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126 .IX Title "FINGERPRINTSVECTOR 1"
127 .TH FINGERPRINTSVECTOR 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 FingerprintsVector
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use Fingerprints::FingerprintsVector;
137 .PP
138 use Fingerprints::FingerprintsVector qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBFingerprintsVector\fR class provides the following methods:
142 .PP
143 new, AddValueIDs, AddValues, CityBlockDistanceCoefficient,
144 CosineSimilarityCoefficient, CzekanowskiSimilarityCoefficient,
145 DiceSimilarityCoefficient, EuclideanDistanceCoefficient, GetDescription,
146 GetFingerprintsVectorString, GetID, GetIDsAndValuesPairsString,
147 GetIDsAndValuesString, GetNumOfNonZeroValues, GetNumOfValueIDs, GetNumOfValues,
148 GetSupportedDistanceAndSimilarityCoefficients, GetSupportedDistanceCoefficients,
149 GetSupportedSimilarityCoefficients, GetType, GetValue, GetValueID, GetValueIDs,
150 GetValueIDsString, GetValues, GetValuesAndIDsPairsString, GetValuesAndIDsString,
151 GetValuesString, GetVectorType, HammingDistanceCoefficient, IsFingerprintsVector,
152 JaccardSimilarityCoefficient, ManhattanDistanceCoefficient,
153 NewFromIDsAndValuesPairsString, NewFromIDsAndValuesString,
154 NewFromValuesAndIDsPairsString, NewFromValuesAndIDsString, NewFromValuesString,
155 OchiaiSimilarityCoefficient, SetDescription, SetID, SetType, SetValue, SetValueID,
156 SetValueIDs, SetValues, SetVectorType, SoergelDistanceCoefficient,
157 SorensonSimilarityCoefficient, StringifyFingerprintsVector,
158 TanimotoSimilarityCoefficient
159 .PP
160 The methods available to create fingerprints vector from strings and to calculate similarity
161 and distance coefficients between two vectors can also be invoked as class functions.
162 .PP
163 \&\fBFingerprintsVector\fR class provides support to perform comparison between vectors
164 containing three different types of values:
165 .PP
166 Type I: OrderedNumericalValues
167 .PP
168 .Vb 3
169 \& o Size of two vectors are same
170 \& o Vectors contain real values in a specific order. For example: MACCS keys
171 \& count, Topological pharmacophore atom pairs and so on.
172 .Ve
173 .PP
174 Type \s-1II:\s0 UnorderedNumericalValues
175 .PP
176 .Vb 3
177 \& o Size of two vectors might not be same
178 \& o Vectors contain unordered real value identified by value IDs. For example:
179 \& Topological atom pairs, Topological atom torsions and so on
180 .Ve
181 .PP
182 Type \s-1III:\s0 AlphaNumericalValues
183 .PP
184 .Vb 3
185 \& o Size of two vectors might not be same
186 \& o Vectors contain unordered alphanumerical values. For example: Extended
187 \& connectivity fingerprints, atom neighborhood fingerprints.
188 .Ve
189 .PP
190 Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
191 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
192 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.
193 .PP
194 Three forms of similarity and distance calculation between two vectors, specified using \fBCalculationMode\fR
195 option, are supported: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR.
196 .PP
197 For \fIBinaryForm\fR, the ordered list of processed final vector values containing the value or
198 count of each unique value type is simply converted into a binary vector containing 1s and 0s
199 corresponding to presence or absence of values before calculating similarity or distance between
200 two vectors.
