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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ESTATEVALUESDESCRIPTORS 1"
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127 .TH ESTATEVALUESDESCRIPTORS 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 EStateValuesDescriptors
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use AtomicDescriptors::EStateValuesDescriptors;
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137 .PP
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138 use AtomicDescriptors::EStateValuesDescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBEStateValuesDescriptors\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, StringifyEStateValuesDescriptors
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144 .PP
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145 \&\fBEStateValuesDescriptors\fR is derived from \fBAtomicValues\fR class which in turn
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146 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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147 in \fBEStateValuesDescriptors\fR, \fBAtomicValues\fR or \fBObjectProperty\fR classes using Perl's
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148 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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149 .PP
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150 .Vb 3
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151 \& Set<PropertyName>(<PropertyValue>);
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152 \& $PropertyValue = Get<PropertyName>();
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153 \& Delete<PropertyName>();
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154 .Ve
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155 .PP
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156 For calculation of electrotopological state (E\-state) values for non-hydrogen atoms:
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157 .PP
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158 Let:
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159 .PP
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160 .Vb 2
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161 \& N = Principal quantum number or period number corresponding to
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162 \& element symbol
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163 \&
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164 \& Sigma = Number of sigma electrons involves in bonds to hydrogen and
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165 \& non\-hydrogen atoms attached to atom
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166 \& = Number of sigma bonds to hydrogen and non\-hydrogen atoms
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167 \& attached to atom
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168 \& PI = Number of PI electrons involved in bonds to non\-hydrogen atoms
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169 \& attached to atom
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170 \& = Number of PI bonds to non\-hydrogen atoms attached to atom
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171 \&
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172 \& LP = Number of lone pair electrons on atom
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173 \&
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174 \& Zv = Number of electrons in valence shell of atom
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175 \&
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176 \& X = Number of non\-hydrogen atom neighbors or heavy atoms attached
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177 \& to atom
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178 \& H = Number of implicit and explicit hydrogens for atom
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179 \&
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180 \& Delta = Number of sigma electrons involved to bonds to non\-hydrogen
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181 \& atoms
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182 \& DeltaV = ValenceDelta = Number of valence shell electrons not involved
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183 \& in bonding to hydrogen atoms
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184 \&
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185 \& Ii = Intrinsic state value for atom i
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186 \&
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187 \& DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i
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188 \& by all other atoms besides atom i
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189 \&
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190 \& DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j
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191 \&
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192 \& Dij = Graph/bond distance between atom i and j
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193 \& Rij = Dij + 1
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194 \&
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195 \& Si = E\-state value for atom i
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196 .Ve
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197 .PP
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198 Then:
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199 .PP
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200 .Vb 1
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201 \& Delta = Sigma \- H = X
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202 \&
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203 \& DeltaV = Zv \- H
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204 \& = Sigma + PI + LP \- H
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205 \&
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206 \& Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta
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207 \&
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208 \& DeltaIi = SUM ( (Ii \- Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i
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209 \&
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210 \& Si = Ii + DeltaIi
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211 .Ve
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212 .PP
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213 The current release of MayaChemTools doesn't support calculation of E\-state
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214 values [ Ref 75\-78 ] for hydrogens.
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215 .SS "\s-1METHODS\s0"
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216 .IX Subsection "METHODS"
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217 .IP "\fBnew\fR" 4
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218 .IX Item "new"
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219 .Vb 2
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220 \& $NewEStateValuesDescriptors = new AtomicDescriptors::
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221 \& EStateValuesDescriptors(%NamesAndValues);
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222 .Ve
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223 .Sp
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224 Using specified \fIEStateValuesDescriptors\fR property names and values hash, \fBnew\fR
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225 method creates a new object and returns a reference to newly created \fBEStateValuesDescriptors\fR
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226 object. By default, the following properties are initialized:
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227 .Sp
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228 .Vb 3
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229 \& Molecule = \*(Aq\*(Aq
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230 \& Type = \*(AqEState\*(Aq
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231 \& IgnoreHydrogens = 1
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232 .Ve
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233 .Sp
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234 Examples:
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235 .Sp
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236 .Vb 3
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237 \& $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors(
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238 \& \*(AqMolecule\*(Aq => $Molecule,
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239 \& \*(AqIgnoreHydrogens\*(Aq => 1);
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240 .Ve
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241 .IP "\fBGenerateDescriptors\fR" 4
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242 .IX Item "GenerateDescriptors"
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243 .Vb 1
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244 \& $EStateValuesDescriptors\->GenerateDescriptors();
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245 .Ve
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246 .Sp
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247 Calculates E\-state atomic descriptors for all the atoms in a molecule and returns
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248 \&\fIEStateValuesDescriptors\fR.
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249 .IP "\fBStringifyEStateValuesDescriptors\fR" 4
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250 .IX Item "StringifyEStateValuesDescriptors"
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251 .Vb 1
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252 \& $String = $EStateValuesDescriptors\->StringifyEStateValuesDescriptors();
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253 .Ve
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254 .Sp
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255 Returns a string containing information about \fIEStateValuesDescriptors\fR object.
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256 .SH "AUTHOR"
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257 .IX Header "AUTHOR"
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258 Manish Sud <msud@san.rr.com>
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259 .SH "SEE ALSO"
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260 .IX Header "SEE ALSO"
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261 AtomicDescriptors.pm
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262 .SH "COPYRIGHT"
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263 .IX Header "COPYRIGHT"
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264 Copyright (C) 2015 Manish Sud. All rights reserved.
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265 .PP
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266 This file is part of MayaChemTools.
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267 .PP
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268 MayaChemTools is free software; you can redistribute it and/or modify it under
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269 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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270 Software Foundation; either version 3 of the License, or (at your option)
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271 any later version.
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