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diff lib/Fingerprints/FingerprintsVector.pm @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/Fingerprints/FingerprintsVector.pm Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,2579 @@ +package Fingerprints::FingerprintsVector; +# +# $RCSfile: FingerprintsVector.pm,v $ +# $Date: 2015/02/28 20:48:54 $ +# $Revision: 1.31 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# Copyright (C) 2015 Manish Sud. All rights reserved. +# +# This file is part of MayaChemTools. +# +# MayaChemTools is free software; you can redistribute it and/or modify it under +# the terms of the GNU Lesser General Public License as published by the Free +# Software Foundation; either version 3 of the License, or (at your option) any +# later version. +# +# MayaChemTools is distributed in the hope that it will be useful, but without +# any warranty; without even the implied warranty of merchantability of fitness +# for a particular purpose. See the GNU Lesser General Public License for more +# details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or +# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, +# Boston, MA, 02111-1307, USA. +# + +use strict; +use Carp; +use Exporter; +use Scalar::Util (); +use MathUtil (); +use TextUtil (); +use StatisticsUtil (); +use BitVector; +use Vector; + +use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); + +@ISA = qw(Exporter); + +# Distance coefficients +my(@DistanceCoefficients) = qw(CityBlockDistanceCoefficient EuclideanDistanceCoefficient HammingDistanceCoefficient ManhattanDistanceCoefficient SoergelDistanceCoefficient); + +# Similarity coefficients... +my(@SimilarityCoefficients) = qw(CosineSimilarityCoefficient CzekanowskiSimilarityCoefficient DiceSimilarityCoefficient OchiaiSimilarityCoefficient JaccardSimilarityCoefficient SorensonSimilarityCoefficient TanimotoSimilarityCoefficient); + +# New from string... +my(@NewFromString) = qw(NewFromValuesString NewFromValuesAndIDsString NewFromIDsAndValuesString NewFromValuesAndIDsPairsString NewFromIDsAndValuesPairsString); + +@EXPORT = qw(IsFingerprintsVector); +@EXPORT_OK = qw(GetSupportedDistanceCoefficients GetSupportedSimilarityCoefficients GetSupportedDistanceAndSimilarityCoefficients @DistanceCoefficients @SimilarityCoefficients); + +%EXPORT_TAGS = ( + new => [@NewFromString], + distancecoefficients => [@DistanceCoefficients], + similaritycoefficients => [@SimilarityCoefficients], + all => [@EXPORT, @EXPORT_OK] + ); + +# Setup class variables... +my($ClassName); +_InitializeClass(); + +# Overload Perl functions... +use overload '""' => 'StringifyFingerprintsVector'; + +# Class constructor... +sub new { + my($Class, %NamesAndValues) = @_; + + # Initialize object... + my $This = {}; + bless $This, ref($Class) || $Class; + + $This->_InitializeFingerprintsVector(); + + $This->_InitializeFingerprintsVectorProperties(%NamesAndValues); + + return $This; +} + +# Initialize object data... +# +sub _InitializeFingerprintsVector { + my($This) = @_; + + # Type of fingerprint vector... + $This->{Type} = ''; + + # Fingerprint vector values... + @{$This->{Values}} = (); + + # Fingerprint vector value IDs... + @{$This->{ValueIDs}} = (); + + return $This; +} + +# Initialize class ... +sub _InitializeClass { + #Class name... + $ClassName = __PACKAGE__; +} + +# Initialize object properties.... +sub _InitializeFingerprintsVectorProperties { + my($This, %NamesAndValues) = @_; + + my($Name, $Value, $MethodName); + while (($Name, $Value) = each %NamesAndValues) { + $MethodName = "Set${Name}"; + $This->$MethodName($Value); + } + + if (!exists $NamesAndValues{Type}) { + croak "Error: ${ClassName}->New: Object can't be instantiated without specifying type..."; + } + return $This; +} + +# Create a new fingerprints vector using space delimited values string. This functionality can be +# either invoked as a class function or an object method. +# +sub NewFromValuesString ($$;$) { + my($FirstParameter, $SecondParameter, $ThirdParamater) = @_; + my($This, $Type, $ValuesString); + + if (@_ == 3) { + ($This, $Type, $ValuesString) = ($FirstParameter, $SecondParameter, $ThirdParamater); + } + else { + ($This, $Type, $ValuesString) = (undef, $FirstParameter, $SecondParameter); + } + my($FingerprintsVector, @Values); + + @Values = (); + if (defined($ValuesString) && length($ValuesString) && $ValuesString !~ /^None$/i) { + @Values = split(' ', $ValuesString); + } + + $FingerprintsVector = new Fingerprints::FingerprintsVector('Type' => $Type, 'Values' => \@Values); + + return $FingerprintsVector; +} + +# Create a new fingerprints vector using values and IDs string containing semicolon +# delimited value string and value IDs strings. The values within value and value IDs +# string are delimited by spaces. +# +# This functionality can be either invoked as a class function or an object method. +# +sub NewFromValuesAndIDsString ($$;$) { + my($FirstParameter, $SecondParameter, $ThirdParamater) = @_; + my($This, $Type, $ValuesAndIDsString); + + if (@_ == 3) { + ($This, $Type, $ValuesAndIDsString) = ($FirstParameter, $SecondParameter, $ThirdParamater); + } + else { + ($This, $Type, $ValuesAndIDsString) = (undef, $FirstParameter, $SecondParameter); + } + my($FingerprintsVector, $ValuesString, $ValueIDsString, @Values, @ValueIDs); + + ($ValuesString, $ValueIDsString) = split(';', $ValuesAndIDsString); + + @Values = (); + if (defined($ValuesString) && length($ValuesString) && $ValuesString !~ /^None$/i) { + @Values = split(' ', $ValuesString); + } + @ValueIDs = (); + if (defined($ValueIDsString) && length($ValueIDsString) && $ValueIDsString !