201 .PP
202 For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:
203 .PP
204 .Vb 1
205 \& N = Number values in A or B
206 \&
207 \& Xa = Values of vector A
208 \& Xb = Values of vector B
209 \&
210 \& Xai = Value of ith element in A
211 \& Xbi = Value of ith element in B
212 \&
213 \& SUM = Sum of i over N values
214 .Ve
215 .PP
216 For SetTheoreticForm of calculation between two vectors, let:
217 .PP
218 .Vb 2
219 \& SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
220 \& SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) \- SUM ( MIN ( Xai, Xbi ) )
221 .Ve
222 .PP
223 For BinaryForm of calculation between two vectors, let:
224 .PP
225 .Vb 5
226 \& Na = Number of bits set to "1" in A = SUM ( Xai )
227 \& Nb = Number of bits set to "1" in B = SUM ( Xbi )
228 \& Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
229 \& Nd = Number of bits set to "0" in both A and B
230 \& = SUM ( 1 \- Xai \- Xbi + Xai * Xbi)
231 \&
232 \& N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb \- Nc + Nd
233 .Ve
234 .PP
235 Additionally, for BinaryForm various values also correspond to:
236 .PP
237 .Vb 4
238 \& Na = | Xa |
239 \& Nb = | Xb |
240 \& Nc = | SetIntersectionXaXb |
241 \& Nd = N \- | SetDifferenceXaXb |
242 \&
243 \& | SetDifferenceXaXb | = N \- Nd = Na + Nb \- Nc + Nd \- Nd = Na + Nb \- Nc
244 \& = | Xa | + | Xb | \- | SetIntersectionXaXb |
245 .Ve
246 .PP
247 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
248 in \fIAlgebraicForm, BinaryForm and SetTheoreticForm\fR are defined as follows:
249 .PP
250 \&\fBCityBlockDistance\fR: ( same as HammingDistance and ManhattanDistance)
251 .PP
252 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
253 .PP
254 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
255 .PP
256 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
257 .PP
258 \&\fBCosineSimilarity\fR: ( same as OchiaiSimilarityCoefficient)
259 .PP
260 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) )
261 .PP
262 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb)
263 .PP
264 \&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / \s-1SQRT\s0 ( |Xa| * |Xb| ) = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) * \s-1SUM\s0 ( Xbi ) )
265 .PP
266 \&\fBCzekanowskiSimilarity\fR: ( same as DiceSimilarity and SorensonSimilarity)
267 .PP
268 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
269 .PP
270 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
271 .PP
272 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
273 .PP
274 \&\fBDiceSimilarity\fR: ( same as CzekanowskiSimilarity and SorensonSimilarity)
275 .PP
276 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
277 .PP
278 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
279 .PP
280 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
281 .PP
282 \&\fBEuclideanDistance\fR:
283 .PP
284 \&\fIAlgebraicForm\fR: \s-1SQRT\s0 ( \s-1SUM\s0 ( ( ( Xai \- Xbi ) ** 2 ) ) )
285 .PP
286 \&\fIBinaryForm\fR: \s-1SQRT\s0 ( ( Na \- Nc ) + ( Nb \- Nc ) ) = \s-1SQRT\s0 ( Na + Nb \- 2 * Nc )
287 .PP
288 \&\fISetTheoreticForm\fR: \s-1SQRT\s0 ( | SetDifferenceXaXb | \- | SetIntersectionXaXb | ) = \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) )
289 .PP
290 \&\fBHammingDistance\fR: ( same as CityBlockDistance and ManhattanDistance)
291 .PP
292 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
293 .PP
294 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
295 .PP
296 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
297 .PP
298 \&\fBJaccardSimilarity\fR: ( same as TanimotoSimilarity)
299 .PP
300 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) )
301 .PP
302 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc )
303 .PP
304 \&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / | SetDifferenceXaXb | = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
305 .PP
306 \&\fBManhattanDistance\fR: ( same as CityBlockDistance and HammingDistance)
307 .PP
308 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
309 .PP
310 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
311 .PP
312 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
313 .PP
314 \&\fBOchiaiSimilarity\fR: ( same as CosineSimilarity)
315 .PP
316 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) )
317 .PP
318 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb)
319 .PP
320 \&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / \s-1SQRT\s0 ( |Xa| * |Xb| ) = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) * \s-1SUM\s0 ( Xbi ) )
321 .PP
322 \&\fBSorensonSimilarity\fR: ( same as CzekanowskiSimilarity and DiceSimilarity)
323 .PP
324 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
