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124 .\" ========================================================================
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125 .\"
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126 .IX Title "FINGERPRINTSBITVECTOR 1"
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127 .TH FINGERPRINTSBITVECTOR 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 FingerprintsBitVector
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::FingerprintsBitVector;
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137 .PP
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138 use Fingerprints::FingerprintsBitVector qw(:coefficients);
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139 .PP
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140 use Fingerprints::FingerprintsBitVector qw(:all);
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141 .SH "DESCRIPTION"
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142 .IX Header "DESCRIPTION"
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143 \&\fBFingerprintsBitVector\fR class provides the following methods:
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144 .PP
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145 new, BaroniUrbaniSimilarityCoefficient, BuserSimilarityCoefficient,
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146 CosineSimilarityCoefficient, DennisSimilarityCoefficient,
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147 DiceSimilarityCoefficient, FoldFingerprintsBitVectorByDensity,
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148 FoldFingerprintsBitVectorBySize, ForbesSimilarityCoefficient,
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149 FossumSimilarityCoefficient, GetBitsAsBinaryString, GetBitsAsDecimalString,
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150 GetBitsAsHexadecimalString, GetBitsAsOctalString, GetBitsAsRawBinaryString,
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151 GetDescription, GetFingerprintsBitDensity, GetID, GetSpecifiedSize,
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152 GetSupportedSimilarityCoefficients, GetVectorType, HamannSimilarityCoefficient,
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153 IsFingerprintsBitVector, IsSubSet, JacardSimilarityCoefficient,
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154 Kulczynski1SimilarityCoefficient, Kulczynski2SimilarityCoefficient,
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155 MatchingSimilarityCoefficient, McConnaugheySimilarityCoefficient,
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156 NewFromBinaryString, NewFromDecimalString, NewFromHexadecimalString,
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157 NewFromOctalString, NewFromRawBinaryString, OchiaiSimilarityCoefficient,
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158 PearsonSimilarityCoefficient, RogersTanimotoSimilarityCoefficient,
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159 RussellRaoSimilarityCoefficient, SetDescription, SetID, SetSpecifiedSize,
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160 SetVectorType, SimpsonSimilarityCoefficient, SkoalSneath1SimilarityCoefficient,
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161 SkoalSneath2SimilarityCoefficient, SkoalSneath3SimilarityCoefficient,
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162 StringifyFingerprintsBitVector, TanimotoSimilarityCoefficient,
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163 TverskySimilarityCoefficient, WeightedTanimotoSimilarityCoefficient,
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164 WeightedTverskySimilarityCoefficient, YuleSimilarityCoefficient
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165 .PP
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166 The methods available to create fingerprints bit vector from strings and to calculate similarity
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167 coefficient between two bit vectors can also be invoked as class functions.
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168 .PP
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169 \&\fBFingerprintsBitVector\fR class is derived from \fBBitVector\fR class which provides the functionality
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170 to manipulate bits.
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171 .PP
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172 For two fingerprints bit vectors A and B of same size, let:
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173 .PP
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174 .Vb 4
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175 \& Na = Number of bits set to "1" in A
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176 \& Nb = Number of bits set to "1" in B
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177 \& Nc = Number of bits set to "1" in both A and B
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178 \& Nd = Number of bits set to "0" in both A and B
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179 \&
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180 \& Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
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181 \& Nt = Na + Nb \- Nc + Nd
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182 \&
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183 \& Na \- Nc = Number of bits set to "1" in A but not in B
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184 \& Nb \- Nc = Number of bits set to "1" in B but not in A
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185 .Ve
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186 .PP
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187 Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit vectors A and B are
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188 defined as follows:
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189 .PP
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190 BaroniUrbani: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser )
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191 .PP
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192 Buser: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani )
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193 .PP
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194 Cosine: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai)
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195 .PP
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196 Dice: (2 * Nc) / ( Na + Nb )
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197 .PP
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198 Dennis: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb)
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199 .PP
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200 Forbes: ( Nt * Nc ) / ( Na * Nb )
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201 .PP
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202 Fossum: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb )
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203 .PP
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204 Hamann: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt
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205 .PP
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206 Jaccard: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto)
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207 .PP
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208 Kulczynski1: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc )
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209 .PP
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210 Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) )
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211 = 0.5 * ( Nc / Na + Nc / Nb )
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212 .PP
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213 Matching: ( Nc + Nd ) / Nt
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214 .PP
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215 McConnaughey: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb )
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216 .PP
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217 Ochiai: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine)
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218 .PP
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219 Pearson: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) )
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220 .PP
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221 RogersTanimoto: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt)
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222 .PP
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223 RussellRao: Nc / Nt
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224 .PP
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225 Simpson: Nc / \s-1MIN\s0 ( Na, Nb)
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226 .PP
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227 SkoalSneath1: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc )
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228 .PP
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229 SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
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230 .PP
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231 SkoalSneath3: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc )
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232 .PP
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233 Tanimoto: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard)
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234 .PP
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235 Tversky: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb)
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236 .PP
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237 Yule: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) )
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238 .PP
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239 The values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
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240 are set to \*(L"1\*(R" in both A and B. In order to take into account all bit positions, modified versions
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241 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.
