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124 .\" ========================================================================
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125 .\"
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126 .IX Title "CYCLESDETECTION 1"
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127 .TH CYCLESDETECTION 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 CyclesDetection
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Graph::CyclesDetection;
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137 .PP
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138 use Graph::CyclesDetection qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBCyclesDetection\fR class provides the following methods:
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142 .PP
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143 new, Copy, DetectCycles, DetectCyclesUsingCollapsingPathGraphMethodology,
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144 GetAllCyclicPaths, GetIndependentCyclicPaths, StringifyCyclesDetection
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145 .PP
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146 Cycles in a \fBGraph\fR are detected using collapsing path graph [Ref 31]
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147 methodology.
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148 .SS "\s-1METHODS\s0"
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149 .IX Subsection "METHODS"
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150 .IP "\fBnew\fR" 4
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151 .IX Item "new"
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152 .Vb 1
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153 \& $NewCyclesDetection = new Graph::CyclesDetection($Graph);
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154 .Ve
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155 .Sp
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156 Using specified \fIGraph\fR, \fBnew\fR method creates a new \fBCyclesDetection\fR object and returns
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157 newly created \fBCyclesDetection\fR object.
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158 .IP "\fBCopy\fR" 4
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159 .IX Item "Copy"
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160 .Vb 1
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161 \& $NewCyclesDetection = $CyclesDetection\->Copy();
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162 .Ve
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163 .Sp
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164 Copies \fICyclesDetection\fR and its associated data using \fBStorable::dclone\fR and returns a new
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165 \&\fBCyclesDetection\fR object.
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166 .IP "\fBDetectCycles\fR" 4
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167 .IX Item "DetectCycles"
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168 .Vb 1
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169 \& $CyclesDetection\->DetectCycles();
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170 .Ve
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171 .Sp
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172 Detects all cycles in a graph and returns \fICyclesDetection\fR.
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173 .IP "\fBDetectCyclesUsingCollapsingPathGraphMethodology\fR" 4
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174 .IX Item "DetectCyclesUsingCollapsingPathGraphMethodology"
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175 .Vb 1
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176 \& $CyclesDetection\->DetectCyclesUsingCollapsingPathGraphMethodology();
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177 .Ve
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178 .Sp
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179 Detects all cycles in a graph using collapsing path graph [Ref 31] methodology
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180 and returns \fICyclesDetection\fR.
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181 .IP "\fBGetAllCyclicPaths\fR" 4
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182 .IX Item "GetAllCyclicPaths"
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183 .Vb 2
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184 \& @AllCyclicPaths = $CyclesDetection\->GetAllCyclicPaths();
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185 \& $NumOfAllCyclicPaths = $CyclesDetection\->GetAllCyclicPaths();
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186 .Ve
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187 .Sp
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188 Returns an array containing references to all cyclic paths identified during cycles
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189 detection. In scalar text, number of cycles is returned.
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190 .IP "\fBGetIndependentCyclicPaths\fR" 4
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191 .IX Item "GetIndependentCyclicPaths"
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192 .Vb 2
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193 \& @IndependentCyclicPaths = $CyclesDetection\->GetAllCyclicPaths();
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194 \& $NumOfIndependentCyclicPaths = $CyclesDetection\->GetAllCyclicPaths();
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195 .Ve
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196 .Sp
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197 Returns an array containing references to independent cyclic paths identified during cycles
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198 detection. In scalar text, number of cycles is returned.
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199 .Sp
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200 A set of independent cycles identified during cycles detection doesn't correspond to the basis set of
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201 rings or smallest set of smallest rings (\s-1SSSR\s0) [ Refs 29\-30 ]; instead, set of cycles indentified
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202 as independent cycles simply correpond to cycles which contain no other cycle as their
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203 subcycles and can't be described as a linear combination of smaller cycles. And it also happens
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204 to contain all the rings in basis set of rings and \s-1SSSR\s0. In other words, it's a superset of a basis set
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205 of cycles and \s-1SSSR\s0. For example, six four membered cycles are indentified for cubane, which is one
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206 more than the basis set of cycles.
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207 .IP "\fBStringifyCyclesDetection\fR" 4
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208 .IX Item "StringifyCyclesDetection"
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209 .Vb 1
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210 \& $String = $CyclesDetection\->StringifyCyclesDetection();
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211 .Ve
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212 .Sp
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213 Returns a string containing information about \fICyclesDetection\fR object.
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214 .SH "AUTHOR"
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215 .IX Header "AUTHOR"
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216 Manish Sud <msud@san.rr.com>
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217 .SH "SEE ALSO"
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218 .IX Header "SEE ALSO"
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219 Graph.pm, Path.pm, PathGraph.pm
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220 .SH "COPYRIGHT"
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221 .IX Header "COPYRIGHT"
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222 Copyright (C) 2015 Manish Sud. All rights reserved.
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223 .PP
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224 This file is part of MayaChemTools.
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225 .PP
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226 MayaChemTools is free software; you can redistribute it and/or modify it under
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227 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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228 Software Foundation; either version 3 of the License, or (at your option)
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229 any later version.
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