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124 .\" ========================================================================
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125 .\"
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126 .IX Title "INFOAMINOACIDS 1"
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127 .TH INFOAMINOACIDS 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 InfoAminoAcids.pl \- List properties of amino acids
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 InfoAminoAcids.pl AminoAcidIDs...
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137 .PP
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138 InfoAminoAcids.pl [\fB\-h, \-\-help\fR] [\fB\-\-outdelim\fR comma | tab | semicolon]
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139 [\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-outputstyle\fR AminoAcidBlock | AminoAcidRows]
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140 [\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-\-propertiesmode\fR Categories | Names | All]
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141 [\fB\-p, \-\-properties\fR CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
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142 [\fB\-\-propertieslinting\fR ByGroup | Alphabetical] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname]
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143 [\fB\-w, \-\-workingdir\fR dirname] AminoAcidIDs...
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144 .SH "DESCRIPTION"
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145 .IX Header "DESCRIPTION"
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146 List amino acid properties. Amino acids identification supports these three types of IDs: one letter
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147 code, three letter code or name. Amino acid properties data, in addition to basic information about
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148 amino acids \- one and three letter codes, name, \s-1DNA\s0 and \s-1RNA\s0 codons, molecular weight \- include
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149 variety of other properties: polarity, acidity, hydrophobicity, and so on.
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150 .SH "PARAMETERS"
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151 .IX Header "PARAMETERS"
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152 .IP "\fBAminoAcidIDs\fR \fIThreeLetterCode [OneLetterCode AminoAcidName...]\fR" 4
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153 .IX Item "AminoAcidIDs ThreeLetterCode [OneLetterCode AminoAcidName...]"
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154 \&\fIAminoAcidIDs\fR is a space delimited list of values to identify amino acids.
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155 .Sp
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156 Input value format is: \fIThreeLetterCode [OneLetterCode AminoAcidName...]\fR. Default: \fIAla\fR.
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157 Examples:
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158 .Sp
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159 .Vb 3
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160 \& Ala
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161 \& Glu A
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162 \& Alanine Glu Y "Aspartic acid"
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163 .Ve
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164 .SH "OPTIONS"
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165 .IX Header "OPTIONS"
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166 .IP "\fB\-h, \-\-help\fR" 4
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167 .IX Item "-h, --help"
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168 Print this help message.
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169 .IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4
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170 .IX Item "--outdelim comma | tab | semicolon"
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171 Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
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172 Default value: \fIcomma\fR.
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173 .IP "\fB\-\-output\fR \fI\s-1STDOUT\s0 | File\fR" 4
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174 .IX Item "--output STDOUT | File"
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175 List information at \s-1STDOUT\s0 or write it to a file. Possible values: \fI\s-1STDOUT\s0 or File\fR. Default:
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176 \&\fI\s-1STDOUT\s0\fR. \fB\-r, \-\-root\fR option is used to generate output file name.
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177 .IP "\fB\-\-outputstyle\fR \fIAminoAcidBlock | AminoAcidRows\fR" 4
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178 .IX Item "--outputstyle AminoAcidBlock | AminoAcidRows"
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179 Specify how to list amino acid information: add a new line for each property and present it as a block
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180 for each amino acid; or include all properties in one line and show it as a single line.
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181 .Sp
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182 Possible values: \fIAminoAcidBlock | AminoAcidRows\fR. Default: \fIAminoAcidBlock\fR
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183 .Sp
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184 An example for \fIAminoAcidBlock\fR output style:
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185 .Sp
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186 .Vb 7
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187 \& ThreeLetterCode: Ala
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188 \& OneLetterCode: A
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189 \& AminoAcid: Alanine
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190 \& MolecularWeight: 89.0941
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191 \& ... ...
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192 \& ... ...
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193 \& ... ...
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194 \&
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195 \& ThreeLetterCode: Glu
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196 \& OneLetterCode: E
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197 \& AminoAcid: Glutamic acid
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198 \& MolecularWeight: 147.1308
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199 \& ... ...
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200 \& ... ...
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201 \& ... ...
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202 .Ve
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203 .Sp
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204 An example for \fIAminoAcidRows\fR output style:
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205 .Sp
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206 .Vb 3
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207 \& ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
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208 \& Ala,A,Alanine,89.0941..
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209 \& Glu,E,Glutamic acid,147.1308..
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210 .Ve
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211 .IP "\fB\-o, \-\-overwrite\fR" 4
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212 .IX Item "-o, --overwrite"
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213 Overwrite existing files.
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214 .IP "\fB\-\-precision\fR \fInumber\fR" 4
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215 .IX Item "--precision number"
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216 Precision for listing numerical values. Default: up to \fI4\fR decimal places.
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217 Valid values: positive integers.
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218 .IP "\fB\-\-propertiesmode\fR \fICategories | Names | All\fR" 4
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219 .IX Item "--propertiesmode Categories | Names | All"
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220 Specify how property names are specified: use category names; explicit list of property names; or
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221 use all available properties. Possible values: \fICategories, Names, or All\fR. Default: \fICategories\fR.
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222 .Sp
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223 This option is used in conjunction with \fB\-p, \-\-properties\fR option to specify properties of
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224 interest.