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242 .PP
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243 Let:
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244 .PP
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245 .Vb 3
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246 \& Na\*(Aq = Number of bits set to "0" in A
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247 \& Nb\*(Aq = Number of bits set to "0" in B
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248 \& Nc\*(Aq = Number of bits set to "0" in both A and B
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249 .Ve
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250 .PP
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251 Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' )
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252 .PP
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253 Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb')
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254 .PP
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255 Then:
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256 .PP
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257 WeightedTanimoto = beta * Tanimoto + (1 \- beta) * Tanimoto'
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258 .PP
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259 WeightedTversky = beta * Tversky + (1 \- beta) * Tversky'
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260 .SS "\s-1METHODS\s0"
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261 .IX Subsection "METHODS"
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262 .IP "\fBnew\fR" 4
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263 .IX Item "new"
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264 .Vb 1
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265 \& $NewFPBitVector = new Fingerprints::FingerprintsBitVector($Size);
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266 .Ve
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267 .Sp
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268 Creates a new \fIFingerprintsBitVector\fR object of size \fISize\fR and returns newly created
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269 \&\fBFingerprintsBitVector\fR. Bit numbers range from 0 to 1 less than \fISize\fR.
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270 .IP "\fBBaroniUrbaniSimilarityCoefficient\fR" 4
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271 .IX Item "BaroniUrbaniSimilarityCoefficient"
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272 .Vb 5
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273 \& $Value = $FingerprintsBitVector\->BaroniUrbaniSimilarityCoefficient(
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274 \& $OtherFingerprintBitVector);
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275 \& $Value = Fingerprints::FingerprintsBitVector::
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276 \& BaroniUrbaniSimilarityCoefficient(
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277 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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278 .Ve
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279 .Sp
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280 Returns value of \fIBaroniUrbani\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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281 .IP "\fBBuserSimilarityCoefficient\fR" 4
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282 .IX Item "BuserSimilarityCoefficient"
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283 .Vb 4
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284 \& $Value = $FingerprintsBitVector\->BuserSimilarityCoefficient(
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285 \& $OtherFingerprintBitVector);
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286 \& $Value = Fingerprints::FingerprintsBitVector::BuserSimilarityCoefficient(
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287 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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288 .Ve
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289 .Sp
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290 Returns value of \fIBuser\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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291 .IP "\fBCosineSimilarityCoefficient\fR" 4
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292 .IX Item "CosineSimilarityCoefficient"
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293 .Vb 4
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294 \& $Value = $FingerprintsBitVector\->CosineSimilarityCoefficient(
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295 \& $OtherFingerprintBitVector);
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296 \& $Value = Fingerprints::FingerprintsBitVector::CosineSimilarityCoefficient(
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297 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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298 .Ve
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299 .Sp
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300 Returns value of \fICosine\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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301 .IP "\fBDennisSimilarityCoefficient\fR" 4
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302 .IX Item "DennisSimilarityCoefficient"
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303 .Vb 4
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304 \& $Value = $FingerprintsBitVector\->DennisSimilarityCoefficient(
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305 \& $OtherFingerprintBitVector);
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306 \& $Value = Fingerprints::FingerprintsBitVector::DennisSimilarityCoefficient(
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307 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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308 .Ve
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309 .Sp
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310 Returns value of \fIDennis\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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311 .IP "\fBDiceSimilarityCoefficient\fR" 4
