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124 .\" ========================================================================
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125 .\"
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126 .IX Title "INFOPDBFILES 1"
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127 .TH INFOPDBFILES 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 InfoPDBFiles.pl \- List information about PDB files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 InfoPDBFiles.pl PDBFile(s) \s-1PDB\s0(s)...
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137 .PP
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138 InfoPDBFiles.pl [\fB\-a, \-\-all\fR] [\fB\-b, \-\-BoundingBox\fR]
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139 [\fB\-c, \-\-count\fR \*(L"RecordType, [RecordType,...]\*(R" | All] [\fB\-\-chains\fR]
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140 [\fB\-d, \-\-detail\fR infolevel] [\fB\-e, \-\-experiment\fR] [\fB\-f, \-\-frequency\fR]
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141 [\fB\-h, \-\-help\fR] [\fB\-\-header\fR] [\fBm, \-\-MasterCheck\fR] [\fB\-\-residues\fR]
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142 [\fB\-\-ResiduesMode\fR InChains | All | Both] [\fB\-\-ResidueNumbers\fR]
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143 [\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)...
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144 .SH "DESCRIPTION"
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145 .IX Header "DESCRIPTION"
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146 List information about contents of \fIPDBFile(s)\fR: number of each record type, number of chains,
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147 count and percent distribution of residues in each chain, bounding box and so on.
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148 Multiple PDBFile names are separated by spaces. The valid file extension is \fI.pdb\fR.
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149 All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files
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150 in a current directory can be specified either by \fI*.pdb\fR or the current directory name.
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151 .PP
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152 In \s-1PDB\s0 files containing data for multiple models, all \s-1ATOM/HETAM\s0 records for chains after the first model
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153 are ignored.
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154 .SH "OPTIONS"
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155 .IX Header "OPTIONS"
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156 .IP "\fB\-a, \-\-all\fR" 4
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157 .IX Item "-a, --all"
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158 List all the available information.
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159 .IP "\fB\-b, \-\-BoundingBox\fR" 4
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160 .IX Item "-b, --BoundingBox"
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161 List min/max \s-1XYZ\s0 coordiates of \s-1ATOM/HETATM\s0 records.
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162 .IP "\fB\-c, \-\-count\fR \fIRecordType,[RecordType,...]|All\fR" 4
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163 .IX Item "-c, --count RecordType,[RecordType,...]|All"
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164 Types of \s-1PDB\s0 records to count in \fIPDBFile(s)\fR. You can specify a list of any valid \s-1PDB\s0
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165 record type or count all record types found in the files. Possible values: Comma delimited list
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166 of valid \fIRecordTypes\fR or \fIAll\fR. Default: \fI\s-1ATOM\s0,HETATM\fR. And this is also \fBdefault behavior\fR.
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167 .Sp
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168 The list of valid \s-1PDB\s0 record types includes: \fI\s-1HEADER\s0, \s-1OBSLTE\s0, \s-1TITLE\s0, \s-1CAVEAT\s0, \s-1COMPND\s0, \s-1SOURCE\s0, \s-1KEYWDS\s0,
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169 \&\s-1EXPDTA\s0, \s-1AUTHOR\s0, \s-1REVDAT\s0, \s-1SPRSDE\s0, \s-1JRN\s0, \s-1REMARK\s0, \s-1DBRE\s0, \s-1SEQADV\s0, \s-1SEQRES\s0, \s-1MODRES\s0, \s-1HET\s0, \s-1HETNAM\s0, \s-1HETSYN\s0,
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170 \&\s-1FORMUL\s0, \s-1HELIX\s0, \s-1SHEET\s0, \s-1TURN\s0, \s-1SSBOND\s0, \s-1LINK\s0, \s-1HYDBND\s0, \s-1SLTBRG\s0, \s-1CISPEP\s0, \s-1SITE\s0, \s-1CRYST1\s0, \s-1ORIGX1\s0, \s-1ORIGX2\s0, \s-1ORIGX3\s0,
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171 \&\s-1SCALE1\s0, \s-1SCALE2\s0, \s-1SCALE3\s0, \s-1MTRIX1\s0 \s-1MTRIX2\s0 \s-1MTRIX3\s0, \s-1TVECT\s0, \s-1MODEL\s0, \s-1ATOM\s0, \s-1SIGATM\s0, \s-1ANISOU\s0, \s-1SIGUIJ\s0, \s-1TER\s0,
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172 \&\s-1HETATM\s0, \s-1ENDMDL\s0, \s-1CONECT\s0, \s-1MASTER\s0, \s-1END\s0\fR.
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173 .IP "\fB\-\-chains\fR" 4
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174 .IX Item "--chains"
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175 Count number of chains.
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176 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
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177 .IX Item "-d, --detail infolevel"
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178 Level of information to print about \s-1PDB\s0 during various options. Default: \fI1\fR.
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179 Possible values: \fI1, 2 or 3\fR.
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180 .IP "\fB\-e, \-\-experiment\fR" 4
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181 .IX Item "-e, --experiment"
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182 List experimental technique information along with any applicable resolution.
