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comparison mayachemtools/docs/modules/man3/FingerprintsBitVector.3 @ 0:73ae111cf86f draft
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124 .\" ======================================================================== | |
125 .\" | |
126 .IX Title "FINGERPRINTSBITVECTOR 1" | |
127 .TH FINGERPRINTSBITVECTOR 1 "2015-03-29" "perl v5.14.2" "MayaChemTools" | |
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes | |
129 .\" way too many mistakes in technical documents. | |
130 .if n .ad l | |
131 .nh | |
132 .SH "NAME" | |
133 FingerprintsBitVector | |
134 .SH "SYNOPSIS" | |
135 .IX Header "SYNOPSIS" | |
136 use Fingerprints::FingerprintsBitVector; | |
137 .PP | |
138 use Fingerprints::FingerprintsBitVector qw(:coefficients); | |
139 .PP | |
140 use Fingerprints::FingerprintsBitVector qw(:all); | |
141 .SH "DESCRIPTION" | |
142 .IX Header "DESCRIPTION" | |
143 \&\fBFingerprintsBitVector\fR class provides the following methods: | |
144 .PP | |
145 new, BaroniUrbaniSimilarityCoefficient, BuserSimilarityCoefficient, | |
146 CosineSimilarityCoefficient, DennisSimilarityCoefficient, | |
147 DiceSimilarityCoefficient, FoldFingerprintsBitVectorByDensity, | |
148 FoldFingerprintsBitVectorBySize, ForbesSimilarityCoefficient, | |
149 FossumSimilarityCoefficient, GetBitsAsBinaryString, GetBitsAsDecimalString, | |
150 GetBitsAsHexadecimalString, GetBitsAsOctalString, GetBitsAsRawBinaryString, | |
151 GetDescription, GetFingerprintsBitDensity, GetID, GetSpecifiedSize, | |
152 GetSupportedSimilarityCoefficients, GetVectorType, HamannSimilarityCoefficient, | |
153 IsFingerprintsBitVector, IsSubSet, JacardSimilarityCoefficient, | |
154 Kulczynski1SimilarityCoefficient, Kulczynski2SimilarityCoefficient, | |
155 MatchingSimilarityCoefficient, McConnaugheySimilarityCoefficient, | |
156 NewFromBinaryString, NewFromDecimalString, NewFromHexadecimalString, | |
157 NewFromOctalString, NewFromRawBinaryString, OchiaiSimilarityCoefficient, | |
158 PearsonSimilarityCoefficient, RogersTanimotoSimilarityCoefficient, | |
159 RussellRaoSimilarityCoefficient, SetDescription, SetID, SetSpecifiedSize, | |
160 SetVectorType, SimpsonSimilarityCoefficient, SkoalSneath1SimilarityCoefficient, | |
161 SkoalSneath2SimilarityCoefficient, SkoalSneath3SimilarityCoefficient, | |
162 StringifyFingerprintsBitVector, TanimotoSimilarityCoefficient, | |
163 TverskySimilarityCoefficient, WeightedTanimotoSimilarityCoefficient, | |
164 WeightedTverskySimilarityCoefficient, YuleSimilarityCoefficient | |
165 .PP | |
166 The methods available to create fingerprints bit vector from strings and to calculate similarity | |
167 coefficient between two bit vectors can also be invoked as class functions. | |
168 .PP | |
169 \&\fBFingerprintsBitVector\fR class is derived from \fBBitVector\fR class which provides the functionality | |
170 to manipulate bits. | |
171 .PP | |
172 For two fingerprints bit vectors A and B of same size, let: | |
173 .PP | |
174 .Vb 4 | |
175 \& Na = Number of bits set to "1" in A | |
176 \& Nb = Number of bits set to "1" in B | |
177 \& Nc = Number of bits set to "1" in both A and B | |
178 \& Nd = Number of bits set to "0" in both A and B | |
179 \& | |
180 \& Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) | |
181 \& Nt = Na + Nb \- Nc + Nd | |
182 \& | |
183 \& Na \- Nc = Number of bits set to "1" in A but not in B | |
184 \& Nb \- Nc = Number of bits set to "1" in B but not in A | |
185 .Ve | |
186 .PP | |
