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124 .\" ========================================================================
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125 .\"
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126 .IX Title "INFOSDFILES 1"
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127 .TH INFOSDFILES 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 InfoSDFiles.pl \- List information about SDFile(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 InfoSDFile.pl SDFile(s)...
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137 .PP
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138 InfoSDFile.pl [\fB\-a \-\-all\fR] [\fB\-c \-\-count\fR] [\fB\-\-chiral\fR] [\fB\-\-datacheck\fR]
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139 [\fB\-d \-\-detail\fR infolevel] [\fB\-e \-\-empty\fR] [\fB\-f, \-\-fields\fR] [\fB\-h, \-\-help\fR]
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140 [\fB\-i, \-\-invalidatomnumbers\fR] [\fB\-m, \-\-mismatch\fR] [\fB\-s, \-\-salts\fR] [\fB\-u, \-\-unknownatoms\fR]
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141 [\fB\-w, \-\-workingdir\fR dirname] SDFile(s)...
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142 .SH "DESCRIPTION"
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143 .IX Header "DESCRIPTION"
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144 List information about \fISDFile(s)\fR contents: number of compounds, empty records
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145 and so on. Multiple SDFile names are separated by spaces. The valid file extensions
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146 are \fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current
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147 directory can be specified either by \fI*.sdf\fR or the current directory name.
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148 .SH "OPTIONS"
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149 .IX Header "OPTIONS"
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150 .IP "\fB\-a, \-\-all\fR" 4
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151 .IX Item "-a, --all"
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152 List all the available information.
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153 .IP "\fB\-c, \-\-count\fR" 4
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154 .IX Item "-c, --count"
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155 List number of compounds. This is \fBdefault behavior\fR.
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156 .IP "\fB\-\-chiral\fR" 4
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157 .IX Item "--chiral"
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158 List number of empty atom/bond blocks for compounds with chiral flag set in
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159 count line.
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160 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
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161 .IX Item "-d, --detail infolevel"
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162 Level of information to print. Default: 1. Possible values: \fI1, 2, or 3\fR.
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163 .IP "\fB\-\-datacheck\fR" 4
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164 .IX Item "--datacheck"
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165 List number of numerical and non-numerical values for each data field.
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166 .IP "\fB\-e, \-\-empty\fR" 4
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167 .IX Item "-e, --empty"
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168 List number of empty atom/bond blocks and data fields for compounds.
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169 .IP "\fB\-f, \-\-fields\fR" 4
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170 .IX Item "-f, --fields"
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171 List data field labels present for compounds.
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172 .IP "\fB\-h, \-\-help\fR" 4
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173 .IX Item "-h, --help"
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174 Print this help message.
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175 .IP "\fB\-i, \-\-invalidatomnumbers\fR" 4
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176 .IX Item "-i, --invalidatomnumbers"
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177 List number of bond blocks for compounds which contain invalid atom numbers.
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178 .IP "\fB\-m, \-\-mismatch\fR" 4
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179 .IX Item "-m, --mismatch"
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180 List number of atom/bond blocks for compounds which don't match with counts
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181 line information in header block.
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182 .IP "\fB\-s, \-\-salts\fR" 4
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183 .IX Item "-s, --salts"
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184 List number of atom blocks for compounds which contain salts identified as
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185 disconnected structural units.
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186 .IP "\fB\-u, \-\-unknownatoms\fR" 4
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187 .IX Item "-u, --unknownatoms"
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188 List number of atom blocks for compounds which contain special atom symbols
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189 such as L, Q, * ,LP, X, R#, or any other non periodic table symbols.
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190 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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191 .IX Item "-w, --workingdir dirname"
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192 Location of working directory. Default: current directory.
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193 .SH "EXAMPLES"
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194 .IX Header "EXAMPLES"
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195 To count compounds in \s-1SD\s0 file(s), type:
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196 .PP
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197 .Vb 3
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198 \& % InfoSDFiles.pl Sample1.sdf
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199 \& % InfoSDFiles.pl Sample1.sdf Sample2.sdf
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200 \& % InfoSDFiles.pl *.sdf
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201 .Ve
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202 .PP
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203 To list all available information for \s-1SD\s0 file(s), type:
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204 .PP
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205 .Vb 1
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206 \& % InfoSDFiles.pl \-a *.sdf
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207 .Ve
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208 .PP
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209 To list all data fields present in sample.sdf, type:
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210 .PP
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211 .Vb 1
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212 \& % InfoSDFiles.pl \-f Sample.sdf
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213 .Ve
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214 .PP
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215 To count number of compounds which contain salts and list associated structural
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216 data, type:
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217 .PP
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218 .Vb 1
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219 \& % InfoSDFiles.pl \-s \-d 3 Sample.sdf
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220 .Ve
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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 ExtractFromSDFiles.pl, FilterSDFiles.pl, MergeTextFilesWithSD.pl
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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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