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183 .IP "\fB\-f, \-\-frequency\fR" 4
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184 .IX Item "-f, --frequency"
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185 List distribution of residues: report count and percent of residues in individual chains and
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186 across all the chains, or for all the residues in the file. The value of option \fB\-\-residuesmode\fR
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187 determines how residues are counted and what is listed. The list is sorted by frequency in
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188 descending order. By default, only residue count values are reported. To list percent distribution
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189 of residues, specify \fB\-d, \-\-detail\fR value of \fI2\fR or higher.
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190 .IP "\fB\-h, \-\-help\fR" 4
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191 .IX Item "-h, --help"
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192 Print this help message.
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193 .IP "\fB\-\-header\fR" 4
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194 .IX Item "--header"
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195 List header information.
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196 .IP "\fBm, \-\-MasterCheck\fR" 4
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197 .IX Item "m, --MasterCheck"
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198 Check master record by explicitly counting the number of \s-1REMARK\s0, \s-1HET\s0, \s-1HELIX\s0, \s-1SHEET\s0, \s-1TURN\s0, \s-1SITE\s0,
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199 \&\s-1ORIGX\s0, \s-1SCALE\s0, \s-1MTRIX\s0, \s-1ATOM\s0, \s-1HETATM\s0, \s-1TER\s0, \s-1CONECT\s0 and \s-1SEQRES\s0 records and comparing their
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200 values against contents of master record.
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201 .IP "\fB\-\-residues\fR" 4
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202 .IX Item "--residues"
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203 Count residues in \fIPDBFile(s)\fR. This is also \fBdefault behavior\fR.
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204 .Sp
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205 By default, only residue count values are reported. To list percent distribution of residues,
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206 specify \fB\-d, \-\-detail\fR value of \fI2\fR or higher.
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207 .IP "\fB\-\-ResiduesMode\fR <InChains | All | Both>" 4
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208 .IX Item "--ResiduesMode <InChains | All | Both>"
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209 Specify how to count residues in \fIPDBFile(s)\fR: Count residue in each chain and across all the chains,
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210 list count iof all the residues in the file, or list both. Possible values: \fIInChains, All, or Both\fR.
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211 Default: \fIBoth\fR.
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212 .IP "\fB\-\-ResidueNumbers\fR" 4
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213 .IX Item "--ResidueNumbers"
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214 List information about \s-1ATOM\s0 residue numbers in each chain before \s-1TER\s0 record: start and end residue
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215 number; gaps in residue numbers corresponding to non-sequential residue numbers; residue
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216 numbers not in ascending order.
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217 .IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
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218 .IX Item "-w, --WorkingDir dirname"
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219 Location of working directory. Default: current directory.
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220 .SH "EXAMPLES"
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221 .IX Header "EXAMPLES"
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222 To list total number of records and number of chain(s) residues in \s-1PDB\s0 files, type:
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223 .PP
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224 .Vb 2
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225 \& % InfoPDBFiles.pl Sample1.pdb
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226 \& % InfoPDBFiles.pl Sample2.pdb
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227 .Ve
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228 .PP
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229 To list all available information for \s-1PDB\s0 file Sample2.pdb, type:
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230 .PP
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231 .Vb 1
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232 \& % InfoPDBFiles.pl \-a Sample2.pdb
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233 .Ve
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234 .PP
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235 To list all available information for \s-1PDB\s0 file Sample2.pdb with all available details, type:
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236 .PP
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237 .Vb 1
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238 \& % InfoPDBFiles.pl \-a \-d Sample2.pdb
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239 .Ve
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240 .PP
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241 To count \s-1ATOM\s0 and \s-1HETATM\s0 records in Sample2.pdb file, type:
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242 .PP
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243 .Vb 1
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244 \& % InfoPDBFiles.pl \-c "ATOM,HETATM" Sample2.pdb
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245 .Ve
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246 .PP
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247 To list distribution of residues in chains across the whole \s-1PDB\s0 file Sample2.pdb along with
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248 percent distribution, type
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249 .PP
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250 .Vb 1
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251 \& % InfoPDBFiles.pl \-\-frequency \-d 2 Sample2.pdb
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252 .Ve
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253 .PP
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254 To list distribution of residues only across chains in \s-1PDB\s0 file Sample2.pdb along with
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255 percent distribution, type
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256 .PP
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257 .Vb 1
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258 \& % InfoPDBFiles.pl \-\-frequency \-d 2 \-\-ResiduesMode InChains Sample2.pdb
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259 .Ve
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260 .PP
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261 To list min/max coordinates of the bounding box which encompasses the structure in Sample1.pdb
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262 file, type:
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263 .PP
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264 .Vb 1
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265 \& % InfoPDBFiles.pl \-b Sample1.pdb
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266 .Ve
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267 .SH "AUTHOR"
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268 .IX Header "AUTHOR"
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269 Manish Sud <msud@san.rr.com>
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270 .SH "SEE ALSO"
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271 .IX Header "SEE ALSO"
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272 ExtractFromPDBFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.pl, InfoSequenceFiles.pl, ModifyPDBFiles.pl
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273 .SH "COPYRIGHT"
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274 .IX Header "COPYRIGHT"
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275 Copyright (C) 2015 Manish Sud. All rights reserved.
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276 .PP
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277 This file is part of MayaChemTools.
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278 .PP
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279 MayaChemTools is free software; you can redistribute it and/or modify it under
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280 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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281 Software Foundation; either version 3 of the License, or (at your option)
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282 any later version.
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