325 .PP
326 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
327 .PP
328 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
329 .PP
330 \&\fBSoergelDistance\fR:
331 .PP
332 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) / \s-1SUM\s0 ( \s-1MAX\s0 ( Xai, Xbi ) )
333 .PP
334 \&\fIBinaryForm\fR: 1 \- Nc / ( Na + Nb \- Nc ) = ( Na + Nb \- 2 * Nc ) / ( Na + Nb \- Nc )
335 .PP
336 \&\fISetTheoreticForm\fR: ( | SetDifferenceXaXb | \- | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
337 .PP
338 \&\fBTanimotoSimilarity\fR: ( same as JaccardSimilarity)
339 .PP
340 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) )
341 .PP
342 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc )
343 .PP
344 \&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / | SetDifferenceXaXb | = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
345 .SS "\s-1METHODS\s0"
346 .IX Subsection "METHODS"
347 .IP "\fBnew\fR" 4
348 .IX Item "new"
349 .Vb 1
350 \& $FPVector = new Fingerprints::FingerprintsVector(%NamesAndValues);
351 .Ve
352 .Sp
353 Using specified \fIFingerprintsVector\fR property names and values hash, \fBnew\fR method creates
354 a new object and returns a reference to newly created \fBFingerprintsVectorsVector\fR
355 object. By default, the following properties are initialized:
356 .Sp
357 .Vb 3
358 \& Type = \*(Aq\*(Aq
359 \& @{Values} = ()
360 \& @{ValuesIDs} = ()
361 .Ve
362 .Sp
363 Examples:
364 .Sp
365 .Vb 7
366 \& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqOrderedNumericalValues\*(Aq,
367 \& \*(AqValues\*(Aq => [1, 2, 3, 4]);
368 \& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqNumericalValues\*(Aq,
369 \& \*(AqValues\*(Aq => [10, 22, 33, 44],
370 \& \*(AqValueIDs\*(Aq => [\*(AqID1\*(Aq, \*(AqID2\*(Aq, \*(AqID3\*(Aq, \*(AqID4\*(Aq]);
371 \& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqAlphaNumericalValues\*(Aq,
372 \& \*(AqValues\*(Aq => [\*(Aqa1\*(Aq, 2, \*(Aqa3\*(Aq, 4]);
373 .Ve
374 .IP "\fBAddValueIDs\fR" 4
375 .IX Item "AddValueIDs"
376 .Vb 2
377 \& $FingerprintsVector\->AddValueIDs($ValueIDsRef);
378 \& $FingerprintsVector\->AddValueIDs(@ValueIDs);
379 .Ve
380 .Sp
381 Adds specified \fIValueIDs\fR to \fIFingerprintsVector\fR and returns \fIFingerprintsVector\fR.
382 .IP "\fBAddValues\fR" 4
383 .IX Item "AddValues"
384 .Vb 3
385 \& $FingerprintsVector\->AddValues($ValuesRef);
386 \& $FingerprintsVector\->AddValues(@Values);
387 \& $FingerprintsVector\->AddValues($Vector);
388 .Ve
389 .Sp
390 Adds specified \fIValues\fR to \fIFingerprintsVector\fR and returns \fIFingerprintsVector\fR.
391 .IP "\fBCityBlockDistanceCoefficient\fR" 4
392 .IX Item "CityBlockDistanceCoefficient"
393 .Vb 5
394 \& $Value = $FingerprintsVector\->CityBlockDistanceCoefficient(
395 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
396 \& $Value = Fingerprints::FingerprintsVector::CityBlockDistanceCoefficient(
397 \& $FingerprintsVectorA, $FingerprintVectorB,
398 \& [$CalculationMode, $SkipValuesCheck]);
399 .Ve
400 .Sp
401 Returns value of \fICityBlock\fR distance coefficient between two \fIFingerprintsVectors\fR using
402 optionally specified \fICalculationMode\fR and optional checking of vector values.
403 .Sp
404 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
405 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
406 .IP "\fBCosineSimilarityCoefficient\fR" 4
407 .IX Item "CosineSimilarityCoefficient"
408 .Vb 5
409 \& $Value = $FingerprintsVector\->CosineSimilarityCoefficient(
410 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
411 \& $Value = Fingerprints::FingerprintsVector::CosineSimilarityCoefficient(
412 \& $FingerprintsVectorA, $FingerprintVectorB,
413 \& [$CalculationMode, $SkipValuesCheck]);
414 .Ve
415 .Sp
416 Returns value of \fICosine\fR similarity coefficient between two \fIFingerprintsVectors\fR using
417 optionally specified \fICalculationMode\fR and optional checking of vector values.
418 .Sp
419 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
420 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
421 .IP "\fBCzekanowskiSimilarityCoefficient\fR" 4
422 .IX Item "CzekanowskiSimilarityCoefficient"
423 .Vb 5
424 \& $Value = $FingerprintsVector\->CzekanowskiSimilarityCoefficient(
425 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
426 \& $Value = Fingerprints::FingerprintsVector::CzekanowskiSimilarityCoefficient(
427 \& $FingerprintsVectorA, $FingerprintVectorB,
428 \& [$CalculationMode, $SkipValuesCheck]);
429 .Ve
430 .Sp
431 Returns value of \fICzekanowski\fR similarity coefficient between two \fIFingerprintsVectors\fR using
432 optionally specified \fICalculationMode\fR and optional checking of vector values.
