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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/FingerprintsVector.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,900 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +FingerprintsVector +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::FingerprintsVector; +.PP +use Fingerprints::FingerprintsVector qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBFingerprintsVector\fR class provides the following methods: +.PP +new, AddValueIDs, AddValues, CityBlockDistanceCoefficient, +CosineSimilarityCoefficient, CzekanowskiSimilarityCoefficient, +DiceSimilarityCoefficient, EuclideanDistanceCoefficient, GetDescription, +GetFingerprintsVectorString, GetID, GetIDsAndValuesPairsString, +GetIDsAndValuesString, GetNumOfNonZeroValues, GetNumOfValueIDs, GetNumOfValues, +GetSupportedDistanceAndSimilarityCoefficients, GetSupportedDistanceCoefficients, +GetSupportedSimilarityCoefficients, GetType, GetValue, GetValueID, GetValueIDs, +GetValueIDsString, GetValues, GetValuesAndIDsPairsString, GetValuesAndIDsString, +GetValuesString, GetVectorType, HammingDistanceCoefficient, IsFingerprintsVector, +JaccardSimilarityCoefficient, ManhattanDistanceCoefficient, +NewFromIDsAndValuesPairsString, NewFromIDsAndValuesString, +NewFromValuesAndIDsPairsString, NewFromValuesAndIDsString, NewFromValuesString, +OchiaiSimilarityCoefficient, SetDescription, SetID, SetType, SetValue, SetValueID, +SetValueIDs, SetValues, SetVectorType, SoergelDistanceCoefficient, +SorensonSimilarityCoefficient, StringifyFingerprintsVector, +TanimotoSimilarityCoefficient +.PP +The methods available to create fingerprints vector from strings and to calculate similarity +and distance coefficients between two vectors can also be invoked as class functions. +.PP +\&\fBFingerprintsVector\fR class provides support to perform comparison between vectors +containing three different types of values: +.PP +Type I: OrderedNumericalValues +.PP +.Vb 3 +\& o Size of two vectors are same +\& o Vectors contain real values in a specific order. For example: MACCS keys +\& count, Topological pharmacophore atom pairs and so on. +.Ve +.PP +Type \s-1II:\s0 UnorderedNumericalValues +.PP +.Vb 3 +\& o Size of two vectors might not be same +\& o Vectors contain unordered real value identified by value IDs. For example: +\& Topological atom pairs, Topological atom torsions and so on +.Ve +.PP +Type \s-1III:\s0 AlphaNumericalValues +.PP +.Vb 3 +\& o Size of two vectors might not be same +\& o Vectors contain unordered alphanumerical values. For example: Extended +\& connectivity fingerprints, atom neighborhood fingerprints. +.Ve +.PP +Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues +or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues +using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues. +.PP +Three forms of similarity and distance calculation between two vectors, specified using \fBCalculationMode\fR +option, are supported: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. +.PP +For \fIBinaryForm\fR, the ordered list of processed final vector values containing the value or +count of each unique value type is simply converted into a binary vector containing 1s and 0s +corresponding to presence or absence of values before calculating similarity or distance between +two vectors. +.PP +For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: +.PP +.Vb 1 +\& N = Number values in A or B +\& +\& Xa = Values of vector A +\& Xb = Values of vector B +\& +\& Xai = Value of ith element in A +\& Xbi = Value of ith element in B +\& +\& SUM = Sum of i over N values +.Ve +.PP +For SetTheoreticForm of calculation between two vectors, let: +.PP +.Vb 2 +\& SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) +\& SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) \- SUM ( MIN ( Xai, Xbi ) ) +.Ve +.PP +For BinaryForm of calculation between two vectors, let: +.PP +.Vb 5 +\& Na = Number of bits set to "1" in A = SUM ( Xai ) +\& Nb = Number of bits set to "1" in B = SUM ( Xbi ) +\& Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi ) +\& Nd = Number of bits set to "0" in both A and B +\& = SUM ( 1 \- Xai \- Xbi + Xai * Xbi) +\& +\& N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb \- Nc + Nd +.Ve +.PP +Additionally, for BinaryForm various values also correspond to: +.PP +.Vb 4 +\& Na = | Xa | +\& Nb = | Xb | +\& Nc = | SetIntersectionXaXb | +\& Nd = N \- | SetDifferenceXaXb | +\& +\& | SetDifferenceXaXb | = N \- Nd = Na + Nb \- Nc + Nd \- Nd = Na + Nb \- Nc +\& = | Xa | + | Xb | \- | SetIntersectionXaXb | +.Ve +.PP +Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B +in \fIAlgebraicForm, BinaryForm and SetTheoreticForm\fR are defined as follows: +.PP +\&\fBCityBlockDistance\fR: ( same as HammingDistance and ManhattanDistance) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.PP +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.PP +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.PP +\&\fBCosineSimilarity\fR: ( same as OchiaiSimilarityCoefficient) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) +.PP +\&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) +.PP +\&\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 ) ) +.PP +\&\fBCzekanowskiSimilarity\fR: ( same as DiceSimilarity and SorensonSimilarity) +.PP +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.PP +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.PP +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.PP +\&\fBDiceSimilarity\fR: ( same as CzekanowskiSimilarity and SorensonSimilarity) +.PP +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.PP +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.PP +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.PP +\&\fBEuclideanDistance\fR: +.PP +\&\fIAlgebraicForm\fR: \s-1SQRT\s0 ( \s-1SUM\s0 ( ( ( Xai \- Xbi ) ** 2 ) ) ) +.PP +\&\fIBinaryForm\fR: \s-1SQRT\s0 ( ( Na \- Nc ) + ( Nb \- Nc ) ) = \s-1SQRT\s0 ( Na + Nb \- 2 * Nc ) +.PP +\&\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 ) ) ) ) +.PP +\&\fBHammingDistance\fR: ( same as CityBlockDistance and ManhattanDistance) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.PP +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.PP +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.PP +\&\fBJaccardSimilarity\fR: ( same as TanimotoSimilarity) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) +.PP +\&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) +.PP +\&\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 ) ) ) +.PP +\&\fBManhattanDistance\fR: ( same as CityBlockDistance and HammingDistance) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.PP +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.PP +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.PP +\&\fBOchiaiSimilarity\fR: ( same as CosineSimilarity) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) +.PP +\&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) +.PP +\&\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 ) ) +.PP +\&\fBSorensonSimilarity\fR: ( same as CzekanowskiSimilarity and DiceSimilarity) +.PP +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.PP +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.PP +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.PP +\&\fBSoergelDistance\fR: +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) / \s-1SUM\s0 ( \s-1MAX\s0 ( Xai, Xbi ) ) +.PP +\&\fIBinaryForm\fR: 1 \- Nc / ( Na + Nb \- Nc ) = ( Na + Nb \- 2 * Nc ) / ( Na + Nb \- Nc ) +.PP +\&\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 ) ) ) +.PP +\&\fBTanimotoSimilarity\fR: ( same as JaccardSimilarity) +.PP +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) +.PP +\&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) +.PP +\&\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 ) ) ) +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 1 +\& $FPVector = new Fingerprints::FingerprintsVector(%NamesAndValues); +.Ve +.Sp +Using specified \fIFingerprintsVector\fR property names and values hash, \fBnew\fR method creates +a new object and returns a reference to newly created \fBFingerprintsVectorsVector\fR +object. By default, the following properties are initialized: +.Sp +.Vb 3 +\& Type = \*(Aq\*(Aq +\& @{Values} = () +\& @{ValuesIDs} = () +.Ve +.Sp +Examples: +.Sp +.Vb 7 +\& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqOrderedNumericalValues\*(Aq, +\& \*(AqValues\*(Aq => [1, 2, 3, 