187 Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit vectors A and B are | |
188 defined as follows: | |
189 .PP | |
190 BaroniUrbani: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser ) | |
191 .PP | |
192 Buser: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani ) | |
193 .PP | |
194 Cosine: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai) | |
195 .PP | |
196 Dice: (2 * Nc) / ( Na + Nb ) | |
197 .PP | |
198 Dennis: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb) | |
199 .PP | |
200 Forbes: ( Nt * Nc ) / ( Na * Nb ) | |
201 .PP | |
202 Fossum: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb ) | |
203 .PP | |
204 Hamann: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt | |
205 .PP | |
206 Jaccard: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto) | |
207 .PP | |
208 Kulczynski1: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc ) | |
209 .PP | |
210 Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) ) | |
211 = 0.5 * ( Nc / Na + Nc / Nb ) | |
212 .PP | |
213 Matching: ( Nc + Nd ) / Nt | |
214 .PP | |
215 McConnaughey: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb ) | |
216 .PP | |
217 Ochiai: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine) | |
218 .PP | |
219 Pearson: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) ) | |
220 .PP | |
221 RogersTanimoto: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt) | |
222 .PP | |
223 RussellRao: Nc / Nt | |
224 .PP | |
225 Simpson: Nc / \s-1MIN\s0 ( Na, Nb) | |
226 .PP | |
227 SkoalSneath1: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc ) | |
228 .PP | |
229 SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt ) | |
230 .PP | |
231 SkoalSneath3: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc ) | |
232 .PP | |
233 Tanimoto: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard) | |
234 .PP | |
235 Tversky: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb) | |
236 .PP | |
237 Yule: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) | |
238 .PP | |
239 The values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which | |
240 are set to \*(L"1\*(R" in both A and B. In order to take into account all bit positions, modified versions | |
241 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed. | |
242 .PP | |
243 Let: | |
244 .PP | |
245 .Vb 3 | |
246 \& Na\*(Aq = Number of bits set to "0" in A | |
247 \& Nb\*(Aq = Number of bits set to "0" in B | |
248 \& Nc\*(Aq = Number of bits set to "0" in both A and B | |
249 .Ve | |
250 .PP | |
251 Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' ) | |
252 .PP | |
253 Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb') | |
254 .PP | |
255 Then: | |
256 .PP | |
257 WeightedTanimoto = beta * Tanimoto + (1 \- beta) * Tanimoto' | |
258 .PP | |
259 WeightedTversky = beta * Tversky + (1 \- beta) * Tversky' | |
260 .SS "\s-1METHODS\s0" | |
261 .IX Subsection "METHODS" | |
262 .IP "\fBnew\fR" 4 | |
263 .IX Item "new" | |
264 .Vb 1 | |
265 \& $NewFPBitVector = new Fingerprints::FingerprintsBitVector($Size); | |
266 .Ve | |
267 .Sp | |
268 Creates a new \fIFingerprintsBitVector\fR object of size \fISize\fR and returns newly created | |
269 \&\fBFingerprintsBitVector\fR. Bit numbers range from 0 to 1 less than \fISize\fR. | |
270 .IP "\fBBaroniUrbaniSimilarityCoefficient\fR" 4 | |
271 .IX Item "BaroniUrbaniSimilarityCoefficient" | |
272 .Vb 5 | |
273 \& $Value = $FingerprintsBitVector\->BaroniUrbaniSimilarityCoefficient( | |
274 \& $OtherFingerprintBitVector); | |