433 .Sp
434 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
435 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
436 .IP "\fBDiceSimilarityCoefficient\fR" 4
437 .IX Item "DiceSimilarityCoefficient"
438 .Vb 5
439 \& $Value = $FingerprintsVector\->DiceSimilarityCoefficient(
440 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
441 \& $Value = Fingerprints::FingerprintsVector::DiceSimilarityCoefficient(
442 \& $FingerprintsVectorA, $FingerprintVectorB,
443 \& [$CalculationMode, $SkipValuesCheck]);
444 .Ve
445 .Sp
446 Returns value of \fIDice\fR similarity coefficient between two \fIFingerprintsVectors\fR using
447 optionally specified \fICalculationMode\fR and optional checking of vector values.
448 .Sp
449 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
450 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
451 .IP "\fBEuclideanDistanceCoefficient\fR" 4
452 .IX Item "EuclideanDistanceCoefficient"
453 .Vb 5
454 \& $Value = $FingerprintsVector\->EuclideanDistanceCoefficient(
455 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
456 \& $Value = Fingerprints::FingerprintsVector::EuclideanDistanceCoefficient(
457 \& $FingerprintsVectorA, $FingerprintVectorB,
458 \& [$CalculationMode, $SkipValuesCheck]);
459 .Ve
460 .Sp
461 Returns value of \fIEuclidean\fR distance coefficient between two \fIFingerprintsVectors\fR using
462 optionally specified \fICalculationMode\fR and optional checking of vector values.
463 .Sp
464 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
465 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
466 .IP "\fBGetDescription\fR" 4
467 .IX Item "GetDescription"
468 .Vb 1
469 \& $Description = $FingerprintsVector\->GetDescription();
470 .Ve
471 .Sp
472 Returns a string containing description of fingerprints vector.
473 .IP "\fBGetFingerprintsVectorString\fR" 4
474 .IX Item "GetFingerprintsVectorString"
475 .Vb 1
476 \& $FPString = $FingerprintsVector\->GetFingerprintsVectorString($Format);
477 .Ve
478 .Sp
479 Returns a \fBFingerprintsString\fR containing vector values and/or IDs in \fIFingerprintsVector\fR
480 corresponding to specified \fIFormat\fR.
481 .Sp
482 Possible \fIFormat\fR values: \fIIDsAndValuesString, IDsAndValues, IDsAndValuesPairsString,
483 IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs,
484 ValueIDsString, ValueIDs, ValuesString, or Values\fR.
485 .IP "\fBGetID\fR" 4
486 .IX Item "GetID"
487 .Vb 1
488 \& $ID = $FingerprintsVector\->GetID();
489 .Ve
490 .Sp
491 Returns \fI\s-1ID\s0\fR of \fIFingerprintsVector\fR.
492 .IP "\fBGetVectorType\fR" 4
493 .IX Item "GetVectorType"
494 .Vb 1
495 \& $VectorType = $FingerprintsVector\->GetVectorType();
496 .Ve
497 .Sp
498 Returns \fIVectorType\fR of \fIFingerprintsVector\fR.
499 .IP "\fBGetIDsAndValuesPairsString\fR" 4
500 .IX Item "GetIDsAndValuesPairsString"
501 .Vb 1
502 \& $IDsValuesPairsString = $FingerprintsVector\->GetIDsAndValuesPairsString();
503 .Ve
504 .Sp
505 Returns \fIFingerprintsVector\fR value IDs and values as space delimited ID/value pair
506 string.
507 .IP "\fBGetIDsAndValuesString\fR" 4
508 .IX Item "GetIDsAndValuesString"
509 .Vb 1
510 \& $IDsValuesString = $FingerprintsVector\->GetIDsAndValuesString();
511 .Ve
512 .Sp
513 Returns \fIFingerprintsVector\fR value IDs and values as string containing space delimited IDs followed by
514 values with semicolon as IDs and values delimiter.
515 .IP "\fBGetNumOfNonZeroValues\fR" 4
516 .IX Item "GetNumOfNonZeroValues"
517 .Vb 1
518 \& $NumOfNonZeroValues = $FingerprintsVector\->GetNumOfNonZeroValues();
519 .Ve
520 .Sp
521 Returns number of non-zero values in \fIFingerprintsVector\fR.
522 .IP "\fBGetNumOfValueIDs\fR" 4
523 .IX Item "GetNumOfValueIDs"
524 .Vb 1
525 \& $NumOfValueIDs = $FingerprintsVector\->GetNumOfValueIDs();
526 .Ve
527 .Sp
528 Returns number of value IDs \fIFingerprintsVector\fR.
529 .IP "\fBGetNumOfValues\fR" 4
530 .IX Item "GetNumOfValues"
531 .Vb 1
532 \& $NumOfValues = $FingerprintsVector\->GetNumOfValues();