~ /^None$/i) { + @ValueIDs = split(' ', $ValueIDsString); + } + + if (@Values != @ValueIDs ) { + carp "Warning: ${ClassName}->NewFromValuesAndIDsString: Object can't be instantiated: Number specified values, " . scalar @Values . ", must be equal to number of specified value IDs, " . scalar @ValueIDs . "..."; + return undef; + } + + $FingerprintsVector = new Fingerprints::FingerprintsVector('Type' => $Type, 'Values' => \@Values, 'ValueIDs' => \@ValueIDs); + + return $FingerprintsVector; +} + +# Create a new fingerprints vector using IDs and values string containing semicolon +# delimited value IDs string and values strings. The values within value and value IDs +# string are delimited by spaces. +# +# This functionality can be either invoked as a class function or an object method. +# +sub NewFromIDsAndValuesString ($$;$) { + my($FirstParameter, $SecondParameter, $ThirdParamater) = @_; + my($This, $Type, $IDsAndValuesString); + + if (@_ == 3) { + ($This, $Type, $IDsAndValuesString) = ($FirstParameter, $SecondParameter, $ThirdParamater); + } + else { + ($This, $Type, $IDsAndValuesString) = (undef, $FirstParameter, $SecondParameter); + } + my($FingerprintsVector, $ValuesString, $ValueIDsString, @Values, @ValueIDs); + + ($ValueIDsString, $ValuesString) = split(';', $IDsAndValuesString); + + @Values = (); + if (defined($ValuesString) && length($ValuesString) && $ValuesString !~ /^None$/i) { + @Values = split(' ', $ValuesString); + } + @ValueIDs = (); + if (defined($ValueIDsString) && length($ValueIDsString) && $ValueIDsString !~ /^None$/i) { + @ValueIDs = split(' ', $ValueIDsString); + } + + if (@Values != @ValueIDs ) { + carp "Warning: ${ClassName}->NewFromIDsAndValuesString: Object can't be instantiated: Number specified values, " . scalar @Values . ", must be equal to number of specified value IDs, " . scalar @ValueIDs . "..."; + return undef; + } + + $FingerprintsVector = new Fingerprints::FingerprintsVector('Type' => $Type, 'Values' => \@Values, 'ValueIDs' => \@ValueIDs); + + return $FingerprintsVector; +} + +# Create a new fingerprints vector using values and IDs pairs string containing space +# value and value IDs pairs. +# +# This functionality can be either invoked as a class function or an object method. +# +sub NewFromValuesAndIDsPairsString ($$;$) { + my($FirstParameter, $SecondParameter, $ThirdParamater) = @_; + my($This, $Type, $ValuesAndIDsPairsString); + + if (@_ == 3) { + ($This, $Type, $ValuesAndIDsPairsString) = ($FirstParameter, $SecondParameter, $ThirdParamater); + } + else { + ($This, $Type, $ValuesAndIDsPairsString) = (undef, $FirstParameter, $SecondParameter); + } + my($FingerprintsVector, $Index, @Values, @ValueIDs, @ValuesAndIDsPairs); + + @ValuesAndIDsPairs = split(' ', $ValuesAndIDsPairsString); + if (@ValuesAndIDsPairs % 2) { + carp "Warning: ${ClassName}->NewFromValuesAndIDsPairsString: No fingerprint vector created: Invalid values and IDs pairs data: Input list must contain even number of values and IDs pairs..."; + return undef; + } + + @Values = (); @ValueIDs = (); + if (!(@ValuesAndIDsPairs == 2 && $ValuesAndIDsPairs[0] =~ /^None$/i && $ValuesAndIDsPairs[1] =~ /^None$/i)) { + for ($Index = 0; $Index < $#ValuesAndIDsPairs; $Index += 2) { + push @Values, $ValuesAndIDsPairs[$Index]; + push @ValueIDs, $ValuesAndIDsPairs[$Index + 1]; + } + } + $FingerprintsVector = new Fingerprints::FingerprintsVector('Type' => $Type, 'Values' => \@Values, 'ValueIDs' => \@ValueIDs); + + return $FingerprintsVector; +} + +# Create a new fingerprints vector using IDs and values pairs string containing space +# value IDs and valus pairs. +# +# This functionality can be either invoked as a class function or an object method. +# +sub NewFromIDsAndValuesPairsString ($$;$) { + my($FirstParameter, $SecondParameter, $ThirdParamater) = @_; + my($This, $Type, $IDsAndValuesPairsString); + + if (@_ == 3) { + ($This, $Type, $IDsAndValuesPairsString) = ($FirstParameter, $SecondParameter, $ThirdParamater); + } + else { + ($This, $Type, $IDsAndValuesPairsString) = (undef, $FirstParameter, $SecondParameter); + } + my($FingerprintsVector, $Index, @Values, @ValueIDs, @IDsAndValuesPairs); + + @IDsAndValuesPairs = split(' ', $IDsAndValuesPairsString); + if (@IDsAndValuesPairs % 2) { + croak "Error: ${ClassName}->NewFromIDsAndValuesPairsString: No fingerprint vector created: Invalid values and IDs pairs data: Input list must contain even number of values and IDs pairs..."; + return undef; + } + + @Values = (); @ValueIDs = (); + if (!(@IDsAndValuesPairs == 2 && $IDsAndValuesPairs[0] =~ /^None$/i && $IDsAndValuesPairs[1] =~ /^None$/i)) { + for ($Index = 0; $Index < $#IDsAndValuesPairs; $Index += 2) { + push @ValueIDs, $IDsAndValuesPairs[$Index]; + push @Values, $IDsAndValuesPairs[$Index + 1]; + } + } + $FingerprintsVector = new Fingerprints::FingerprintsVector('Type' => $Type, 'Values' => \@Values, 'ValueIDs' => \@ValueIDs); + + return $FingerprintsVector; +} + +# Set type of fingerprint vector. Supported types are: OrderedNumericalValues, NumericalValues, and +# AlphaNumericalValues +# +# . For OrderedNumericalValues type, both vectors must be of the same size and contain similar +# types of numerical values in the same order. +# +# . 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. +# +# . For AlphaNumericalValues type, vectors may contain both numerical and alphanumerical values +# and their sizes may be different. +# +sub SetType { + my($This, $Type) = @_; + + if ($Type !