275 \& $Value = Fingerprints::FingerprintsBitVector:: | |
276 \& BaroniUrbaniSimilarityCoefficient( | |
277 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
278 .Ve | |
279 .Sp | |
280 Returns value of \fIBaroniUrbani\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
281 .IP "\fBBuserSimilarityCoefficient\fR" 4 | |
282 .IX Item "BuserSimilarityCoefficient" | |
283 .Vb 4 | |
284 \& $Value = $FingerprintsBitVector\->BuserSimilarityCoefficient( | |
285 \& $OtherFingerprintBitVector); | |
286 \& $Value = Fingerprints::FingerprintsBitVector::BuserSimilarityCoefficient( | |
287 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
288 .Ve | |
289 .Sp | |
290 Returns value of \fIBuser\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
291 .IP "\fBCosineSimilarityCoefficient\fR" 4 | |
292 .IX Item "CosineSimilarityCoefficient" | |
293 .Vb 4 | |
294 \& $Value = $FingerprintsBitVector\->CosineSimilarityCoefficient( | |
295 \& $OtherFingerprintBitVector); | |
296 \& $Value = Fingerprints::FingerprintsBitVector::CosineSimilarityCoefficient( | |
297 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
298 .Ve | |
299 .Sp | |
300 Returns value of \fICosine\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
301 .IP "\fBDennisSimilarityCoefficient\fR" 4 | |
302 .IX Item "DennisSimilarityCoefficient" | |
303 .Vb 4 | |
304 \& $Value = $FingerprintsBitVector\->DennisSimilarityCoefficient( | |
305 \& $OtherFingerprintBitVector); | |
306 \& $Value = Fingerprints::FingerprintsBitVector::DennisSimilarityCoefficient( | |
307 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
308 .Ve | |
309 .Sp | |
310 Returns value of \fIDennis\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
311 .IP "\fBDiceSimilarityCoefficient\fR" 4 | |
312 .IX Item "DiceSimilarityCoefficient" | |
313 .Vb 4 | |
314 \& $Value = $FingerprintsBitVector\->DiceSimilarityCoefficient( | |
315 \& $OtherFingerprintBitVector); | |
316 \& $Value = Fingerprints::FingerprintsBitVector::DiceSimilarityCoefficient( | |
317 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
318 .Ve | |
319 .Sp | |
320 Returns value of \fIDice\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
321 .IP "\fBFoldFingerprintsBitVectorByDensity\fR" 4 | |
322 .IX Item "FoldFingerprintsBitVectorByDensity" | |
323 .Vb 1 | |
324 \& $FingerprintsBitVector\->FoldFingerprintsBitVectorByDensity($Density); | |
325 .Ve | |
326 .Sp | |
327 Folds \fIFingerprintsBitVector\fR by recursively reducing its size by half until bit density of set bits is | |
328 greater than or equal to specified \fIDensity\fR and returns folded \fIFingerprintsBitVector\fR. | |
329 .IP "\fBFoldFingerprintsBitVectorBySize\fR" 4 | |
330 .IX Item "FoldFingerprintsBitVectorBySize" | |
331 .Vb 1 | |
332 \& $FingerprintsBitVector\->FoldFingerprintsBitVectorBySize($Size); | |
333 .Ve | |
334 .Sp | |
335 Folds \fIFingerprintsBitVector\fR by recursively reducing its size by half until size is less than or equal to | |
336 specified \fISize\fR and returns folded \fIFingerprintsBitVector\fR. | |
337 .IP "\fBForbesSimilarityCoefficient\fR" 4 | |
338 .IX Item "ForbesSimilarityCoefficient" | |
339 .Vb 4 | |
340 \& $Value = $FingerprintsBitVector\->ForbesSimilarityCoefficient( | |
341 \& $OtherFingerprintBitVector); | |
342 \& $Value = Fingerprints::FingerprintsBitVector::ForbesSimilarityCoefficient( | |
343 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
344 .Ve | |
345 .Sp | |
346 Returns value of \fIForbes\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