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225 .IP "\fB\-p, \-\-properties\fR \fICategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]\fR" 4
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226 .IX Item "-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]"
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227 This option is \fB\-\-propertiesmode\fR specific. In general, it's a list of comma separated category or
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228 property names.
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229 .Sp
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230 Specify which amino acid properties information to list for the amino acid IDs specified using command:
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231 line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma
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232 separated list of amino acid property names.
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233 .Sp
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234 Possible values: \fIBasic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]\fR.
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235 Default: \fIBasic\fR.
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236 .Sp
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237 \&\fIBasic\fR includes: \fIThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4\fR
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238 .Sp
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239 \&\fIBasicPlus\fR includes: \fIThreeLetterCode, 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\fR
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240 .Sp
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241 \&\fIBasicAndHydrophobicity\fR includes: \fIThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers\fR
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242 .Sp
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243 \&\fIBasicAndHydrophobicityPlus\fR includes: \fI(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\fR
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244 .Sp
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245 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, \f(CW%AccessibleResidues\fR, \f(CW%BuriedResidues\fR, 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
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246 .IP "\fB\-\-propertieslisting\fR \fIByGroup | Alphabetical\fR" 4
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247 .IX Item "--propertieslisting ByGroup | Alphabetical"
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248 Specify how to list properties for amino acids: group by category or an alphabetical by
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249 property names. Possible values: \fIByGroup or Alphabetical\fR. Default: \fIByGroup\fR.
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250 .IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4
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251 .IX Item "-q, --quote yes | no"
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252 Put quotes around column values in output text file. Possible values: \fIyes or
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253 no\fR. Default value: \fIyes\fR.
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254 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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255 .IX Item "-r, --root rootname"
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256 New text file name is generated using the root: <Root>.<Ext>. File name is only
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257 used during \fIFile\fR value of \fB\-o, \-\-output\fR option.
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258 .Sp
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259 Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv
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260 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
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261 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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262 .IX Item "-w, --workingdir dirname"
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263 Location of working directory. Default: current directory.
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264 .SH "EXAMPLES"
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265 .IX Header "EXAMPLES"
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266 To list basic properties information for amino acid Ala, type:
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267 .PP
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268 .Vb 1
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269 \& % InfoAminoAcids.pl
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270 .Ve
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271 .PP
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272 To list all available properties information for amino acid Ala, type:
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273 .PP
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274 .Vb 1
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275 \& % InfoAminoAcids.pl \-\-propertiesmode all
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276 .Ve
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277 .PP
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278 To list basic properties information for amino acids Ala, Arg, and Asp type:
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279 .PP
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280 .Vb 2
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281 \& % InfoAminoAcids.pl Ala Arg Asp
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282 \& % InfoAminoAcids.pl A Arg "Aspartic acid"
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283 .Ve
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284 .PP
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285 To list all available properties information for amino acids Ala, Arg, and Asp type:
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286 .PP
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287 .Vb 1
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288 \& % InfoAminoAcids.pl \-\-propertiesmode all Ala Arg Asp
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289 .Ve
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290 .PP
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291 To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:
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292 .PP
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293 .Vb 2
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294 \& % InfoAminoAcids.pl \-\-propertiesmode Categories
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295 \& \-\-properties BasicAndHydrophobicity Ala Arg Asp
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296 .Ve
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297 .PP
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298 To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino
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299 acids Ala, Arg, and Asp type:
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300 .PP
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301 .Vb 3
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302 \& % InfoAminoAcids.pl \-\-propertiesmode Names
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303 \& \-\-properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
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304 \& Ala Arg Asp
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305 .Ve
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306 .PP
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307 To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
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308 in rows insetad of amino acid blocks with quotes around the values, type:
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309 .PP
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310 .Vb 3
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311 \& % InfoAminoAcids.pl \-\-propertiesmode Categories
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312 \& \-\-properties BasicAndHydrophobicity \-\-propertieslisting alphabetical
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313 \& \-\-outdelim comma \-\-outputstyle AminoAcidRows \-\-quote yes Ala Arg Asp
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314 .Ve
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315 .PP
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316 To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
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317 in rows insetad of amino acid blocks with quotes around the values and write them into a file
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318 AminoAcidProperties.csv, type:
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319 .PP
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320 .Vb 4
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321 \& % InfoAminoAcids.pl \-\-propertiesmode Categories
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322 \& \-\-properties BasicAndHydrophobicity \-\-propertieslisting alphabetical
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323 \& \-\-outdelim comma \-\-outputstyle AminoAcidRows \-\-quote yes
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324 \& \-\-output File \-r AminoAcidProperties \-o Ala Arg Asp
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325 .Ve
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326 .SH "AUTHOR"
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327 .IX Header "AUTHOR"
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328 Manish Sud <msud@san.rr.com>
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329 .SH "SEE ALSO"
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330 .IX Header "SEE ALSO"
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331 InfoNucleicAcids.pl InfoPeriodicTableElements.pl
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332 .SH "COPYRIGHT"
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333 .IX Header "COPYRIGHT"
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334 Copyright (C) 2015 Manish Sud. All rights reserved.
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335 .PP
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336 This file is part of MayaChemTools.
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337 .PP
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338 MayaChemTools is free software; you can redistribute it and/or modify it under
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339 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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340 Software Foundation; either version 3 of the License, or (at your option)
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341 any later version.
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