533 .Ve
534 .Sp
535 Returns number of values \fIFingerprintsVector\fR.
536 .IP "\fBGetSupportedDistanceAndSimilarityCoefficients\fR" 4
537 .IX Item "GetSupportedDistanceAndSimilarityCoefficients"
538 .Vb 2
539 \& @SupportedDistanceAndSimilarityCoefficientsReturn =
540 \& Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients();
541 .Ve
542 .Sp
543 Returns an array containing names of supported distance and similarity coefficients.
544 .IP "\fBGetSupportedDistanceCoefficients\fR" 4
545 .IX Item "GetSupportedDistanceCoefficients"
546 .Vb 2
547 \& @SupportedDistanceCoefficientsReturn =
548 \& Fingerprints::FingerprintsVector::GetSupportedDistanceCoefficients();
549 .Ve
550 .Sp
551 Returns an array containing names of supported disyance coefficients.
552 .IP "\fBGetSupportedSimilarityCoefficients\fR" 4
553 .IX Item "GetSupportedSimilarityCoefficients"
554 .Vb 2
555 \& @SupportedSimilarityCoefficientsReturn =
556 \& Fingerprints::FingerprintsVector::GetSupportedSimilarityCoefficients();
557 .Ve
558 .Sp
559 Returns an array containing names of supported similarity coefficients.
560 .IP "\fBGetType\fR" 4
561 .IX Item "GetType"
562 .Vb 1
563 \& $VectorType = $FingerprintsVector\->GetType();
564 .Ve
565 .Sp
566 Returns \fIFingerprintsVector\fR vector type.
567 .IP "\fBGetValue\fR" 4
568 .IX Item "GetValue"
569 .Vb 1
570 \& $Value = $FingerprintsVector\->GetValue($Index);
571 .Ve
572 .Sp
573 Returns fingerprints vector \fBValue\fR specified using \fIIndex\fR starting at 0.
574 .IP "\fBGetValueID\fR" 4
575 .IX Item "GetValueID"
576 .Vb 1
577 \& $ValueID = $FingerprintsVector\->GetValueID();
578 .Ve
579 .Sp
580 Returns fingerprints vector \fBValueID\fR specified using \fIIndex\fR starting at 0.
581 .IP "\fBGetValueIDs\fR" 4
582 .IX Item "GetValueIDs"
583 .Vb 2
584 \& $ValueIDs = $FingerprintsVector\->GetValueIDs();
585 \& @ValueIDs = $FingerprintsVector\->GetValueIDs();
586 .Ve
587 .Sp
588 Returns fingerprints vector \fBValueIDs\fR as an array or reference to an array.
589 .IP "\fBGetValueIDsString\fR" 4
590 .IX Item "GetValueIDsString"
591 .Vb 1
592 \& $ValueIDsString = $FingerprintsVector\->GetValueIDsString();
593 .Ve
594 .Sp
595 Returns fingerprints vector \fBValueIDsString\fR with value IDs delimited by space.
596 .IP "\fBGetValues\fR" 4
597 .IX Item "GetValues"
598 .Vb 2
599 \& $ValuesRef = $FingerprintsVector\->GetValues();
600 \& @Values = $FingerprintsVector\->GetValues();
601 .Ve
602 .Sp
603 Returns fingerprints vector \fBValues\fR as an array or reference to an array.
604 .IP "\fBGetValuesAndIDsPairsString\fR" 4
605 .IX Item "GetValuesAndIDsPairsString"
606 .Vb 1
607 \& $ValuesIDsPairsString = $FingerprintsVector\->GetValuesAndIDsPairsString();
608 .Ve
609 .Sp
610 Returns \fIFingerprintsVector\fR value and value IDs as space delimited ID/value pair
611 string.
612 .IP "\fBGetValuesAndIDsString\fR" 4
613 .IX Item "GetValuesAndIDsString"
614 .Vb 1
615 \& $ValuesIDsString = $FingerprintsVector\->GetValuesAndIDsString();
616 .Ve
617 .Sp
618 Returns \fIFingerprintsVector\fR values and value IDs as string containing space delimited IDs followed by
619 values with semicolon as IDs and values delimiter.