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312 .IX Item "DiceSimilarityCoefficient"
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313 .Vb 4
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314 \& $Value = $FingerprintsBitVector\->DiceSimilarityCoefficient(
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315 \& $OtherFingerprintBitVector);
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316 \& $Value = Fingerprints::FingerprintsBitVector::DiceSimilarityCoefficient(
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317 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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318 .Ve
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319 .Sp
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320 Returns value of \fIDice\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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321 .IP "\fBFoldFingerprintsBitVectorByDensity\fR" 4
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322 .IX Item "FoldFingerprintsBitVectorByDensity"
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323 .Vb 1
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324 \& $FingerprintsBitVector\->FoldFingerprintsBitVectorByDensity($Density);
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325 .Ve
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326 .Sp
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327 Folds \fIFingerprintsBitVector\fR by recursively reducing its size by half until bit density of set bits is
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328 greater than or equal to specified \fIDensity\fR and returns folded \fIFingerprintsBitVector\fR.
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329 .IP "\fBFoldFingerprintsBitVectorBySize\fR" 4
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330 .IX Item "FoldFingerprintsBitVectorBySize"
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331 .Vb 1
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332 \& $FingerprintsBitVector\->FoldFingerprintsBitVectorBySize($Size);
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333 .Ve
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334 .Sp
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335 Folds \fIFingerprintsBitVector\fR by recursively reducing its size by half until size is less than or equal to
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336 specified \fISize\fR and returns folded \fIFingerprintsBitVector\fR.
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337 .IP "\fBForbesSimilarityCoefficient\fR" 4
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338 .IX Item "ForbesSimilarityCoefficient"
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339 .Vb 4
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340 \& $Value = $FingerprintsBitVector\->ForbesSimilarityCoefficient(
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341 \& $OtherFingerprintBitVector);
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342 \& $Value = Fingerprints::FingerprintsBitVector::ForbesSimilarityCoefficient(
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343 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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344 .Ve
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345 .Sp
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346 Returns value of \fIForbes\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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347 .IP "\fBFossumSimilarityCoefficient\fR" 4
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348 .IX Item "FossumSimilarityCoefficient"
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349 .Vb 4
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350 \& $Value = $FingerprintsBitVector\->FossumSimilarityCoefficient(
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351 \& $OtherFingerprintBitVector);
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352 \& $Value = Fingerprints::FingerprintsBitVector::FossumSimilarityCoefficient(
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353 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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354 .Ve
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355 .Sp
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356 Returns value of \fIFossum\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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357 .IP "\fBGetBitsAsBinaryString\fR" 4
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358 .IX Item "GetBitsAsBinaryString"
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359 .Vb 1
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360 \& $BinaryASCIIString = $FingerprintsBitVector\->GetBitsAsBinaryString();
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361 .Ve
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362 .Sp
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363 Returns fingerprints as a binary \s-1ASCII\s0 string containing 0s and 1s.
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364 .IP "\fBGetBitsAsHexadecimalString\fR" 4
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365 .IX Item "GetBitsAsHexadecimalString"
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366 .Vb 1
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367 \& $HexadecimalString = $FingerprintsBitVector\->GetBitsAsHexadecimalString();
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368 .Ve
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369 .Sp
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370 Returns fingerprints as a hexadecimal string.
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371 .IP "\fBGetBitsAsRawBinaryString\fR" 4
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372 .IX Item "GetBitsAsRawBinaryString"
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373 .Vb 1
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374 \& $RawBinaryString = $FingerprintsBitVector\->GetBitsAsRawBinaryString();
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375 .Ve
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376 .Sp
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377 Returns fingerprints as a raw binary string containing packed bit values for each byte.