4]); +\& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqNumericalValues\*(Aq, +\& \*(AqValues\*(Aq => [10, 22, 33, 44], +\& \*(AqValueIDs\*(Aq => [\*(AqID1\*(Aq, \*(AqID2\*(Aq, \*(AqID3\*(Aq, \*(AqID4\*(Aq]); +\& $FPVector = new Fingerprints::FingerprintsVector(\*(AqType\*(Aq => \*(AqAlphaNumericalValues\*(Aq, +\& \*(AqValues\*(Aq => [\*(Aqa1\*(Aq, 2, \*(Aqa3\*(Aq, 4]); +.Ve +.IP "\fBAddValueIDs\fR" 4 +.IX Item "AddValueIDs" +.Vb 2 +\& $FingerprintsVector\->AddValueIDs($ValueIDsRef); +\& $FingerprintsVector\->AddValueIDs(@ValueIDs); +.Ve +.Sp +Adds specified \fIValueIDs\fR to \fIFingerprintsVector\fR and returns \fIFingerprintsVector\fR. +.IP "\fBAddValues\fR" 4 +.IX Item "AddValues" +.Vb 3 +\& $FingerprintsVector\->AddValues($ValuesRef); +\& $FingerprintsVector\->AddValues(@Values); +\& $FingerprintsVector\->AddValues($Vector); +.Ve +.Sp +Adds specified \fIValues\fR to \fIFingerprintsVector\fR and returns \fIFingerprintsVector\fR. +.IP "\fBCityBlockDistanceCoefficient\fR" 4 +.IX Item "CityBlockDistanceCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->CityBlockDistanceCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::CityBlockDistanceCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fICityBlock\fR distance coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBCosineSimilarityCoefficient\fR" 4 +.IX Item "CosineSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->CosineSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::CosineSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fICosine\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBCzekanowskiSimilarityCoefficient\fR" 4 +.IX Item "CzekanowskiSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->CzekanowskiSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::CzekanowskiSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fICzekanowski\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBDiceSimilarityCoefficient\fR" 4 +.IX Item "DiceSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->DiceSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::DiceSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIDice\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBEuclideanDistanceCoefficient\fR" 4 +.IX Item "EuclideanDistanceCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->EuclideanDistanceCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::EuclideanDistanceCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIEuclidean\fR distance coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Description = $FingerprintsVector\->GetDescription(); +.Ve +.Sp +Returns a string containing description of fingerprints vector. +.IP "\fBGetFingerprintsVectorString\fR" 4 +.IX Item "GetFingerprintsVectorString" +.Vb 1 +\& $FPString = $FingerprintsVector\->GetFingerprintsVectorString($Format); +.Ve +.Sp +Returns a \fBFingerprintsString\fR containing vector values and/or IDs in \fIFingerprintsVector\fR +corresponding to specified \fIFormat\fR. +.Sp +Possible \fIFormat\fR values: \fIIDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, +IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, +ValueIDsString, ValueIDs, ValuesString, or Values\fR. +.IP "\fBGetID\fR" 4 +.IX Item "GetID" +.Vb 1 +\& $ID = $FingerprintsVector\->GetID(); +.Ve +.Sp +Returns \fI\s-1ID\s0\fR of \fIFingerprintsVector\fR. +.IP "\fBGetVectorType\fR" 4 +.IX Item "GetVectorType" +.Vb 1 +\& $VectorType = $FingerprintsVector\->GetVectorType(); +.Ve +.Sp +Returns \fIVectorType\fR of \fIFingerprintsVector\fR. +.IP "\fBGetIDsAndValuesPairsString\fR" 4 +.IX Item "GetIDsAndValuesPairsString" +.Vb 1 +\& $IDsValuesPairsString = $FingerprintsVector\->GetIDsAndValuesPairsString(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR value IDs and values as space delimited ID/value pair +string. +.IP "\fBGetIDsAndValuesString\fR" 4 +.IX Item "GetIDsAndValuesString" +.Vb 1 +\& $IDsValuesString = $FingerprintsVector\->GetIDsAndValuesString(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR value IDs and values as string containing space delimited IDs followed by +values with semicolon as IDs and values delimiter. +.IP "\fBGetNumOfNonZeroValues\fR" 4 +.IX Item "GetNumOfNonZeroValues" +.Vb 1 +\& $NumOfNonZeroValues = $FingerprintsVector\->GetNumOfNonZeroValues(); +.Ve +.Sp +Returns number of