you can redistribute it and/or modify it under
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234 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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235 Software Foundation; either version 3 of the License, or (at your option)
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236 any later version.
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