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378 .IP "\fBGetDescription\fR" 4
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|
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379 .IX Item "GetDescription"
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|
|
380 .Vb 1
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|
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381 \& $Description = $FingerprintsBitVector\->GetDescription();
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|
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382 .Ve
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|
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383 .Sp
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|
|
384 Returns a string containing description of fingerprints bit vector.
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385 .IP "\fBGetFingerprintsBitDensity\fR" 4
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|
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386 .IX Item "GetFingerprintsBitDensity"
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|
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387 .Vb 1
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|
|
388 \& $BitDensity = $FingerprintsBitVector\->GetFingerprintsBitDensity();
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|
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389 .Ve
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|
|
390 .Sp
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|
|
391 Returns \fIBitDensity\fR of \fIFingerprintsBitVector\fR corresponding to bits set to 1s.
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|
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392 .IP "\fBGetID\fR" 4
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|
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393 .IX Item "GetID"
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|
|
394 .Vb 1
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|
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395 \& $ID = $FingerprintsBitVector\->GetID();
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396 .Ve
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|
|
397 .Sp
|
|
|
398 Returns \fI\s-1ID\s0\fR of \fIFingerprintsBitVector\fR.
|
|
|
399 .IP "\fBGetVectorType\fR" 4
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|
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400 .IX Item "GetVectorType"
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|
|
401 .Vb 1
|
|
|
402 \& $VectorType = $FingerprintsBitVector\->GetVectorType();
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|
|
403 .Ve
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|
|
404 .Sp
|
|
|
405 Returns \fIVectorType\fR of \fIFingerprintsBitVector\fR.
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|
|
406 .IP "\fBGetSpecifiedSize\fR" 4
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|
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407 .IX Item "GetSpecifiedSize"
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|
|
408 .Vb 1
|
|
|
409 \& $Size = $FingerprintsBitVector\->GetSpecifiedSize();
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|
|
410 .Ve
|
|
|
411 .Sp
|
|
|
412 Returns value of specified size for bit vector.
|
|
|
413 .IP "\fBGetSupportedSimilarityCoefficients\fR" 4
|
|
|
414 .IX Item "GetSupportedSimilarityCoefficients"
|
|
|
415 .Vb 2
|
|
|
416 \& @SimilarityCoefficient =
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|
|
417 \& Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients();
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|
|
418 .Ve
|
|
|
419 .Sp
|
|
|
420 Returns an array containing names of supported similarity coefficients.
|
|
|
421 .IP "\fBHamannSimilarityCoefficient\fR" 4
|
|
|
422 .IX Item "HamannSimilarityCoefficient"
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|
|
423 .Vb 4
|
|
|
424 \& $Value = $FingerprintsBitVector\->HamannSimilarityCoefficient(
|
|
|
425 \& $OtherFingerprintBitVector);
|
|
|
426 \& $Value = Fingerprints::FingerprintsBitVector::HamannSimilarityCoefficient(
|
|
|
427 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
428 .Ve
|
|
|
429 .Sp
|
|
|
430 Returns value of \fIHamann\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
431 .IP "\fBIsFingerprintsBitVector\fR" 4
|
|
|
432 .IX Item "IsFingerprintsBitVector"
|
|
|
433 .Vb 2
|
|
|
434 \& $Status = Fingerprints::FingerprintsBitVector::
|
|
|
435 \& IsFingerprintsBitVector($Object);
|
|
|
436 .Ve
|
|
|
437 .Sp
|
|
|
438 Returns 1 or 0 based on whether \fIObject\fR is a \fBFingerprintsBitVector\fR object.
|
|
|
439 .IP "\fBIsSubSet\fR" 4
|
|
|
440 .IX Item "IsSubSet"
|
|
|
441 .Vb 3
|
|
|
442 \& $Status = $FingerprintsBitVector\->IsSubSet($OtherFPBitVector);
|
|
|
443 \& $Status = Fingerprints::FingerprintsBitVector::IsSubSet(
|
|
|
444 \& $FPBitVectorA, $FPBitVectorB);
|
|
|
445 .Ve
|
|
|
446 .Sp
|
|
|
447 Returns 1 or 0 based on whether first firngerprints bit vector is a subset of second
|
|
|
448 fingerprints bit vector.
