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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ELEMENTALANALYSISSDFILES 1"
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127 .TH ELEMENTALANALYSISSDFILES 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 ElementalAnalysisSDFiles.pl \- Perform elemental analysis using formula data field in SDFile(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ElementalAnalysisSDFiles.pl SDFile(s)...
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137 .PP
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138 ElementalAnalysisSDFiles.pl [\fB\-d, \-\-detail\fR infolevel] [\fB\-\-fast\fR]
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139 [\fB\-\-formulafield\fR \s-1SD\s0 data field name] [\fB\-f, \-\-formulamode\fR \fIDataField | StructureData\fR]
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140 [\fB\-\-formulaout\fR yes or no] [\fB\-m, \-\-mode\fR All | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"]
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141 [\fB\-h, \-\-help\fR] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname]
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142 [\fB\-v \-\-valuefieldnames\fR Name, Label, [Name, Label,...]] [\fB\-w, \-\-workingdir\fR dirname] SDFile(s)...
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143 .SH "DESCRIPTION"
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144 .IX Header "DESCRIPTION"
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145 Perform elemental analysis using molecular formula specified by a data field name or generated
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146 from structure data in \fISDFile(s)\fR.
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147 .PP
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148 In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \-
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149 other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)6]4\-, C37H42N2O6+2, Na2CO3.10H2O,
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150 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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151 D and T, are not supported.
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152 .PP
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153 The file names are separated by space.The valid file extensions are \fI.sdf\fR and \fI.sd\fR.
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154 All other file names are ignored. All the \s-1SD\s0 files in a current directory can be specified
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155 either by \fI*.sdf\fR or the current directory name.
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156 .SH "OPTIONS"
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157 .IX Header "OPTIONS"
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158 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
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159 .IX Item "-d, --detail infolevel"
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160 Level of information to print about compound records being ignored. Default: \fI1\fR. Possible
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161 values: \fI1, 2 or 3\fR.
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162 .IP "\fB\-\-fast\fR" 4
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163 .IX Item "--fast"
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164 In this mode, the formula data field specified using \fB\-f, \-\-formulafield\fR option is assumed
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165 to contain valid molecular formula data and initial formula validation check is skipped.
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166 .IP "\fB\-\-formulafield\fR \fI\s-1SD\s0 data field name\fR" 4
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167 .IX Item "--formulafield SD data field name"
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168 \&\fISDFile(s)\fR data field name containing molecular formulas used for performing
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169 elemental analysis during \fIDataField\fR value of \fB\-f, \-\-formulamode\fR option.
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170 Default value: \fI\s-1SD\s0 data field containing the word formula in its name\fR.
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171 .Sp
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172 This option is ignore during \fIStructureData\fR value of \fB\-f, \-\-formulamode\fR option.
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173 .IP "\fB\-f, \-\-formulamode\fR \fIDataField | StructureData\fR" 4
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174 .IX Item "-f, --formulamode DataField | StructureData"
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175 Specify source of molecular formula used for performing elemental analysis: retrieve
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176 formula using \fISDFile(s)\fR data field name or generate formula from structure. Possible
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177 values: \fIDataField or StructureData\fR. Default value: \fIDataField\fR.
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178 .IP "\fB\-\-formulaout\fR \fIyes or no\fR" 4
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179 .IX Item "--formulaout yes or no"
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180 Specify whether to write out formula to \s-1SD\s0 file during \fIStructureData\fR value of
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181 \&\fB\-f, \-\-formulamode\fR option. Possible values: \fIYes or No\fR. Default: \fINo\fR.
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182 .ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4
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183 .el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4
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184 .IX Item "-m, --mode All | ElementalAnalysis,[MolecularWeight,ExactMass]"
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185 Specify what values to calculate using molecular formula data field or structure data from
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186 \&\fISDFile(s)\fR: calculate all supported values or specify a comma delimited list of values.
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187 Possible values: \fIAll | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR
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188 .IP "\fB\-h, \-\-help\fR" 4
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189 .IX Item "-h, --help"
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190 Print this help message.