non-zero values in \fIFingerprintsVector\fR. +.IP "\fBGetNumOfValueIDs\fR" 4 +.IX Item "GetNumOfValueIDs" +.Vb 1 +\& $NumOfValueIDs = $FingerprintsVector\->GetNumOfValueIDs(); +.Ve +.Sp +Returns number of value IDs \fIFingerprintsVector\fR. +.IP "\fBGetNumOfValues\fR" 4 +.IX Item "GetNumOfValues" +.Vb 1 +\& $NumOfValues = $FingerprintsVector\->GetNumOfValues(); +.Ve +.Sp +Returns number of values \fIFingerprintsVector\fR. +.IP "\fBGetSupportedDistanceAndSimilarityCoefficients\fR" 4 +.IX Item "GetSupportedDistanceAndSimilarityCoefficients" +.Vb 2 +\& @SupportedDistanceAndSimilarityCoefficientsReturn = +\& Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients(); +.Ve +.Sp +Returns an array containing names of supported distance and similarity coefficients. +.IP "\fBGetSupportedDistanceCoefficients\fR" 4 +.IX Item "GetSupportedDistanceCoefficients" +.Vb 2 +\& @SupportedDistanceCoefficientsReturn = +\& Fingerprints::FingerprintsVector::GetSupportedDistanceCoefficients(); +.Ve +.Sp +Returns an array containing names of supported disyance coefficients. +.IP "\fBGetSupportedSimilarityCoefficients\fR" 4 +.IX Item "GetSupportedSimilarityCoefficients" +.Vb 2 +\& @SupportedSimilarityCoefficientsReturn = +\& Fingerprints::FingerprintsVector::GetSupportedSimilarityCoefficients(); +.Ve +.Sp +Returns an array containing names of supported similarity coefficients. +.IP "\fBGetType\fR" 4 +.IX Item "GetType" +.Vb 1 +\& $VectorType = $FingerprintsVector\->GetType(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR vector type. +.IP "\fBGetValue\fR" 4 +.IX Item "GetValue" +.Vb 1 +\& $Value = $FingerprintsVector\->GetValue($Index); +.Ve +.Sp +Returns fingerprints vector \fBValue\fR specified using \fIIndex\fR starting at 0. +.IP "\fBGetValueID\fR" 4 +.IX Item "GetValueID" +.Vb 1 +\& $ValueID = $FingerprintsVector\->GetValueID(); +.Ve +.Sp +Returns fingerprints vector \fBValueID\fR specified using \fIIndex\fR starting at 0. +.IP "\fBGetValueIDs\fR" 4 +.IX Item "GetValueIDs" +.Vb 2 +\& $ValueIDs = $FingerprintsVector\->GetValueIDs(); +\& @ValueIDs = $FingerprintsVector\->GetValueIDs(); +.Ve +.Sp +Returns fingerprints vector \fBValueIDs\fR as an array or reference to an array. +.IP "\fBGetValueIDsString\fR" 4 +.IX Item "GetValueIDsString" +.Vb 1 +\& $ValueIDsString = $FingerprintsVector\->GetValueIDsString(); +.Ve +.Sp +Returns fingerprints vector \fBValueIDsString\fR with value IDs delimited by space. +.IP "\fBGetValues\fR" 4 +.IX Item "GetValues" +.Vb 2 +\& $ValuesRef = $FingerprintsVector\->GetValues(); +\& @Values = $FingerprintsVector\->GetValues(); +.Ve +.Sp +Returns fingerprints vector \fBValues\fR as an array or reference to an array. +.IP "\fBGetValuesAndIDsPairsString\fR" 4 +.IX Item "GetValuesAndIDsPairsString" +.Vb 1 +\& $ValuesIDsPairsString = $FingerprintsVector\->GetValuesAndIDsPairsString(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR value and value IDs as space delimited ID/value pair +string. +.IP "\fBGetValuesAndIDsString\fR" 4 +.IX Item "GetValuesAndIDsString" +.Vb 1 +\& $ValuesIDsString = $FingerprintsVector\->GetValuesAndIDsString(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR values and value IDs as string containing space delimited IDs followed by +values with semicolon as IDs and values delimiter. +.IP "\fBGetValuesString\fR" 4 +.IX Item "GetValuesString" +.Vb 1 +\& $Return = $FingerprintsVector\->GetValuesString(); +.Ve +.Sp +Returns \fIFingerprintsVector\fR values as space delimited string. +.IP "\fBHammingDistanceCoefficient\fR" 4 +.IX Item "HammingDistanceCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->HammingDistanceCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::HammingDistanceCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIHamming\fR distance coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBIsFingerprintsVector\fR" 4 +.IX Item "IsFingerprintsVector" +.Vb 1 +\& $Status = Fingerprints::FingerprintsVector::IsFingerprintsVector($Object); +.Ve +.Sp +Returns 1 or 0 based on whether \fIObject\fR is a \fIFingerprintsVector\fR. +.IP "\fBJaccardSimilarityCoefficient\fR" 4 +.IX Item "JaccardSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->JaccardSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::JaccardSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIJaccard\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBManhattanDistanceCoefficient\fR" 4 +.IX Item "ManhattanDistanceCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->ManhattanDistanceCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::ManhattanDistanceCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIManhattan\fR distance coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBNewFromIDsAndValuesPairsString\fR" 4 +.IX Item "NewFromIDsAndValuesPairsString" +.Vb 4 +\& $FingerprintsVector = $FingerprintsVector\->NewFromIDsAndValuesPairsString( +\& $ValuesType, $IDsAndValuesPairsString); +\& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString( +\& $ValuesType, $IDsAndValuesPairsString); +.Ve +.Sp +Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIIDsAndValuesPairsString\fR containing +space delimited value IDs and values pairs and returns new \fBFingerprintsVector\fR object. +Possible \fIValuesType\fR values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR. +.IP "\fBNewFromIDsAndValuesString\fR" 4 +.IX Item "NewFromIDsAndValuesString" +.Vb 4 +\& $FingerprintsVector = $FingerprintsVector\->NewFromIDsAndValuesString( +\& $ValuesType, $IDsAndValuesString); +\& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString( +\& $ValuesType, $IDsAndValuesString); +.Ve +.Sp +Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIIDsAndValuesString\fR containing +semicolon delimited value IDs string followed by values strings and returns new \fBFingerprintsVector\fR +object. The values within value and value IDs tring are delimited by spaces. Possible \fIValuesType\fR +values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR. +.IP "\fBNewFromValuesAndIDsPairsString\fR" 4 +.IX Item "NewFromValuesAndIDsPairsString" +.Vb 4 +\& $FingerprintsVector = $FingerprintsVector\->NewFromValuesAndIDsPairsString( +\& $ValuesType, $ValuesAndIDsPairsString); +\& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString( +\& $ValuesType, $ValuesAndIDsPairsString); +.Ve +.Sp +Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesAndIDsPairsString\fR containing +space delimited value and value IDs pairs and returns new \fBFingerprintsVector\fR object. +Possible \fIValuesType\fR values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR. +.IP "\fBNewFromValuesAndIDsString\fR" 4 +.IX Item "NewFromValuesAndIDsString" +.Vb 4 +\& $FingerprintsVector = $FingerprintsVector\->NewFromValuesAndIDsString( +\& $ValuesType, $IDsAndValuesString); +\& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString( +\& $ValuesType, $IDsAndValuesString); +.Ve +.Sp +Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesAndIDsString\fR containing +semicolon delimited values string followed by value IDs strings and returns new \fBFingerprintsVector\fR +object. The values within values and value IDs tring are delimited by spaces. Possible \fIValuesType\fR +values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR. +.IP "\fBNewFromValuesString\fR" 4 +.IX Item "NewFromValuesString" +.Vb 4 +\& $FingerprintsVector = $FingerprintsVector\->NewFromValuesString( +\& $ValuesType, $ValuesString); +\& $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString( +\& $ValuesType, $ValuesString); +.Ve +.Sp +Creates a new \fIFingerprintsVector\fR of \fIValuesType\fR using \fIValuesString\fR containing space +delimited values string and returns new \fBFingerprintsVector\fR object. The values within values +and value IDs tring are delimited by spaces. Possible \fIValuesType\fR values: \fIOrderedNumericalValues, +NumericalValues, or AlphaNumericalValues\fR. +.IP "\fBOchiaiSimilarityCoefficient\fR" 4 +.IX Item "OchiaiSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->OchiaiSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::OchiaiSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fIOchiai\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBSetDescription\fR" 4 +.IX Item "SetDescription" +.Vb 1 +\& $FingerprintsVector\->SetDescription($Description); +.Ve +.Sp +Sets \fIDescription\fR of fingerprints vector and returns \fIFingerprintsVector\fR. +.IP "\fBSetID\fR" 4 +.IX Item "SetID" +.Vb 1 +\& $FingerprintsVector\->SetID($ID); +.Ve +.Sp +Sets \fI\s-1ID\s0\fR of fingerprints