|
|
|
449 .Sp
|
|
|
450 For a bit vector to be a subset of another bit vector, both vectors must be of
|
|
|
451 the same size and the bit positions set in first vector must also be set in the
|
|
|
452 second bit vector.
|
|
|
453 .IP "\fBJacardSimilarityCoefficient\fR" 4
|
|
|
454 .IX Item "JacardSimilarityCoefficient"
|
|
|
455 .Vb 4
|
|
|
456 \& $Value = $FingerprintsBitVector\->JacardSimilarityCoefficient(
|
|
|
457 \& $OtherFingerprintBitVector);
|
|
|
458 \& $Value = Fingerprints::FingerprintsBitVector::JacardSimilarityCoefficient(
|
|
|
459 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
460 .Ve
|
|
|
461 .Sp
|
|
|
462 Returns value of \fIJacard\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
463 .IP "\fBKulczynski1SimilarityCoefficient\fR" 4
|
|
|
464 .IX Item "Kulczynski1SimilarityCoefficient"
|
|
|
465 .Vb 5
|
|
|
466 \& $Value = $FingerprintsBitVector\->Kulczynski1SimilarityCoefficient(
|
|
|
467 \& $OtherFingerprintBitVector);
|
|
|
468 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
469 \& Kulczynski1SimilarityCoefficient(
|
|
|
470 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
471 .Ve
|
|
|
472 .Sp
|
|
|
473 Returns value of \fIKulczynski1\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
474 .IP "\fBKulczynski2SimilarityCoefficient\fR" 4
|
|
|
475 .IX Item "Kulczynski2SimilarityCoefficient"
|
|
|
476 .Vb 5
|
|
|
477 \& $Value = $FingerprintsBitVector\->Kulczynski2SimilarityCoefficient(
|
|
|
478 \& $OtherFingerprintBitVector);
|
|
|
479 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
480 \& Kulczynski2SimilarityCoefficient(
|
|
|
481 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
482 .Ve
|
|
|
483 .Sp
|
|
|
484 Returns value of \fIKulczynski2\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
485 .IP "\fBMatchingSimilarityCoefficient\fR" 4
|
|
|
486 .IX Item "MatchingSimilarityCoefficient"
|
|
|
487 .Vb 5
|
|
|
488 \& $Value = $FingerprintsBitVector\->MatchingSimilarityCoefficient(
|
|
|
489 \& $OtherFingerprintBitVector);
|
|
|
490 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
491 \& MatchingSimilarityCoefficient(
|
|
|
492 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
493 .Ve
|
|
|
494 .Sp
|
|
|
495 Returns value of \fIMatching\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
496 .IP "\fBMcConnaugheySimilarityCoefficient\fR" 4
|
|
|
497 .IX Item "McConnaugheySimilarityCoefficient"
|
|
|
498 .Vb 5
|
|
|
499 \& $Value = $FingerprintsBitVector\->McConnaugheySimilarityCoefficient(
|
|
|
500 \& $OtherFingerprintBitVector);
|
|
|
501 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
502 \& McConnaugheySimilarityCoefficient(
|
|
|
503 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
504 .Ve
|
|
|
505 .Sp
|
|
|
506 Returns value of \fIMcConnaughey\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
507 .IP "\fBNewFromBinaryString\fR" 4
|
|
|
508 .IX Item "NewFromBinaryString"
|
|
|
509 .Vb 4
|
|
|
510 \& $NewFPBitVector = $FingerprintsBitVector\->NewFromBinaryString(
|
|
|
511 \& $BinaryString);
|
|
|
512 \& $NewFPBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString(
|
|
|
513 \& $BinaryString);
|
|
|
514 .Ve
|
|
|
515 .Sp
|
|
|
516 Creates a new \fIFingerprintsBitVector\fR using \fIBinaryString\fR and returns new
|
|
|
517 \&\fBFingerprintsBitVector\fR object.