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191 .IP "\fB\-o, \-\-overwrite\fR" 4
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192 .IX Item "-o, --overwrite"
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193 Overwrite existing files.
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194 .IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4
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195 .IX Item "-p, --precision number"
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196 Precision of calculated values in the output file. Default: up to \fI2\fR decimal places.
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197 Valid values: positive integers.
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198 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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199 .IX Item "-r, --root rootname"
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200 New \s-1SD\s0 file name is generated using the root: <Root>.<Ext>. Default new file
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201 name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple
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202 input files.
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203 .IP "\fB\-v \-\-valuefieldnames\fR \fIName,Label,[Name,Label,...]\fR" 4
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204 .IX Item "-v --valuefieldnames Name,Label,[Name,Label,...]"
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205 Specify \s-1SD\s0 data field names to use for calculated values. In general, it's a comma delimited
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206 list of value name and \s-1SD\s0 field name pairs. Supported value names: \fIElementalAnalysis,
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207 MolecularWeight, ExactMass, and MolecularFormula\fR. Default labels: \fIElementalAnalysis,
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208 MolecularWeight, ExactMass, and MolecularFormula\fR.
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209 .Sp
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210 \&\fIMolecularFormula\fR label is only used during \fIStructureData\fR value of
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211 \&\fB\-f, \-\-formulamode\fR option.
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212 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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213 .IX Item "-w, --workingdir dirname"
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214 Location of working directory. Default: current directory.
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215 .SH "EXAMPLES"
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216 .IX Header "EXAMPLES"
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217 To perform elemental analysis, calculate molecular weight and exact mass using \s-1SD\s0
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218 field name value with the word Formula in its name and generate a new \s-1SD\s0 file
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219 NewSample1.sdf, type:
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220 .PP
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221 .Vb 1
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222 \& % ElementalAnalysisSDFiles.pl \-o \-r NewSample1 Sample1.sdf
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223 .Ve
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224 .PP
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225 To perform elemental analysis, calculate molecular weight and exact mass using
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226 structure data in \s-1SD\s0 file and generate a new \s-1SD\s0 file NewSample1.sdf, type:
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227 .PP
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228 .Vb 2
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229 \& % ElementalAnalysisSDFiles.pl \-\-formulamode StructureData \-o
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230 \& \-r NewSample1 Sample1.sdf
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231 .Ve
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232 .PP
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233 To perform elemental analysis using formulas in \s-1SD\s0 field name Formula, use field name
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234 Analysis for calculated data, and generate a new \s-1SD\s0 file NewSample1.sdf, type:
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235 .PP
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236 .Vb 3
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237 \& % ElementalAnalysisSDFiles.pl \-\-m ElementalAnalysis \-\-formulafield
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238 \& Formula \-\-valuefieldnames "ElementalAnalysis,Analysis" \-o
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239 \& \-r NewSample1 Sample1.sdf
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240 .Ve
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241 .PP
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242 To calculate molecular weight, using formulas in \s-1SD\s0 field name Formula, with four decimal
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243 precision and generate a new \s-1SD\s0 file NewSample1.sdf, type
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244 .PP
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245 .Vb 2
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246 \& % ElementalAnalysisSDFiles.pl \-\-m MolecularWeight \-\-formulafield
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247 \& Formula \-\-precision 4 \-o \-r NewSample1 Sample1.sdf
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248 .Ve
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249 .SH "AUTHOR"
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250 .IX Header "AUTHOR"
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251 Manish Sud <msud@san.rr.com>
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252 .SH "SEE ALSO"
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253 .IX Header "SEE ALSO"
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254 AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
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255 .SH "COPYRIGHT"
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256 .IX Header "COPYRIGHT"
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257 Copyright (C) 2015 Manish Sud. All rights reserved.
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258 .PP
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259 This file is part of MayaChemTools.
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260 .PP
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261 MayaChemTools is free software; you can redistribute it and/or modify it under
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262 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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263 Software Foundation; either version 3 of the License, or (at your option)
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264 any later version.
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