~ /^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i) { + croak "Error: ${ClassName}->SetType: Specified value, $Type, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues"; + } + + if ($This->{Type}) { + croak "Error: ${ClassName}->SetType: Can't change intial fingerprints vector type: It's already set..."; + } + $This->{Type} = $Type; + + return $This; +} + +# Get fingerpints vector type... +# +sub GetType { + my($This) = @_; + + return $This->{Type}; +} + +# Set ID... +sub SetID { + my($This, $Value) = @_; + + $This->{ID} = $Value; + + return $This; +} + +# Get ID... +sub GetID { + my($This) = @_; + + return exists $This->{ID} ? $This->{ID} : 'None'; +} + +# Set description... +sub SetDescription { + my($This, $Value) = @_; + + $This->{Description} = $Value; + + return $This; +} + +# Get description... +sub GetDescription { + my($This) = @_; + + return exists $This->{Description} ? $This->{Description} : 'No description available'; +} + +# Set vector type... +sub SetVectorType { + my($This, $Value) = @_; + + $This->{VectorType} = $Value; + + return $This; +} + +# Get vector type... +sub GetVectorType { + my($This) = @_; + + return exists $This->{VectorType} ? $This->{VectorType} : 'FingerprintsVector'; +} + +# Set values of a fingerprint vector using a vector, reference to an array or an array... +# +sub SetValues { + my($This, @Values) = @_; + + $This->_SetOrAddValuesOrValueIDs("SetValues", @Values); + + return $This; +} + +# Set value IDs of a fingerprint vector using a vector, reference to an array or an array... +# +sub SetValueIDs { + my($This, @Values) = @_; + + $This->_SetOrAddValuesOrValueIDs("SetValueIDs", @Values); + + return $This; +} + +# Add values to a fingerprint vector using a vector, reference to an array or an array... +# +sub AddValues { + my($This, @Values) = @_; + + $This->_SetOrAddValuesOrValueIDs("AddValues", @Values); + + return $This; +} + +# Add value IDs to a fingerprint vector using a vector, reference to an array or an array... +# +sub AddValueIDs { + my($This, @Values) = @_; + + $This->_SetOrAddValuesOrValueIDs("AddValueIDs", @Values); + + return $This; +} + +# Set or add values or value IDs using: +# +# o List of values or ValueIDs +# o Reference to an list of values or ValuesIDs +# o A vector containing values or ValueIDs +# +sub _SetOrAddValuesOrValueIDs { + my($This, $Mode, @Values) = @_; + + if (!@Values) { + return; + } + + # Collect specified values or valueIDs... + my($FirstValue, $TypeOfFirstValue, $ValuesRef); + + $FirstValue = $Values[0]; + $TypeOfFirstValue = ref $FirstValue; + if ($TypeOfFirstValue =~ /^(SCALAR|HASH|CODE|REF|GLOB)/) { + croak "Error: ${ClassName}-> _SetOrAddValuesOrValueIDs: Trying to add values to vector object with a reference to unsupported value format..."; + } + + if (Vector::IsVector($FirstValue)) { + # It's a vector... + $ValuesRef = $FirstValue->GetValues(); + } + elsif ($TypeOfFirstValue =~ /^ARRAY/) { + # It's an array refernce... + $ValuesRef = $FirstValue; + } + else { + # It's a list of values... + $ValuesRef = \@Values; + } + + # Set or add values or value IDs... + MODE: { + if ($Mode =~ /^SetValues$/i) { @{$This->{Values}} = (); push @{$This->{Values}}, @{$ValuesRef}; last MODE; } + if ($Mode =~ /^SetValueIDs$/i) { @{$This->{ValueIDs}} = (); push @{$This->{ValueIDs}}, @{$ValuesRef}; last MODE; } + if ($Mode =~ /^AddValues$/i) { push @{$This->{Values}}, @{$ValuesRef}; last MODE; } + if ($Mode =~ /^AddValueIDs$/i) { push @{$This->{ValueIDs}}, @{$ValuesRef}; last MODE; } + croak "Error: ${ClassName}-> _SetOrAddValuesOrValueIDs: Unknown mode $Mode..."; + } + return $This; +} + +# Set a specific value in fingerprint vector with indicies starting from 0.. +# +sub SetValue { + my($This, $Index, $Value, $SkipCheck) = @_; + + # Just set it... + if ($SkipCheck) { + return $This->_SetValue($Index, $Value); + } + + # Check and set... + if ($Index < 0) { + croak "Error: ${ClassName}->SetValue: Index value must be a positive number..."; + } + if ($Index >= $This->GetNumOfValues()) { + croak "Error: ${ClassName}->SetValue: Index vaue must be less than number of values..."; + } + + return $This->_SetValue($Index, $Value); +} + +# Set a fingerprint vector value... +# +sub _SetValue { + my($This, $Index, $Value) = @_; + + $This->{Values}[$Index] = $Value; + + return $This; +} + +# Get a specific value from fingerprint vector with indicies starting from 0... +# +sub GetValue { + my($This, $Index) = @_; + + if ($Index < 0) { + croak "Error: ${ClassName}->GetValue: Index value must be a positive number..."; + } + if ($Index >= $This->GetNumOfValues()) { + croak "Error: ${ClassName}->GetValue: Index value must be less than number of values..."; + } + return $This->_GetValue($Index); +} + +# Get a fingerprint vector value... +sub _GetValue { + my($This, $Index) = @_; + + return $This->{Values}[$Index]; +} + +# Return vector values as an array or reference to an array... +# +sub GetValues { + my($This) = @_; + + return wantarray ? @{$This->{Values}} : \@{$This->{Values}}; +} + +# Set a specific value ID in fingerprint vector with indicies starting from 0.. +# +sub SetValueID { + my($This, $Index, $Value, $SkipCheck) = @_; + + # Just set it... + if ($SkipCheck) { + return $This->_SetValueID($Index, $Value); + } + + # Check and set... + if ($Index < 0) { + croak "Error: ${ClassName}->SetValueID: Index value must be a positive number..."; + } + if ($Index >= $This->GetNumOfValueIDs()) { + croak "Error: ${ClassName}->SetValueID: Index vaue must be less than number of value IDs..."; + } + + return $This->_SetValueID($Index, $Value); +} + +# Set a fingerprint vector value ID... +# +sub _SetValueID { + my($This, $Index, $Value) = @_; + + $This->{ValueIDs}[$Index] = $Value; + + return $This; +} + +# Get a specific value ID from fingerprint vector with indicies starting from 0... +# +sub GetValueID { + my($This, $Index) = @_; + + if ($Index < 0) { + croak "Error: ${ClassName}->GetValueID: Index value must be a positive number..."; + } + if ($Index >= $This->GetNumOfValueIDs()) { + croak "Error: ${ClassName}->GetValueID: Index value must be less than number of value IDs..."; + } + return $This->_GetValueID($Index); +} + +# Get a fingerprint vector value ID... +# +sub _GetValueID { + my($This, $Index) = @_; + + return $This->{ValueIDs}[$Index]; +} + +# Return vector value IDs as an array or reference to an array... +# +sub GetValueIDs { + my($This) = @_; + + return wantarray ? @{$This->{ValueIDs}} : \@{$This->{ValueIDs}}; +} + +# Get fingerprints vector string containing values and/or IDs string in a specifed format... +# +sub GetFingerprintsVectorString { + my($This, $Format) = @_; + + FORMAT : { + if ($Format =~ /^(IDsAndValuesString|IDsAndValues)$/i) { return $This->GetIDsAndValuesString(); last FORMAT; } + if ($Format =~ /^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i) { return $This->GetIDsAndValuesPairsString(); last FORMAT; } + if ($Format =~ /^(ValuesAndIDsString|ValuesAndIDs)$/i) { return $This->GetValuesAndIDsString(); last FORMAT; } + if ($Format =~ /^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i) { return $This->GetValuesAndIDsPairsString(); last FORMAT;} + if ($Format =~ /^(ValueIDsString|ValueIDs)$/i) { return $This->GetValueIDsString(); last FORMAT; } + if ($Format =~ /^(ValuesString|Values)$/i) { return $This->GetValuesString(); last FORMAT; } + croak "Error: ${ClassName}->GetFingerprintsVectorString: Specified vector string format, $Format, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValueIDsString, ValueIDs, ValuesString, Values..."; + } + return ''; +} +# Get vector value IDs and values string as space delimited ASCII string separated +# by semicolon... +# +sub GetIDsAndValuesString { + my($This) = @_; + + if (@{$This->{ValueIDs}} && @{$This->{Values}}) { + # Both IDs and values are available... + return join(' ', @{$This->{ValueIDs}}) . ";" . join(' ', @{$This->{Values}}); + } + elsif (@{$This->{Values}}) { + # Only values are available... + return "None;" . join(' ', @{$This->{Values}}); + } + else { + # Values are not available... + return "None;None"; + } +} + +# Get vector value IDs and value pairs string as space delimited ASCII string... +# +sub GetIDsAndValuesPairsString { + my($This) = @_; + my($Index, $ValueIDsPresent, @IDsAndValuesPairs); + + if (!@{$This->{Values}}) { + # Values are unavailable... + return "None None"; + } + + $ValueIDsPresent = @{$This->{ValueIDs}} ? 1 : 0; + + @IDsAndValuesPairs = (); + for $Index (0 .. $#{$This->{Values}}) { + if ($ValueIDsPresent) { + push @IDsAndValuesPairs, ($This->{ValueIDs}->[$Index], $This->{Values}->[$Index]); + } + else { + push @IDsAndValuesPairs, ('None', $This->{Values}->[$Index]); + } + } + return join(' ', @IDsAndValuesPairs); +} + +# Get vector value and value IDs string as space delimited ASCII string separated +# by semicolon... +# +sub GetValuesAndIDsString { + my($This) = @_; + + if (@{$This->{ValueIDs}} && @{$This->{Values}}) { + # Both IDs and values are available... + return join(' ', @{$This->{Values}}) . ";" . join(' ', @{$This->{ValueIDs}}); + } + elsif (@{$This->{Values}}) { + # Only values are available... + return join(' ', @{$This->{Values}}) . ";None"; + } + else { + # Values are not available... + return "None;None"; + } +} + +# Get vector value and value ID pairs string as space delimited ASCII string... +# +sub GetValuesAndIDsPairsString { + my($This) = @_; + my($Index, $ValueIDsPresent, @ValuesAndIDsPairs); + + if (!@{$This->{Values}}) { + # Values are unavailable... + return "None None"; + } + + $ValueIDsPresent = @{$This->{ValueIDs}} ? 1 : 0; + + @ValuesAndIDsPairs = (); + for $Index (0 .. $#{$This->{Values}}) { + if ($ValueIDsPresent) { + push @ValuesAndIDsPairs, ($This->{Values}->[$Index], $This->{ValueIDs}->[$Index]); + } + else { + push @ValuesAndIDsPairs, ($This->{Values}->[$Index], 'None'); + } + } + return join(' ', @ValuesAndIDsPairs); +} + +# Get vector value IDs string as space delimited ASCII string... +# +sub GetValueIDsString { + my($This) = @_; + + return @{$This->{ValueIDs}} ? join(' ', @{$This->{ValueIDs}}) : 'None'; +} + +# Get vector value string as space delimited ASCII string... +# +sub GetValuesString { + my($This) = @_; + + return @{$This->{Values}} ? join(' ', @{$This->{Values}}) : 'None'; +} + +# Get number of values... +sub GetNumOfValues { + my($This) = @_; + + return scalar @{$This->{Values}}; +} + +# Get number of non-zero values... +sub GetNumOfNonZeroValues { + my($This) = @_; + my($Count, $Index, $Size); + + $Count = 0; + $Size = $This->GetNumOfValues(); + + for $Index (0 .. ($Size -1)) { + if ($This->{Values}[$Index] != 0) { + $Count++; + } + } + return $Count; +} + +# Get number of value IDs... +sub GetNumOfValueIDs { + my($This) = @_; + + return scalar @{$This->{ValueIDs}}; +} + +# FinegerprintsVectors class provides methods to calculate similarity between vectors +# containing three different types of values: +# +# Type I: OrderedNumericalValues +# +# . Size of two vectors are same +# . Vectors contain real values in a specific order. For example: MACCS keys count, Topological +# pharnacophore atom pairs and so on. +# . Option to calculate similarity value using continious values or binary values +# +# Type II: UnorderedNumericalValues +# +# . Size of two vectors might not be same +# . Vectors contain