|
|
|
518 .IP "\fBNewFromHexadecimalString\fR" 4
|
|
|
519 .IX Item "NewFromHexadecimalString"
|
|
|
520 .Vb 5
|
|
|
521 \& $NewFPBitVector = $FingerprintsBitVector\->NewFromHexadecimalString(
|
|
|
522 \& $HexdecimalString);
|
|
|
523 \& $NewFPBitVector = Fingerprints::FingerprintsBitVector::
|
|
|
524 \& NewFromHexadecimalString(
|
|
|
525 \& $HexdecimalString);
|
|
|
526 .Ve
|
|
|
527 .Sp
|
|
|
528 Creates a new \fIFingerprintsBitVector\fR using \fIHexdecimalString\fR and returns new
|
|
|
529 \&\fBFingerprintsBitVector\fR object.
|
|
|
530 .IP "\fBNewFromRawBinaryString\fR" 4
|
|
|
531 .IX Item "NewFromRawBinaryString"
|
|
|
532 .Vb 5
|
|
|
533 \& $NewFPBitVector = $FingerprintsBitVector\->NewFromRawBinaryString(
|
|
|
534 \& $RawBinaryString);
|
|
|
535 \& $NewFPBitVector = Fingerprints::FingerprintsBitVector::
|
|
|
536 \& NewFromRawBinaryString(
|
|
|
537 \& $RawBinaryString);
|
|
|
538 .Ve
|
|
|
539 .Sp
|
|
|
540 Creates a new \fIFingerprintsBitVector\fR using \fIRawBinaryString\fR and returns new
|
|
|
541 \&\fBFingerprintsBitVector\fR object.
|
|
|
542 .IP "\fBOchiaiSimilarityCoefficient\fR" 4
|
|
|
543 .IX Item "OchiaiSimilarityCoefficient"
|
|
|
544 .Vb 4
|
|
|
545 \& $Value = $FingerprintsBitVector\->OchiaiSimilarityCoefficient(
|
|
|
546 \& $OtherFingerprintBitVector);
|
|
|
547 \& $Value = Fingerprints::FingerprintsBitVector::OchiaiSimilarityCoefficient(
|
|
|
548 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
549 .Ve
|
|
|
550 .Sp
|
|
|
551 Returns value of \fIOchiai\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
552 .IP "\fBPearsonSimilarityCoefficient\fR" 4
|
|
|
553 .IX Item "PearsonSimilarityCoefficient"
|
|
|
554 .Vb 4
|
|
|
555 \& $Value = $FingerprintsBitVector\->PearsonSimilarityCoefficient(
|
|
|
556 \& $OtherFingerprintBitVector);
|
|
|
557 \& $Value = Fingerprints::FingerprintsBitVector::PearsonSimilarityCoefficient(
|
|
|
558 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
559 .Ve
|
|
|
560 .Sp
|
|
|
561 Returns value of \fIPearson\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
562 .IP "\fBRogersTanimotoSimilarityCoefficient\fR" 4
|
|
|
563 .IX Item "RogersTanimotoSimilarityCoefficient"
|
|
|
564 .Vb 5
|
|
|
565 \& $Value = $FingerprintsBitVector\->RogersTanimotoSimilarityCoefficient(
|
|
|
566 \& $OtherFingerprintBitVector);
|
|
|
567 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
568 \& RogersTanimotoSimilarityCoefficient(
|
|
|
569 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
570 .Ve
|
|
|
571 .Sp
|
|
|
572 Returns value of \fIRogersTanimoto\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
573 .IP "\fBRussellRaoSimilarityCoefficient\fR" 4
|
|
|
574 .IX Item "RussellRaoSimilarityCoefficient"
|
|
|
575 .Vb 5
|
|
|
576 \& $Value = $FingerprintsBitVector\->RussellRaoSimilarityCoefficient(
|
|
|
577 \& $OtherFingerprintBitVector);
|
|
|
578 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
579 \& RussellRaoSimilarityCoefficient(
|
|
|
580 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
581 .Ve
|
|
|
582 .Sp
|
|
|
583 Returns value of \fIRussellRao\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
584 .IP "\fBSetSpecifiedSize\fR" 4
|
|
|
585 .IX Item "SetSpecifiedSize"
|
|
|
586 .Vb 1
|
|
|
587 \& $FingerprintsBitVector\->SetSpecifiedSize($Size);
|
|
|
588 .Ve
|
|
|
589 .Sp
|
|
|
590 Sets specified size for fingerprints bit vector.
|
|
|
591 .Sp
|
|
|
592 Irrespective of specified size, Perl functions used to handle bit data in \fBBitVector\fR class
|
|
|
593 automatically sets the size to the next nearest power of 2. \fISpecifiedSize\fR is used by
|
|
|
594 \&\fBFingerprintsBitVector\fR class to process any aribitray size during similarity coefficient calculations.