347 .IP "\fBFossumSimilarityCoefficient\fR" 4 | |
348 .IX Item "FossumSimilarityCoefficient" | |
349 .Vb 4 | |
350 \& $Value = $FingerprintsBitVector\->FossumSimilarityCoefficient( | |
351 \& $OtherFingerprintBitVector); | |
352 \& $Value = Fingerprints::FingerprintsBitVector::FossumSimilarityCoefficient( | |
353 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
354 .Ve | |
355 .Sp | |
356 Returns value of \fIFossum\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
357 .IP "\fBGetBitsAsBinaryString\fR" 4 | |
358 .IX Item "GetBitsAsBinaryString" | |
359 .Vb 1 | |
360 \& $BinaryASCIIString = $FingerprintsBitVector\->GetBitsAsBinaryString(); | |
361 .Ve | |
362 .Sp | |
363 Returns fingerprints as a binary \s-1ASCII\s0 string containing 0s and 1s. | |
364 .IP "\fBGetBitsAsHexadecimalString\fR" 4 | |
365 .IX Item "GetBitsAsHexadecimalString" | |
366 .Vb 1 | |
367 \& $HexadecimalString = $FingerprintsBitVector\->GetBitsAsHexadecimalString(); | |
368 .Ve | |
369 .Sp | |
370 Returns fingerprints as a hexadecimal string. | |
371 .IP "\fBGetBitsAsRawBinaryString\fR" 4 | |
372 .IX Item "GetBitsAsRawBinaryString" | |
373 .Vb 1 | |
374 \& $RawBinaryString = $FingerprintsBitVector\->GetBitsAsRawBinaryString(); | |
375 .Ve | |
376 .Sp | |
377 Returns fingerprints as a raw binary string containing packed bit values for each byte. | |
378 .IP "\fBGetDescription\fR" 4 | |
379 .IX Item "GetDescription" | |
380 .Vb 1 | |
381 \& $Description = $FingerprintsBitVector\->GetDescription(); | |
382 .Ve | |
383 .Sp | |
384 Returns a string containing description of fingerprints bit vector. | |
385 .IP "\fBGetFingerprintsBitDensity\fR" 4 | |
386 .IX Item "GetFingerprintsBitDensity" | |
387 .Vb 1 | |
388 \& $BitDensity = $FingerprintsBitVector\->GetFingerprintsBitDensity(); | |
389 .Ve | |
390 .Sp | |
391 Returns \fIBitDensity\fR of \fIFingerprintsBitVector\fR corresponding to bits set to 1s. | |
392 .IP "\fBGetID\fR" 4 | |
393 .IX Item "GetID" | |
394 .Vb 1 | |
395 \& $ID = $FingerprintsBitVector\->GetID(); | |
396 .Ve | |
397 .Sp | |
398 Returns \fI\s-1ID\s0\fR of \fIFingerprintsBitVector\fR. | |
399 .IP "\fBGetVectorType\fR" 4 | |
400 .IX Item "GetVectorType" | |
401 .Vb 1 | |
402 \& $VectorType = $FingerprintsBitVector\->GetVectorType(); | |
403 .Ve | |
404 .Sp | |
405 Returns \fIVectorType\fR of \fIFingerprintsBitVector\fR. | |
406 .IP "\fBGetSpecifiedSize\fR" 4 | |
407 .IX Item "GetSpecifiedSize" | |
408 .Vb 1 | |
409 \& $Size = $FingerprintsBitVector\->GetSpecifiedSize(); | |
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 = | |
417 \& Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients(); | |
418 .Ve | |
419 .Sp | |
420 Returns an array containing names of supported similarity coefficients. | |
421 .IP "\fBHamannSimilarityCoefficient\fR" 4 | |
422 .IX Item "HamannSimilarityCoefficient" | |
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" | |
650 .Vb 5 | |
651 \& $Value = $FingerprintsBitVector\->SkoalSneath3SimilarityCoefficient( | |
652 \& $OtherFingerprintBitVector); | |
653 \& $Value = Fingerprints::FingerprintsBitVector:: | |
654 \& SkoalSneath3SimilarityCoefficient( | |
655 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
656 .Ve | |
657 .Sp | |
658 Returns value of \fISkoalSneath3\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR | |
659 .IP "\fBStringifyFingerprintsBitVector\fR" 4 | |
660 .IX Item "StringifyFingerprintsBitVector" | |
661 .Vb 1 | |
