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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ELEMENTALANALYSIS 1"
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127 .TH ELEMENTALANALYSIS 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 ElementalAnalysis.pl \- Perform elemental analysis using specified formulas
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ElementalAnalysis.pl Formula(s)...
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137 .PP
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138 ElementalAnalysis.pl [\fB\-h, \-\-help\fR]
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139 [\fB\-m, \-\-mode\fR All | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"]
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140 [\fB\-\-outdelim\fR comma | tab | semicolon]
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141 [\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-outputstyle\fR FormulaBlock | FormulaRows]
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142 [\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname]
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143 [\fB\-v \-\-valuelabels\fR [Name, Label, [Name, Label,...]]
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144 [\fB\-w, \-\-workingdir\fR dirname] Formula(s)...
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145 .SH "DESCRIPTION"
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146 .IX Header "DESCRIPTION"
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147 Perform elemental analysis using molecular formula(s) specified on the command line.
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148 .PP
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149 In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \-
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150 other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)6]4\-, C37H42N2O6+2, Na2CO3.10H2O,
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151 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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152 D and T, are not supported.
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153 .SH "PARAMETERS"
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154 .IX Header "PARAMETERS"
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155 .IP "\fBFormulas\fR \fIFormula1 [Formula2...]\fR" 4
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156 .IX Item "Formulas Formula1 [Formula2...]"
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157 \&\fIFormulas\fR is a space delimited list of molecular formulas to use for elemental analysis.
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158 .Sp
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159 Input value format is: \fIFormula1 [Formula2 Formula3...]\fR. Default: \fIH2O\fR.
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160 Examples:
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161 .Sp
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162 .Vb 3
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163 \& HCl
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164 \& HCl, C3H7O2N
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165 \& H2O2 Ca3(PO4)2 [PCl4]+
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166 .Ve
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167 .SH "OPTIONS"
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168 .IX Header "OPTIONS"
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169 .IP "\fB\-h, \-\-help\fR" 4
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170 .IX Item "-h, --help"
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171 Print this help message.
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172 .IP "\fB\-\-fast\fR" 4
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173 .IX Item "--fast"
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174 In this mode, the specified formulas are considered valid and initial formula
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175 validation check is skipped.
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176 .ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4
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177 .el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4
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178 .IX Item "-m, --mode All | ElementalAnalysis,[MolecularWeight,ExactMass]"
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179 Specify what values to calculate using molecular formulas specified on command
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180 line: calculate all supported values or specify a comma delimited list of values. Possible
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181 values: \fIAll | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR.
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182 .IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4
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183 .IX Item "--outdelim comma | tab | semicolon"
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184 Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
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185 Default value: \fIcomma\fR.
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186 .IP "\fB\-\-output\fR \fI\s-1STDOUT\s0 | File\fR" 4
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187 .IX Item "--output STDOUT | File"
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188 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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189 \&\fI\s-1STDOUT\s0\fR. \fB\-r, \-\-root\fR option is used to generate output file name.
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190 .IP "\fB\-\-outputstyle\fR \fIFormulaBlock | FormulaRows\fR" 4
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191 .IX Item "--outputstyle FormulaBlock | FormulaRows"
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192 Specify how to list calculated values: add a new line for each property and present it as a block
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193 for each formula; or include all properties in one line and show it as a single line.
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194 .Sp
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195 Possible values: \fIFormulaBlock | FormulaRows\fR. Default: \fIFormulaBlock\fR
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196 .Sp
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197 An example for \fIFormulaBlock\fR output style:
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198 .Sp
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199 .Vb 7
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200 \& Formula: H2O
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201 \& ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
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202 \& MolecularWeight: 18.0153
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203 \& ExactMass: 18.0106
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204 \& ... ...
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205 \& ... ...
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206 \& ... ...
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207 \&
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208 \& Formula: H2O2
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209 \& ElementalAnalysis: H: 5.9265%; O: 94.0735%
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210 \& MolecularWeight: 34.0147
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211 \& ExactMass: 34.0055
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212 \& ... ...