|
|
|
595 .IP "\fBSetDescription\fR" 4
|
|
|
596 .IX Item "SetDescription"
|
|
|
597 .Vb 1
|
|
|
598 \& $FingerprintsBitVector\->SetDescription($Description);
|
|
|
599 .Ve
|
|
|
600 .Sp
|
|
|
601 Sets \fIDescription\fR of fingerprints bit vector and returns \fIFingerprintsBitVector\fR.
|
|
|
602 .IP "\fBSetID\fR" 4
|
|
|
603 .IX Item "SetID"
|
|
|
604 .Vb 1
|
|
|
605 \& $FingerprintsBitVector\->SetID($ID);
|
|
|
606 .Ve
|
|
|
607 .Sp
|
|
|
608 Sets \fI\s-1ID\s0\fR of fingerprints bit vector and returns \fIFingerprintsBitVector\fR.
|
|
|
609 .IP "\fBSetVectorType\fR" 4
|
|
|
610 .IX Item "SetVectorType"
|
|
|
611 .Vb 1
|
|
|
612 \& $FingerprintsBitVector\->SetVectorType($VectorType);
|
|
|
613 .Ve
|
|
|
614 .Sp
|
|
|
615 Sets \fIVectorType\fR of fingerprints bit vector and returns \fIFingerprintsBitVector\fR.
|
|
|
616 .IP "\fBSimpsonSimilarityCoefficient\fR" 4
|
|
|
617 .IX Item "SimpsonSimilarityCoefficient"
|
|
|
618 .Vb 4
|
|
|
619 \& $Value = $FingerprintsBitVector\->SimpsonSimilarityCoefficient(
|
|
|
620 \& $OtherFingerprintBitVector);
|
|
|
621 \& $Value = Fingerprints::FingerprintsBitVector::SimpsonSimilarityCoefficient(
|
|
|
622 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
623 .Ve
|
|
|
624 .Sp
|
|
|
625 Returns value of \fISimpson\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
626 .IP "\fBSkoalSneath1SimilarityCoefficient\fR" 4
|
|
|
627 .IX Item "SkoalSneath1SimilarityCoefficient"
|
|
|
628 .Vb 5
|
|
|
629 \& $Value = $FingerprintsBitVector\->SkoalSneath1SimilarityCoefficient(
|
|
|
630 \& $OtherFingerprintBitVector);
|
|
|
631 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
632 \& SkoalSneath1SimilarityCoefficient(
|
|
|
633 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
634 .Ve
|
|
|
635 .Sp
|
|
|
636 Returns value of \fISkoalSneath1\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
637 .IP "\fBSkoalSneath2SimilarityCoefficient\fR" 4
|
|
|
638 .IX Item "SkoalSneath2SimilarityCoefficient"
|
|
|
639 .Vb 5
|
|
|
640 \& $Value = $FingerprintsBitVector\->SkoalSneath2SimilarityCoefficient(
|
|
|
641 \& $OtherFingerprintBitVector);
|
|
|
642 \& $Value = Fingerprints::FingerprintsBitVector::
|
|
|
643 \& SkoalSneath2SimilarityCoefficient(
|
|
|
644 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
|
|
|
645 .Ve
|
|
|
646 .Sp
|
|
|
647 Returns value of \fISkoalSneath2\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
|
|
|
648 .IP "\fBSkoalSneath3SimilarityCoefficient\fR" 4
|
|
|
649 .IX Item "SkoalSneath3SimilarityCoefficient"
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650 .Vb 5
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651 \& $Value = $FingerprintsBitVector\->SkoalSneath3SimilarityCoefficient(
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652 \& $OtherFingerprintBitVector);
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653 \& $Value = Fingerprints::FingerprintsBitVector::
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654 \& SkoalSneath3SimilarityCoefficient(
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655 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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656 .Ve
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657 .Sp
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658 Returns value of \fISkoalSneath3\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR
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659 .IP "\fBStringifyFingerprintsBitVector\fR" 4
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660 .IX Item "StringifyFingerprintsBitVector"
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661 .Vb 1
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662 \& $String = $FingerprintsBitVector\->StringifyFingerprintsBitVector();
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663 .Ve
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664 .Sp
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665 Returns a string containing information about \fIFingerprintsBitVector\fR object.
