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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ROTATABLEBONDSDESCRIPTORS 1"
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127 .TH ROTATABLEBONDSDESCRIPTORS 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 RotatableBondsDescriptors
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::RotatableBondsDescriptors;
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137 .PP
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138 use MolecularDescriptors::RotatableBondsDescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBRotatableBondsDescriptors\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, GetDescriptorNames,
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144 StringifyRotatableBondsDescriptors
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145 .PP
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146 \&\fBRotatableBondsDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
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147 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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148 in \fBRotatableBondsDescriptors\fR, \fBMolecularDescriptors\fR or \fBObjectProperty\fR classes using Perl's
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149 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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150 .PP
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151 .Vb 3
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152 \& Set<PropertyName>(<PropertyValue>);
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153 \& $PropertyValue = Get<PropertyName>();
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154 \& Delete<PropertyName>();
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155 .Ve
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156 .PP
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157 A rotatable bond [ Ref 92 ] is defined as any single bond which is not in a ring and involves only non-hydrogen
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158 atoms. By default, the following types of single bonds are not considered rotatable bonds:
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159 .PP
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160 .Vb 5
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161 \& o Terminal bonds
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162 \& o Bonds attached to triple bonds
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163 \& o Amide C\-N bonds
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164 \& o Thioamide C\-N bond bonds
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165 \& o Sulfonamide S\-N bonds
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166 .Ve
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167 .SS "\s-1METHODS\s0"
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168 .IX Subsection "METHODS"
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169 .IP "\fBnew\fR" 4
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170 .IX Item "new"
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171 .Vb 3
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172 \& $RotatableBondsDescriptors = new MolecularDescriptors::
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173 \& RotatableBondsDescriptors(
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174 \& %NamesAndValues);
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175 .Ve
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176 .Sp
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177 Using specified \fIRotatableBondsDescriptors\fR property names and values hash, \fBnew\fR
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178 method creates a new object and returns a reference to newly created \fBRotatableBondsDescriptors\fR
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179 object. By default, the following properties are initialized:
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180 .Sp
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181 .Vb 9
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182 \& Molecule = \*(Aq\*(Aq
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183 \& Type = \*(AqRotatableBonds\*(Aq
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184 \& IgnoreTerminalBonds = 1
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185 \& IgnoreBondsToTripleBonds = 1
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186 \& IgnoreAmideBonds = 1
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187 \& IgnoreThioamideBonds = 1
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188 \& IgnoreSulfonamideBonds = 1
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189 \& @DescriptorNames = (\*(AqRotatableBonds\*(Aq)
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190 \& @DescriptorValues = (\*(AqNone\*(Aq)
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191 .Ve
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192 .Sp
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193 Examples:
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194 .Sp
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195 .Vb 2
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196 \& $RotatableBondsDescriptors = new MolecularDescriptors::
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197 \& RotatableBondsDescriptors();
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198 \&
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199 \& $RotatableBondsDescriptors = new MolecularDescriptors::
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200 \& RotatableBondsDescriptors(
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201 \& \*(AqIgnoreAmideBonds\*(Aq => 0,
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202 \& \*(AqIgnoreThioamideBonds\*(Aq => 0,
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203 \& \*(AqIgnoreSulfonamideBonds\*(Aq => 0);
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204 \&
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205 \& $RotatableBondsDescriptors\->SetMolecule($Molecule);
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206 \& $RotatableBondsDescriptors\->GenerateDescriptors();
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207 \& print "RotatableBondsDescriptors: $RotatableBondsDescriptors\en";
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208 .Ve
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209 .IP "\fBGenerateDescriptors\fR" 4
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210 .IX Item "GenerateDescriptors"
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211 .Vb 1
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212 \& $RotatableBondsDescriptors\->GenerateDescriptors();
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213 .Ve
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214 .Sp
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215 Calculates number of rotatable bonds descriptors in a molecule and returns
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216 \&\fIRotatableBondsDescriptors\fR.
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217 .IP "\fBGetDescriptorNames\fR" 4
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218 .IX Item "GetDescriptorNames"
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219 .Vb 3
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220 \& @DescriptorNames = $RotatableBondsDescriptors\->GetDescriptorNames();
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221 \& @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors::
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222 \& GetDescriptorNames();
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223 .Ve
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224 .Sp
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225 Returns all available descriptor names as an array.
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226 .IP "\fBStringifyRotatableBondsDescriptors\fR" 4
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227 .IX Item "StringifyRotatableBondsDescriptors"
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228 .Vb 1
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229 \& $String = $RotatableBondsDescriptors\->StringifyRotatableBondsDescriptors();
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230 .Ve
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231 .Sp
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232 Returns a string containing information about \fIRotatableBondsDescriptors\fR object.
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233 .SH "AUTHOR"
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234 .IX Header "AUTHOR"
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235 Manish Sud <msud@san.rr.com>
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236 .SH "SEE ALSO"
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237 .IX Header "SEE ALSO"
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238 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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239 .SH "COPYRIGHT"
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240 .IX Header "COPYRIGHT"
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241 Copyright (C) 2015 Manish Sud. All rights reserved.
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242 .PP
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243 This file is part of MayaChemTools.
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244 .PP
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245 MayaChemTools is free software; you can redistribute it and/or modify it under
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246 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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247 Software Foundation; either version 3 of the License, or (at your option)
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248 any later version.
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