vector and returns \fIFingerprintsVector\fR. +.IP "\fBSetVectorType\fR" 4 +.IX Item "SetVectorType" +.Vb 1 +\& $FingerprintsVector\->SetVectorType($VectorType); +.Ve +.Sp +Sets \fIVectorType\fR of fingerprints vector and returns \fIFingerprintsVector\fR. +.IP "\fBSetType\fR" 4 +.IX Item "SetType" +.Vb 1 +\& $FingerprintsVector\->SetType($Type); +.Ve +.Sp +Sets \fIFingerprintsVector\fR values \fIType\fR and returns \fIFingerprintsVector\fR. Possible \fIType\fR +values: \fIOrderedNumericalValues, NumericalValues, or AlphaNumericalValues\fR. +.Sp +During calculation of similarity and distance coefficients between two \fIFingerprintsVectors\fR, the +following conditions apply to vector type, size, value and value IDs: +.Sp +.Vb 2 +\& o For OrderedNumericalValues type, both vectors must be of the same size +\& and contain similar types of numerical values in the same order. +\& +\& o For NumericalValues type, vector value IDs for both vectors must be +\& specified; however, their size and order of IDs and numerical values may +\& be different. For each vector, value IDs must correspond to vector values. +\& +\& o For AlphaNumericalValues type, vectors may contain both numerical and +\& alphanumerical values and their sizes may be different. +.Ve +.IP "\fBSetValue\fR" 4 +.IX Item "SetValue" +.Vb 1 +\& $FingerprintsVector\->SetValue($Index, $Value, [$SkipIndexCheck]); +.Ve +.Sp +Sets a \fIFingerprintsVector\fR value specified by \fIIndex\fR starting at 0 to \fIValue\fR along with +optional index range check and returns \fIFingerprintsVector\fR. +.IP "\fBSetValueID\fR" 4 +.IX Item "SetValueID" +.Vb 1 +\& $FingerprintsVector\->SetValueID($Index, $ValueID, [$SkipIndexCheck]); +.Ve +.Sp +Sets a \fIFingerprintsVector\fR value \s-1ID\s0 specified by \fIIndex\fR starting at 0 to \fIValueID\fR along with +optional index range check and returns \fIFingerprintsVector\fR. +.IP "\fBSetValueIDs\fR" 4 +.IX Item "SetValueIDs" +.Vb 2 +\& $FingerprintsVector\->SetValueIDs($ValueIDsRef); +\& $FingerprintsVector\->SetValueIDs(@ValueIDs); +.Ve +.Sp +Sets \fIFingerprintsVector\fR value IDs to specified \fIValueIDs\fR and returns \fIFingerprintsVector\fR. +.IP "\fBSetValues\fR" 4 +.IX Item "SetValues" +.Vb 2 +\& $FingerprintsVector\->SetValues($ValuesRef); +\& $FingerprintsVector\->SetValues(@Values); +.Ve +.Sp +Sets \fIFingerprintsVector\fR value to specified \fIValues\fR and returns \fIFingerprintsVector\fR. +.IP "\fBSoergelDistanceCoefficient\fR" 4 +.IX Item "SoergelDistanceCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->SoergelDistanceCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::SoergelDistanceCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fISoergel\fR distance coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBSorensonSimilarityCoefficient\fR" 4 +.IX Item "SorensonSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->SorensonSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::SorensonSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fISorenson\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBTanimotoSimilarityCoefficient\fR" 4 +.IX Item "TanimotoSimilarityCoefficient" +.Vb 5 +\& $Value = $FingerprintsVector\->TanimotoSimilarityCoefficient( +\& $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); +\& $Value = Fingerprints::FingerprintsVector::TanimotoSimilarityCoefficient( +\& $FingerprintsVectorA, $FingerprintVectorB, +\& [$CalculationMode, $SkipValuesCheck]); +.Ve +.Sp +Returns value of \fITanimoto\fR similarity coefficient between two \fIFingerprintsVectors\fR using +optionally specified \fICalculationMode\fR and optional checking of vector values. +.Sp +Possible \fICalculationMode\fR values: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. Default +\&\fICalculationMode\fR value: \fIAlgebraicForm\fR. Default \fISkipValuesCheck\fR value: \fI0\fR. +.IP "\fBStringifyFingerprintsVector\fR" 4 +.IX Item "StringifyFingerprintsVector" +.Vb 1 +\& $String = $FingerprintsVector\->StringifyFingerprintsVector(); +.Ve +.Sp +Returns a string containing information about \fIFingerprintsVector\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +BitVector.pm, FingerprintsStringUtil.pm, FingerprintsBitVector.pm, Vector.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.