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666 .IP "\fBTanimotoSimilarityCoefficient\fR" 4
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667 .IX Item "TanimotoSimilarityCoefficient"
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668 .Vb 5
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669 \& $Value = $FingerprintsBitVector\->TanimotoSimilarityCoefficient(
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670 \& $OtherFingerprintBitVector);
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671 \& $Value = Fingerprints::FingerprintsBitVector::
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672 \& TanimotoSimilarityCoefficient(
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673 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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674 .Ve
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675 .Sp
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676 Returns value of \fITanimoto\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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677 .IP "\fBTverskySimilarityCoefficient\fR" 4
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678 .IX Item "TverskySimilarityCoefficient"
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679 .Vb 5
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680 \& $Value = $FingerprintsBitVector\->TverskySimilarityCoefficient(
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681 \& $OtherFingerprintBitVector, $Alpha);
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682 \& $Value = Fingerprints::FingerprintsBitVector::
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683 \& TverskySimilarityCoefficient(
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684 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha);
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685 .Ve
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686 .Sp
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687 Returns value of \fITversky\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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688 .IP "\fBWeightedTanimotoSimilarityCoefficient\fR" 4
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689 .IX Item "WeightedTanimotoSimilarityCoefficient"
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690 .Vb 7
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691 \& $Value =
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692 \& $FingerprintsBitVector\->WeightedTanimotoSimilarityCoefficient(
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693 \& $OtherFingerprintBitVector, $Beta);
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694 \& $Value =
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695 \& Fingerprints::FingerprintsBitVector::
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696 \& WeightedTanimotoSimilarityCoefficient(
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697 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Beta);
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698 .Ve
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699 .Sp
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700 Returns value of \fIWeightedTanimoto\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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701 .IP "\fBWeightedTverskySimilarityCoefficient\fR" 4
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702 .IX Item "WeightedTverskySimilarityCoefficient"
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703 .Vb 7
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704 \& $Value =
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705 \& $FingerprintsBitVector\->WeightedTverskySimilarityCoefficient(
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706 \& $OtherFingerprintBitVector, $Alpha, $Beta);
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707 \& $Value =
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708 \& Fingerprints::FingerprintsBitVector::
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709 \& WeightedTverskySimilarityCoefficient(
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710 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha, $Beta);
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711 .Ve
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712 .Sp
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713 Returns value of \fIWeightedTversky\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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714 .IP "\fBYuleSimilarityCoefficient\fR" 4
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715 .IX Item "YuleSimilarityCoefficient"
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716 .Vb 4
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717 \& $Value = $FingerprintsBitVector\->YuleSimilarityCoefficient(
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718 \& $OtherFingerprintBitVector);
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719 \& $Value = Fingerprints::FingerprintsBitVector::YuleSimilarityCoefficient(
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720 \& $FingerprintsBitVectorA, $FingerprintBitVectorB);
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721 .Ve
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722 .Sp
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723 Returns value of \fIYule\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR.
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724 .SH "AUTHOR"
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725 .IX Header "AUTHOR"
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726 Manish Sud <msud@san.rr.com>
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727 .SH "SEE ALSO"
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728 .IX Header "SEE ALSO"
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729 BitVector.pm, FingerprintsStringUtil.pm, FingerprintsVector.pm, Vector.pm
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730 .SH "COPYRIGHT"
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731 .IX Header "COPYRIGHT"
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732 Copyright (C) 2015 Manish Sud. All rights reserved.
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733 .PP
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734 This file is part of MayaChemTools.
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735 .PP
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736 MayaChemTools is free software; you can redistribute it and/or modify it under
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737 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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738 Software Foundation; either version 3 of the License, or (at your option)
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739 any later version.
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