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124 .\" ========================================================================
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125 .\"
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126 .IX Title "RINGSCOUNTDESCRIPTORS 1"
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127 .TH RINGSCOUNTDESCRIPTORS 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 RingsCountDescriptors
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::RingsCountDescriptors;
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137 .PP
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138 use MolecularDescriptors::RingsCountDescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBRingsCountDescriptors\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, GetDescriptorNames, StringifyRingsCountDescriptors
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144 .PP
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145 \&\fBRingsCountDescriptors\fR is derived from \fBMolecularDescriptors\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 \fBRingsCountDescriptors\fR, \fBMolecularDescriptors\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 \&\fBRingsCountDescriptors\fR class doesn't perform any ring or aromaticity detection before
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157 counting their number in a molecule. Instead, it assumes ring and aromaticity detection have
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158 been performed by caller using \fBDetectRings\fR [Ref 31] and \fBDetectAromaticity\fR methods
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159 available in \fBMolecule\fR.
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160 .PP
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161 \&\fBDetectAromaticity\fR method available in \fBMolecule\fR class assigns aromaticity to rings
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162 using Huckel rule as explained below:
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163 .PP
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164 o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is
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165 considered aromatic.
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166 .PP
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167 o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and
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168 Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a
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169 double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have
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170 an attached hydrogen atom and the remaining lone pair contribute to electron delocalization
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171 and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)
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172 .PP
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173 o For molecules containing fused rings, each fused ring set is considered as one aromatic
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174 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
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175 fused set are treated individually for aromaticity detection. Additionally, non-fused
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176 rings are handled on their own during aromaticity detection.
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177 .SS "\s-1METHODS\s0"
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178 .IX Subsection "METHODS"
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179 .IP "\fBnew\fR" 4
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180 .IX Item "new"
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181 .Vb 3
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182 \& $NewRingsCountDescriptors = new MolecularDescriptors::
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183 \& RingsCountDescriptors(
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184 \& %NamesAndValues);
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185 .Ve
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186 .Sp
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187 Using specified \fIRingsCountDescriptors\fR property names and values hash, \fBnew\fR
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188 method creates a new object and returns a reference to newly created \fBRingsCountDescriptors\fR
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189 object. By default, the following properties are initialized:
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190 .Sp
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191 .Vb 2
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192 \& Molecule = \*(Aq\*(Aq
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193 \& Type = \*(AqRingsCount\*(Aq
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194 \&
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195 \& @DescriptorNames = (\*(AqRings\*(Aq, \*(AqAromaticRings\*(Aq)
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196 \& @DescriptorValues = (\*(AqNone\*(Aq, \*(AqNone\*(Aq)
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197 .Ve
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198 .Sp
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199 Examples:
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200 .Sp
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201 .Vb 2
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202 \& $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
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203 \& \*(AqMolecule\*(Aq => $Molecule);
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204 \&
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205 \& $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
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206 \&
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207 \& $RingsCountDescriptors\->SetMolecule($Molecule);
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208 \& $RingsCountDescriptors\->GenerateDescriptors();
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209 \& print "RingsCountDescriptors: $RingsCountDescriptors\en";
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210 .Ve
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211 .IP "\fBGenerateDescriptors\fR" 4
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212 .IX Item "GenerateDescriptors"
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213 .Vb 1
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214 \& $RingsCountDescriptors\->GenerateDescriptors();
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215 .Ve
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216 .Sp
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217 Calculate number of rings and aromatic rings in a molecule and returns
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218 \&\fIRingsCountDescriptors\fR.
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219 .IP "\fBGetDescriptorNames\fR" 4
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220 .IX Item "GetDescriptorNames"
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221 .Vb 3
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222 \& @DescriptorNames = $RingsCountDescriptors\->GetDescriptorNames();
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223 \& @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
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224 \& GetDescriptorNames();
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225 .Ve
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226 .Sp
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227 Returns all available descriptor names as an array.
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228 .IP "\fBStringifyRingsCountDescriptors\fR" 4
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229 .IX Item "StringifyRingsCountDescriptors"
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230 .Vb 2
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231 \& $String = $RingsCountDescriptors\->
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232 \& StringifyRingsCountDescriptors();
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233 .Ve
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234 .Sp
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235 Returns a string containing information about \fIRingsCountDescriptors\fR object.
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236 .SH "AUTHOR"
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237 .IX Header "AUTHOR"
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238 Manish Sud <msud@san.rr.com>
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239 .SH "SEE ALSO"
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240 .IX Header "SEE ALSO"
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241 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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242 .SH "COPYRIGHT"
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243 .IX Header "COPYRIGHT"
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244 Copyright (C) 2015 Manish Sud. All rights reserved.
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245 .PP
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246 This file is part of MayaChemTools.
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247 .PP
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248 MayaChemTools is free software; you can redistribute it and/or modify it under
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249 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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250 Software Foundation; either version 3 of the License, or (at your option)
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251 any later version.
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