662 \& $String = $FingerprintsBitVector\->StringifyFingerprintsBitVector(); | |
663 .Ve | |
664 .Sp | |
665 Returns a string containing information about \fIFingerprintsBitVector\fR object. | |
666 .IP "\fBTanimotoSimilarityCoefficient\fR" 4 | |
667 .IX Item "TanimotoSimilarityCoefficient" | |
668 .Vb 5 | |
669 \& $Value = $FingerprintsBitVector\->TanimotoSimilarityCoefficient( | |
670 \& $OtherFingerprintBitVector); | |
671 \& $Value = Fingerprints::FingerprintsBitVector:: | |
672 \& TanimotoSimilarityCoefficient( | |
673 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
674 .Ve | |
675 .Sp | |
676 Returns value of \fITanimoto\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
677 .IP "\fBTverskySimilarityCoefficient\fR" 4 | |
678 .IX Item "TverskySimilarityCoefficient" | |
679 .Vb 5 | |
680 \& $Value = $FingerprintsBitVector\->TverskySimilarityCoefficient( | |
681 \& $OtherFingerprintBitVector, $Alpha); | |
682 \& $Value = Fingerprints::FingerprintsBitVector:: | |
683 \& TverskySimilarityCoefficient( | |
684 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha); | |
685 .Ve | |
686 .Sp | |
687 Returns value of \fITversky\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
688 .IP "\fBWeightedTanimotoSimilarityCoefficient\fR" 4 | |
689 .IX Item "WeightedTanimotoSimilarityCoefficient" | |
690 .Vb 7 | |
691 \& $Value = | |
692 \& $FingerprintsBitVector\->WeightedTanimotoSimilarityCoefficient( | |
693 \& $OtherFingerprintBitVector, $Beta); | |
694 \& $Value = | |
695 \& Fingerprints::FingerprintsBitVector:: | |
696 \& WeightedTanimotoSimilarityCoefficient( | |
697 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Beta); | |
698 .Ve | |
699 .Sp | |
700 Returns value of \fIWeightedTanimoto\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
701 .IP "\fBWeightedTverskySimilarityCoefficient\fR" 4 | |
702 .IX Item "WeightedTverskySimilarityCoefficient" | |
703 .Vb 7 | |
704 \& $Value = | |
705 \& $FingerprintsBitVector\->WeightedTverskySimilarityCoefficient( | |
706 \& $OtherFingerprintBitVector, $Alpha, $Beta); | |
707 \& $Value = | |
708 \& Fingerprints::FingerprintsBitVector:: | |
709 \& WeightedTverskySimilarityCoefficient( | |
710 \& $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha, $Beta); | |
711 .Ve | |
712 .Sp | |
713 Returns value of \fIWeightedTversky\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
714 .IP "\fBYuleSimilarityCoefficient\fR" 4 | |
715 .IX Item "YuleSimilarityCoefficient" | |
716 .Vb 4 | |
717 \& $Value = $FingerprintsBitVector\->YuleSimilarityCoefficient( | |
718 \& $OtherFingerprintBitVector); | |
719 \& $Value = Fingerprints::FingerprintsBitVector::YuleSimilarityCoefficient( | |
720 \& $FingerprintsBitVectorA, $FingerprintBitVectorB); | |
721 .Ve | |
722 .Sp | |
723 Returns value of \fIYule\fR similarity coefficient between two same size \fIFingerprintsBitVectors\fR. | |
724 .SH "AUTHOR" | |
725 .IX Header "AUTHOR" | |
726 Manish Sud <msud@san.rr.com> | |
727 .SH "SEE ALSO" | |
728 .IX Header "SEE ALSO" | |
729 BitVector.pm, FingerprintsStringUtil.pm, FingerprintsVector.pm, Vector.pm | |
730 .SH "COPYRIGHT" | |
731 .IX Header "COPYRIGHT" | |
732 Copyright (C) 2015 Manish Sud. All rights reserved. | |
733 .PP | |
734 This file is part of MayaChemTools. | |
735 .PP | |
736 MayaChemTools is free software; you can redistribute it and/or modify it under | |
737 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free | |
738 Software Foundation; either version 3 of the License, or (at your option) | |
739 any later version. |