unordered real value identified by value IDs. For example: Toplogical atom pairs, +# Topological atom torsions and so on +# . Option to calculate similarity value using continous values or binary values +# +# Type III: AlphaNumericalValues +# +# . Size of two vectors might not be same +# . Vectors contain unordered alphanumerical values. For example: Extended connectivity fingerprints, +# atom neighbothood fingerpritns. +# . The vector values are treated as keys or bit indices and similarity value is calculated accordingly. +# +# Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues +# or AlphaNumericalValues, the vectors are tranformed into vectors containing unique OrderedNumericalValues +# using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues. +# +# Three forms similarity or distance calculation between two vectors: AlgebraicForm, BinaryForm or +# SetTheoreticForm. +# +# The value of an extra paramter, CalculationMode, passed to each similarity or distance function +# controls the calculation. Supported values for CalculationMode: AlgebraicForm, BinaryForm and +# SetTheoreticForm. Default: AlgebraicForm. +# +# For BinaryForm CalculationMode, 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. +# +# For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: +# +# 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 +# +# For SetTheoreticForm of calculation between two vectors, let: +# +# SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) +# SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) +# +# For BinaryForm of calculation between two vectors, let: +# +# 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 +# +# Additionally, for BinaryForm various values also correspond to: +# +# Na = | Xa | +# Nb = | Xb | +# Nc = | SetIntersectionXaXb | +# Nd = N - | SetDifferenceXaXb | +# +# | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc +# = | Xa | + | Xb | - | SetIntersectionXaXb | +# +# Various distance coefficients and similarity coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair vectors A and B +# in AlgebraicForm and BinaryForm are defined as follows: +# +# . CityBlockDistanceCoefficient: ( same as HammingDistanceCoefficient and ManhattanDistanceCoefficient) +# +# . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) ) +# +# . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc +# +# . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb | +# = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) +# +# . CosineSimilarityCoefficient: ( same as OchiaiSimilarityCoefficient) +# +# . AlgebraicForm: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) +# +# . BinaryForm: Nc / SQRT ( Na * Nb) +# +# . SetTheoreticForm: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) +# = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) +# +# . CzekanowskiSimilarityCoefficient: ( same as DiceSimilarityCoefficient and SorensonSimilarityCoefficient) +# +# . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) +# +# . BinaryForm: 2 * Nc / ( Na + Nb ) +# +# . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) +# = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) +# +# . DiceSimilarityCoefficient: ( same as CzekanowskiSimilarityCoefficient and SorensonSimilarityCoefficient) +# +# . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) +# +# . BinaryForm: 2 * Nc / ( Na + Nb ) +# +# . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) +# = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) +# +# . EuclideanDistanceCoefficient: +# +# . AlgebraicForm: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) ) +# +# . BinaryForm: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc ) +# +# . SetTheoreticForm: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) +# = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) +# +# . HammingDistanceCoefficient: ( same as CityBlockDistanceCoefficient and ManhattanDistanceCoefficient) +# +# . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) ) +# +# . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc +# +# . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb | +# = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) +# +# . JaccardSimilarityCoefficient: ( same as TanimotoSimilarityCoefficient) +# +# . AlgebraicForm: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) +# +# . BinaryForm: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) +# +# . SetTheoreticForm: | SetIntersectionXaXb | / | SetDifferenceXaXb | +# = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) +# +# . ManhattanDistanceCoefficient: ( same as CityBlockDistanceCoefficient and HammingDistanceCoefficient) +# +# . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) ) +# +# . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc +# +# . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb | +# = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) +# +# . OchiaiSimilarityCoefficient: ( same as CosineSimilarityCoefficient) +# +# . AlgebraicForm: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) +# +# . BinaryForm: Nc / SQRT ( Na * Nb) +# +# . SetTheoreticForm: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) +# = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) +# +# . SorensonSimilarityCoefficient: ( same as CzekanowskiSimilarityCoefficient and DiceSimilarityCoefficient) +# +# . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) +# +# . BinaryForm: 2 * Nc / ( Na + Nb ) +# +# . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) +# = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) +# +# . SoergelDistanceCoefficient: +# +# . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) ) +# +# . BinaryForm: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc ) +# +# . SetTheoreticForm: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | +# = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) +# +# . TanimotoSimilarityCoefficient: ( same as JaccardSimilarityCoefficient) +# +# . AlgebraicForm: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) +# +# . BinaryForm: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) +# +# . SetTheoreticForm: | SetIntersectionXaXb | / | SetDifferenceXaXb | +# = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) +# +# + +# Calculate Hamming distance coefficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub HammingDistanceCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return CityBlockDistanceCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate Hamming distance coefficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub ManhattanDistanceCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return CityBlockDistanceCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate CityBlock distance coefficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub CityBlockDistanceCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("CityBlockDistanceCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _CityBlockDistanceCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _CityBlockDistanceCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _CityBlockDistanceCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate CityBlock distance coefficient using algebraic form... +# +sub _CityBlockDistanceCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumAbsSubtractionXaiXbi); + + $SumAbsSubtractionXaiXbi = _GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + + return $SumAbsSubtractionXaiXbi; +} + +# Calculate CityBlock distance coefficient using binary form... +# +sub _CityBlockDistanceCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + return ($Na + $Nb - 2 * $Nc); +} + +# Calculate CityBlock distance coefficient using set theoretic form... +# +sub _CityBlockDistanceCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + return ($SumXai + $SumXbi - 2 * $SumMinXaiXbi); +} + +# Calculate Ochiai similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub OchiaiSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return CosineSimilarityCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate Cosine similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub CosineSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("CosineSimilarityCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _CosineSimilarityCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _CosineSimilarityCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _CosineSimilarityCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate Cosine similarity coefficient using algebraic form... +# +sub _CosineSimilarityCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumProductXaiXbi, $SumXai2, $SumXbi2, $Numerator, $Denominator); + + $SumXai2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumProductXaiXbi = _GetSumOfProductOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumProductXaiXbi; + $Denominator = sqrt($SumXai2 * $SumXbi2); + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# CalculateCosine similarity coefficient using binary form... +# +sub _CosineSimilarityCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc, $Numerator, $Denominator); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $Nc; + $Denominator = sqrt($Na * $Nb); + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Cosine similarity coefficient using set theoretic form... +# +sub _CosineSimilarityCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi, $Numerator, $Denominator); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumMinXaiXbi; + $Denominator = sqrt($SumXai * $SumXbi); + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Czekanowski similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub CzekanowskiSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return DiceSimilarityCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate Sorenson similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub SorensonSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return DiceSimilarityCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate Dice similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub DiceSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("DiceSimilarityCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _DiceSimilarityCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _DiceSimilarityCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _DiceSimilarityCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate Dice similarity coefficient using algebraic form... +# +sub _DiceSimilarityCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumProductXaiXbi, $SumXai2, $SumXbi2, $Numerator, $Denominator); + + $SumXai2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumProductXaiXbi = _GetSumOfProductOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = 2 * $SumProductXaiXbi; + $Denominator = $SumXai2 + $SumXbi2; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Dice similarity coefficient using binary form... +# +sub _DiceSimilarityCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc, $Numerator, $Denominator); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = 2 * $Nc; + $Denominator = $Na + $Nb; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Dice similarity coefficient