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213 \& ... ...
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214 \& ... ...
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215 .Ve
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216 .Sp
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217 An example for \fIFormulaRows\fR output style:
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218 .Sp
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219 .Vb 3
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220 \& Formula,ElementalAnalysis,MolecularWeight,ExactMass
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221 \& H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
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222 \& H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055
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223 .Ve
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224 .IP "\fB\-o, \-\-overwrite\fR" 4
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225 .IX Item "-o, --overwrite"
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226 Overwrite existing files.
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227 .IP "\fB\-\-precision\fR \fInumber\fR" 4
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228 .IX Item "--precision number"
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229 Precision for listing numerical values. Default: up to \fI4\fR decimal places.
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230 Valid values: positive integers.
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231 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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232 .IX Item "-r, --root rootname"
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233 New text file name is generated using the root: <Root>.<Ext>. File name is only
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234 used during \fIFile\fR value of \fB\-o, \-\-output\fR option.
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235 .Sp
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236 Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
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237 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
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238 .IP "\fB\-v \-\-valuelabels\fR \fIName,Label,[Name,Label,...]\fR" 4
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239 .IX Item "-v --valuelabels Name,Label,[Name,Label,...]"
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240 Specify labels to use for calculated values. In general, it's a comma delimited
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241 list of value name and column label pairs. Supported value names: \fIElementalAnalysis,
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242 MolecularWeight, and ExactMass\fR. Default labels: \fIElementalAnalysis, MolecularWeight,
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243 and ExactMass\fR.
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244 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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245 .IX Item "-w, --workingdir dirname"
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246 Location of working directory. Default: current directory.
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247 .SH "EXAMPLES"
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248 .IX Header "EXAMPLES"
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249 To perform elemental analysis, calculate molecular weight and exact mass for H2O,
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250 type:
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251 .PP
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252 .Vb 1
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253 \& % ElementalAnalysis.pl
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254 .Ve
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255 .PP
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256 To perform elemental analysis, calculate molecular weight and exact mass for
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257 Ca3(\s-1PO4\s0)2 and [PCl4]+, type:
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258 .PP
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259 .Vb 1
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260 \& % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
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261 .Ve
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262 .PP
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263 To perform elemental analysis, use label analysis for calculated data, and generate a
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264 new \s-1CSV\s0 file ElementalAnalysis.csv for H2O and H2O2, type:
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265 .PP
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266 .Vb 3
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267 \& % ElementalAnalysis.pl \-\-m ElementalAnalysis \-\-output File
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268 \& \-\-valuelabels "ElementalAnalysis,Analysis" \-o \-r ElementalAnalysis.csv
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269 \& H2O H2O2
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270 .Ve
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271 .PP
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272 To calculate molecular weight and exact mass with four decimal precision and
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273 generate a new \s-1CSV\s0 file WeightAndMass.csv with data rows for H2O and H2O2, type:
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274 .PP
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275 .Vb 3
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276 \& % ElementalAnalysis.pl \-\-m "MolecularWeight,ExactMass" \-\-output File
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277 \& \-\-outputstyle FormulaRows \-o \-r WeightAndMass.csv
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278 \& H2O H2O2
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279 .Ve
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280 .SH "AUTHOR"
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281 .IX Header "AUTHOR"
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282 Manish Sud <msud@san.rr.com>
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283 .SH "SEE ALSO"
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284 .IX Header "SEE ALSO"
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285 ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl
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286 .SH "COPYRIGHT"
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287 .IX Header "COPYRIGHT"
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288 Copyright (C) 2015 Manish Sud. All rights reserved.
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289 .PP
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290 This file is part of MayaChemTools.
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291 .PP
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292 MayaChemTools is free software; you can redistribute it and/or modify it under
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293 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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294 Software Foundation; either version 3 of the License, or (at your option)
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295 any later version.
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