620 .IP "\fBGetValuesString\fR" 4
621 .IX Item "GetValuesString"
622 .Vb 1
623 \& $Return = $FingerprintsVector\->GetValuesString();
624 .Ve
625 .Sp
626 Returns \fIFingerprintsVector\fR values as space delimited string.
627 .IP "\fBHammingDistanceCoefficient\fR" 4
628 .IX Item "HammingDistanceCoefficient"
629 .Vb 5
630 \& $Value = $FingerprintsVector\->HammingDistanceCoefficient(
631 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
632 \& $Value = Fingerprints::FingerprintsVector::HammingDistanceCoefficient(
633 \& $FingerprintsVectorA, $FingerprintVectorB,
634 \& [$CalculationMode, $SkipValuesCheck]);
635 .Ve
636 .Sp
637 Returns value of \fIHamming\fR distance coefficient between two \fIFingerprintsVectors\fR using
638 optionally specified \fICalculationMode\fR and optional checking of vector values.
639 .Sp
640 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
641 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
642 .IP "\fBIsFingerprintsVector\fR" 4
643 .IX Item "IsFingerprintsVector"
644 .Vb 1
645 \& $Status = Fingerprints::FingerprintsVector::IsFingerprintsVector($Object);
646 .Ve
647 .Sp
648 Returns 1 or 0 based on whether \fIObject\fR is a \fIFingerprintsVector\fR.
649 .IP "\fBJaccardSimilarityCoefficient\fR" 4
650 .IX Item "JaccardSimilarityCoefficient"
651 .Vb 5
652 \& $Value = $FingerprintsVector\->JaccardSimilarityCoefficient(
653 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
654 \& $Value = Fingerprints::FingerprintsVector::JaccardSimilarityCoefficient(
655 \& $FingerprintsVectorA, $FingerprintVectorB,
656 \& [$CalculationMode, $SkipValuesCheck]);
657 .Ve
658 .Sp
659 Returns value of \fIJaccard\fR similarity coefficient between two \fIFingerprintsVectors\fR using
660 optionally specified \fICalculationMode\fR and optional checking of vector values.
661 .Sp
662 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
663 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
664 .IP "\fBManhattanDistanceCoefficient\fR" 4
665 .IX Item "ManhattanDistanceCoefficient"
666 .Vb 5
667 \& $Value = $FingerprintsVector\->ManhattanDistanceCoefficient(
668 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
669 \& $Value = Fingerprints::FingerprintsVector::ManhattanDistanceCoefficient(
670 \& $FingerprintsVectorA, $FingerprintVectorB,
671 \& [$CalculationMode, $SkipValuesCheck]);
672 .Ve
673 .Sp
674 Returns value of \fIManhattan\fR distance coefficient between two \fIFingerprintsVectors\fR using
675 optionally specified \fICalculationMode\fR and optional checking of vector values.
676 .Sp
677 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
678 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
679 .IP "\fBNewFromIDsAndValuesPairsString\fR" 4
680 .IX Item "NewFromIDsAndValuesPairsString"
681 .Vb 4
682 \& $FingerprintsVector = $FingerprintsVector\->NewFromIDsAndValuesPairsString(
683 \& $ValuesType, $IDsAndValuesPairsString);
684 \& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString(
685 \& $ValuesType, $IDsAndValuesPairsString);
686 .Ve
687 .Sp
688 Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIIDsAndValuesPairsString\fR containing
689 space delimited value IDs and values pairs and returns new \fBFingerprintsVector\fR object.
690 Possible \fIValuesType\fR values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR.
691 .IP "\fBNewFromIDsAndValuesString\fR" 4
692 .IX Item "NewFromIDsAndValuesString"
693 .Vb 4
694 \& $FingerprintsVector = $FingerprintsVector\->NewFromIDsAndValuesString(
695 \& $ValuesType, $IDsAndValuesString);
696 \& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString(
697 \& $ValuesType, $IDsAndValuesString);
698 .Ve
699 .Sp
700 Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIIDsAndValuesString\fR containing
701 semicolon delimited value IDs string followed by values strings and returns new \fBFingerprintsVector\fR
702 object. The values within value and value IDs tring are delimited by spaces. Possible \fIValuesType\fR
703 values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR.
704 .IP "\fBNewFromValuesAndIDsPairsString\fR" 4
705 .IX Item "NewFromValuesAndIDsPairsString"
706 .Vb 4
707 \& $FingerprintsVector = $FingerprintsVector\->NewFromValuesAndIDsPairsString(
708 \& $ValuesType, $ValuesAndIDsPairsString);
709 \& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString(
710 \& $ValuesType, $ValuesAndIDsPairsString);
711 .Ve
712 .Sp
713 Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesAndIDsPairsString\fR containing
714 space delimited value and value IDs pairs and returns new \fBFingerprintsVector\fR object.