using set theoretic form... +# +sub _DiceSimilarityCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi, $Numerator, $Denominator); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = 2 * $SumMinXaiXbi; + $Denominator = $SumXai + $SumXbi; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + + +# Calculate Euclidean distance coefficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub EuclideanDistanceCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("EuclideanDistanceCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _EuclideanDistanceCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _EuclideanDistanceCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _EuclideanDistanceCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate Euclidean distance coefficient using algebraic form... +# +sub _EuclideanDistanceCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumSquaresSubtractionXaiXbi); + + $SumSquaresSubtractionXaiXbi = _GetSumOfSquaresOfSubtractionOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + + return sqrt($SumSquaresSubtractionXaiXbi); +} + +# Calculate Euclidean distance coefficient using binary form... +# +sub _EuclideanDistanceCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + return (sqrt($Na + $Nb - 2 * $Nc)); +} + +# Calculate Euclidean distance coefficient using set theoretic form... +# +sub _EuclideanDistanceCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + return (sqrt($SumXai + $SumXbi - 2 * $SumMinXaiXbi)); +} + +# Calculate Jaccard similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub JaccardSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + return TanimotoSimilarityCoefficient($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); +} + +# Calculate Tanimoto similarity cofficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub TanimotoSimilarityCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("TanimotoSimilarityCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _TanimotoSimilarityCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _TanimotoSimilarityCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _TanimotoSimilarityCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate Tanimoto similarity coefficient using algebraic form... +# +sub _TanimotoSimilarityCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumProductXaiXbi, $SumXai2, $SumXbi2, $Numerator, $Denominator); + + $SumXai2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi2 = _GetSumOfSquaresOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumProductXaiXbi = _GetSumOfProductOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumProductXaiXbi; + $Denominator = $SumXai2 + $SumXbi2 - $SumProductXaiXbi; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Tanimoto similarity coefficient using binary form... +# +sub _TanimotoSimilarityCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc, $Numerator, $Denominator); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $Nc; + $Denominator = $Na + $Nb - $Nc; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Tanimoto similarity coefficient using set theoretic form... +# +sub _TanimotoSimilarityCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi, $Numerator, $Denominator); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumMinXaiXbi; + $Denominator = $SumXai + $SumXbi - $SumMinXaiXbi; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + + +# Calculate Soergel distance coefficient between two fingerprint vectors. +# +# This functionality can be either invoked as a class function or an object method. +# +sub SoergelDistanceCoefficient ($$;$$) { + my($FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + # Validate and process fingerprints vectors for similarity calculations... + # + _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation("SoergelDistanceCoefficient: Calculation failed", $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck); + + # Perform the calculation... + if ($CalculationMode =~ /^AlgebraicForm$/i) { + return _SoergelDistanceCoefficientUsingAlgebraicForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^BinaryForm$/i) { + return _SoergelDistanceCoefficientUsingBinaryForm($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($CalculationMode =~ /^SetTheoreticForm$/i) { + return _SoergelDistanceCoefficientUsingSetTheoreticForm($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + return undef; + } +} + +# Calculate Soergel distance coefficientusing algebraic form... +# +sub _SoergelDistanceCoefficientUsingAlgebraicForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumAbsSubtractionXaiXbi, $SumMaxXaiXbi, $Numerator, $Denominator); + + $SumAbsSubtractionXaiXbi = _GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues($FingerprintsVectorA, $FingerprintsVectorB); + $SumMaxXaiXbi = _GetSumOfMaximumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumAbsSubtractionXaiXbi; + $Denominator = $SumMaxXaiXbi; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate Soergel distance coefficient using binary form... +# +sub _SoergelDistanceCoefficientUsingBinaryForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc, $Numerator, $Denominator); + + ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $Na + $Nb - 2 * $Nc; + $Denominator = $Na + $Nb - $Nc; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Calculate SoergelDistanceCoefficient using set theoretic form... +# +sub _SoergelDistanceCoefficientUsingSetTheoreticForm { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($SumMinXaiXbi, $SumXai, $SumXbi, $Numerator, $Denominator); + + $SumXai = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorA); + $SumXbi = _GetSumOfFingerprintsOrderedValues($FingerprintsVectorB); + $SumMinXaiXbi = _GetSumOfMinimumOfFingerprintsOrderdedValues($FingerprintsVectorA, $FingerprintsVectorB); + + $Numerator = $SumXai + $SumXbi - 2 * $SumMinXaiXbi; + $Denominator = $SumXai + $SumXbi - $SumMinXaiXbi; + + return $Denominator ? ($Numerator/$Denominator) : 0; +} + +# Validate and process fingerprints vectors for similarity calculations... +# +sub _ValidateAndProcessFingerprintsVectorsForSimilarityCalculation { + my($ErrorMsg, $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode, $SkipValuesCheck) = @_; + + $CalculationMode = defined $CalculationMode ? $CalculationMode : 'AlgebraicForm'; + $SkipValuesCheck = defined $SkipValuesCheck ? $SkipValuesCheck : 0; + + if (!