715 Possible \fIValuesType\fR values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR.
716 .IP "\fBNewFromValuesAndIDsString\fR" 4
717 .IX Item "NewFromValuesAndIDsString"
718 .Vb 4
719 \& $FingerprintsVector = $FingerprintsVector\->NewFromValuesAndIDsString(
720 \& $ValuesType, $IDsAndValuesString);
721 \& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString(
722 \& $ValuesType, $IDsAndValuesString);
723 .Ve
724 .Sp
725 Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesAndIDsString\fR containing
726 semicolon delimited values string followed by value IDs strings and returns new \fBFingerprintsVector\fR
727 object. The values within values and value IDs tring are delimited by spaces. Possible \fIValuesType\fR
728 values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR.
729 .IP "\fBNewFromValuesString\fR" 4
730 .IX Item "NewFromValuesString"
731 .Vb 4
732 \& $FingerprintsVector = $FingerprintsVector\->NewFromValuesString(
733 \& $ValuesType, $ValuesString);
734 \& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString(
735 \& $ValuesType, $ValuesString);
736 .Ve
737 .Sp
738 Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesString\fR containing space
739 delimited values string and returns new \fBFingerprintsVector\fR object. The values within values
740 and value IDs tring are delimited by spaces. Possible \fIValuesType\fR values: \fIOrderedNumericalValues,
741 NumericalValues, or AlphaNumericalValues\fR.
742 .IP "\fBOchiaiSimilarityCoefficient\fR" 4
743 .IX Item "OchiaiSimilarityCoefficient"
744 .Vb 5
745 \& $Value = $FingerprintsVector\->OchiaiSimilarityCoefficient(
746 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
747 \& $Value = Fingerprints::FingerprintsVector::OchiaiSimilarityCoefficient(
748 \& $FingerprintsVectorA, $FingerprintVectorB,
749 \& [$CalculationMode, $SkipValuesCheck]);
750 .Ve
751 .Sp
752 Returns value of \fIOchiai\fR similarity coefficient between two \fIFingerprintsVectors\fR using
753 optionally specified \fICalculationMode\fR and optional checking of vector values.
754 .Sp
755 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
756 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
757 .IP "\fBSetDescription\fR" 4
758 .IX Item "SetDescription"
759 .Vb 1
760 \& $FingerprintsVector\->SetDescription($Description);
761 .Ve
762 .Sp
763 Sets \fIDescription\fR of fingerprints vector and returns \fIFingerprintsVector\fR.
764 .IP "\fBSetID\fR" 4
765 .IX Item "SetID"
766 .Vb 1
767 \& $FingerprintsVector\->SetID($ID);
768 .Ve
769 .Sp
770 Sets \fI\s-1ID\s0\fR of fingerprints vector and returns \fIFingerprintsVector\fR.
771 .IP "\fBSetVectorType\fR" 4
772 .IX Item "SetVectorType"
773 .Vb 1
774 \& $FingerprintsVector\->SetVectorType($VectorType);
775 .Ve
776 .Sp
777 Sets \fIVectorType\fR of fingerprints vector and returns \fIFingerprintsVector\fR.
778 .IP "\fBSetType\fR" 4
779 .IX Item "SetType"
780 .Vb 1
781 \& $FingerprintsVector\->SetType($Type);
782 .Ve
783 .Sp
784 Sets \fIFingerprintsVector\fR values \fIType\fR and returns \fIFingerprintsVector\fR. Possible \fIType\fR
785 values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR.
786 .Sp
787 During calculation of similarity and distance coefficients between two \fIFingerprintsVectors\fR, the
788 following conditions apply to vector type, size, value and value IDs:
789 .Sp
790 .Vb 2
791 \& o For OrderedNumericalValues type, both vectors must be of the same size
792 \& and contain similar types of numerical values in the same order.
793 \&
794 \& o For NumericalValues type, vector value IDs for both vectors must be
795 \& specified; however, their size and order of IDs and numerical values may
796 \& be different. For each vector, value IDs must correspond to vector values.
797 \&
798 \& o For AlphaNumericalValues type, vectors may contain both numerical and
799 \& alphanumerical values and their sizes may be different.
800 .Ve
801 .IP "\fBSetValue\fR" 4
802 .IX Item "SetValue"
803 .Vb 1
804 \& $FingerprintsVector\->SetValue($Index, $Value, [$SkipIndexCheck]);
805 .Ve
806 .Sp
807 Sets a \fIFingerprintsVector\fR value specified by \fIIndex\fR starting at 0 to \fIValue\fR along with
808 optional index range check and returns \fIFingerprintsVector\fR.
809 .IP "\fBSetValueID\fR" 4
810 .IX Item "SetValueID"
811 .Vb 1
812 \& $FingerprintsVector\->SetValueID($Index, $ValueID, [$SkipIndexCheck]);
813 .Ve
814 .Sp
815 Sets a \fIFingerprintsVector\fR value \s-1ID\s0 specified by \fIIndex\fR starting at 0 to \fIValueID\fR along with
816 optional index range check and returns \fIFingerprintsVector\fR.
817 .IP "\fBSetValueIDs\fR" 4
818 .IX Item "SetValueIDs"
819 .Vb 2
820 \& $FingerprintsVector\->SetValueIDs($ValueIDsRef);
821 \& $FingerprintsVector\->SetValueIDs(@ValueIDs);
822 .Ve
823 .Sp
824 Sets \fIFingerprintsVector\fR value IDs to specified \fIValueIDs\fR and returns \fIFingerprintsVector\fR.
825 .IP "\fBSetValues\fR" 4
826 .IX Item "SetValues"
827 .Vb 2
828 \& $FingerprintsVector\->SetValues($ValuesRef);
829 \& $FingerprintsVector\->SetValues(@Values);
830 .Ve
831 .Sp
832 Sets \fIFingerprintsVector\fR value to specified \fIValues\fR and returns \fIFingerprintsVector\fR.
833 .IP "\fBSoergelDistanceCoefficient\fR" 4
834 .IX Item "SoergelDistanceCoefficient"
835 .Vb 5
836 \& $Value = $FingerprintsVector\->SoergelDistanceCoefficient(
837 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
838 \& $Value = Fingerprints::FingerprintsVector::SoergelDistanceCoefficient(
839 \& $FingerprintsVectorA, $FingerprintVectorB,
840 \& [$CalculationMode, $SkipValuesCheck]);
841 .Ve
842 .Sp
843 Returns value of \fISoergel\fR distance coefficient between two \fIFingerprintsVectors\fR using
844 optionally specified \fICalculationMode\fR and optional checking of vector values.
845 .Sp
846 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
847 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
848 .IP "\fBSorensonSimilarityCoefficient\fR" 4
849 .IX Item "SorensonSimilarityCoefficient"
850 .Vb 5
851 \& $Value = $FingerprintsVector\->SorensonSimilarityCoefficient(
852 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
853 \& $Value = Fingerprints::FingerprintsVector::SorensonSimilarityCoefficient(
854 \& $FingerprintsVectorA, $FingerprintVectorB,
855 \& [$CalculationMode, $SkipValuesCheck]);
856 .Ve
857 .Sp
858 Returns value of \fISorenson\fR similarity coefficient between two \fIFingerprintsVectors\fR using
859 optionally specified \fICalculationMode\fR and optional checking of vector values.
860 .Sp
861 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
862 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
863 .IP "\fBTanimotoSimilarityCoefficient\fR" 4
864 .IX Item "TanimotoSimilarityCoefficient"
865 .Vb 5
866 \& $Value = $FingerprintsVector\->TanimotoSimilarityCoefficient(
867 \& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]);
868 \& $Value = Fingerprints::FingerprintsVector::TanimotoSimilarityCoefficient(
869 \& $FingerprintsVectorA, $FingerprintVectorB,
870 \& [$CalculationMode, $SkipValuesCheck]);
871 .Ve
872 .Sp
873 Returns value of \fITanimoto\fR similarity coefficient between two \fIFingerprintsVectors\fR using
874 optionally specified \fICalculationMode\fR and optional checking of vector values.
875 .Sp
876 Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default
877 \&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR.
878 .IP "\fBStringifyFingerprintsVector\fR" 4
879 .IX Item "StringifyFingerprintsVector"
880 .Vb 1
881 \& $String = $FingerprintsVector\->StringifyFingerprintsVector();
882 .Ve
883 .Sp
884 Returns a string containing information about \fIFingerprintsVector\fR object.
885 .SH "AUTHOR"
886 .IX Header "AUTHOR"
887 Manish Sud <msud@san.rr.com>
888 .SH "SEE ALSO"
889 .IX Header "SEE ALSO"
890 BitVector.pm, FingerprintsStringUtil.pm, FingerprintsBitVector.pm, Vector.pm
891 .SH "COPYRIGHT"
892 .IX Header "COPYRIGHT"
893 Copyright (C) 2015 Manish Sud. All rights reserved.
894 .PP
895 This file is part of MayaChemTools.
896 .PP
897 MayaChemTools is free software; you can redistribute it and/or modify it under
898 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
899 Software Foundation; either version 3 of the License, or (at your option)
900 any later version.