$SkipValuesCheck) { + _ValidateFingerprintsVectorsForSimilarityCalculation($ErrorMsg, $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode); + } + _ProcessFingerprintsVectorsForSimilarityCalculation($ErrorMsg, $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode); +} + +# Make sure fingerprint vectors are good for performing similarity/distance calculation... +# +sub _ValidateFingerprintsVectorsForSimilarityCalculation { + my($ErrorMsg, $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode) = @_; + + # Make sure both are fingerprint vectors.. + if (!(IsFingerprintsVector($FingerprintsVectorA) && IsFingerprintsVector($FingerprintsVectorB))) { + croak "Error: ${ClassName}->${ErrorMsg}: Both objects must be fingerprint vectors..."; + } + + # Check types... + if ($FingerprintsVectorA->{Type} ne $FingerprintsVectorB->{Type}) { + croak "Error: ${ClassName}->${ErrorMsg}: Type of first fingerprint vector, $FingerprintsVectorA->{Type}, must be same as type of second fingerprint vector, $FingerprintsVectorB->{Type}..."; + } + + # Check calculation mode... + if ($CalculationMode !~ /^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i) { + croak "Error: ${ClassName}->${ErrorMsg}: Specified similarity calculation mode, $CalculationMode, is not valid. Supported values: AlgebraicForm, BinaryForm, and SetTheoreticForm..."; + } + + # Check values and value IDs... + my($Na, $Nb, $NIDa, $NIDb); + $Na = $FingerprintsVectorA->GetNumOfValues(); $Nb = $FingerprintsVectorB->GetNumOfValues(); + $NIDa = $FingerprintsVectorA->GetNumOfValueIDs(); $NIDb = $FingerprintsVectorB->GetNumOfValueIDs(); + + if ($Na == 0) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of values in first fingerprint vector, $Na, must be > 0 for fingerprint vector type $FingerprintsVectorA->{Type} ..."; + } + if ($Nb == 0) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of values in second fingerprint vector, $Nb, must be > 0 for fingerprint vector type $FingerprintsVectorB->{Type} ..."; + } + + if ($FingerprintsVectorA->{Type} =~ /^OrderedNumericalValues$/i) { + if ($Na != $Nb) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of values in first fingerprint vector, $Na, must be equal to number of values, $Nb, in second fingerprint vector for fingerprint vector types $FingerprintsVectorA->{Type} ..."; + } + } + elsif ($FingerprintsVectorA->{Type} =~ /^NumericalValues$/i) { + if ($NIDa == 0) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDa, must be > 0 for fingerprint vector type $FingerprintsVectorA->{Type} ..."; + } + if ($NIDb == 0) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDb, must be > 0 for fingerprint vector type $FingerprintsVectorB->{Type} ..."; + } + + if ($NIDa != $Na) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDa, must be equal to its number of values, $Na, for fingerprint vector type $FingerprintsVectorA->{Type} ..."; + } + if ($NIDb != $Nb) { + croak "Error: ${ClassName}->${ErrorMsg}: Number of value IDs in second fingerprint vector, $NIDb, must be equal to its number of values, $Nb, for fingerprint vector type $FingerprintsVectorA->{Type} ..."; + } + } + elsif ($FingerprintsVectorA->{Type} =~ /^AlphaNumericalValues$/i) { + if ($NIDa || $NIDb) { + croak "Error: ${ClassName}->${ErrorMsg}: ValueIDs cann't be specified for fingerprint vector types $FingerprintsVectorA->{Type} ..."; + } + } + else { + croak "Error: ${ClassName}->${ErrorMsg}: Fingerprint vector types $FingerprintsVectorA->{Type} is not valid..."; + } +} + +# Process fingerprints vectors for similarity calculation by generating vectors +# containing ordered list of values... +# +sub _ProcessFingerprintsVectorsForSimilarityCalculation { + my($ErrorMsg, $FingerprintsVectorA, $FingerprintsVectorB, $CalculationMode) = @_; + + $FingerprintsVectorA->{OrderedValuesRef} = undef; $FingerprintsVectorB->{OrderedValuesRef} = undef; + $FingerprintsVectorA->{BitVector} = undef; $FingerprintsVectorB->{BitVector} = undef; + + if ($FingerprintsVectorA->{Type} =~ /^OrderedNumericalValues$/i) { + _ProcessOrderedNumericalValuesFingerprintsVectorsForSimilarityCalculation($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($FingerprintsVectorA->{Type} =~ /^NumericalValues$/i) { + _ProcessNumericalValuesFingerprintsVectorsForSimilarityCalculation($FingerprintsVectorA, $FingerprintsVectorB); + } + elsif ($FingerprintsVectorA->{Type} =~ /^AlphaNumericalValues$/i) { + _ProcessAlphaNumericalValuesFingerprintsVectorsForSimilarityCalculation($FingerprintsVectorA, $FingerprintsVectorB); + } + else { + croak "Error: ${ClassName}->${ErrorMsg}: Fingerprint vector types $FingerprintsVectorA->{Type} is not valid..."; + } + if ($CalculationMode =~ /^BinaryForm$/i) { + _TransformFinalOrderedValuesIntoBitVectorsForSimilarityCalculation($FingerprintsVectorA, $FingerprintsVectorB); + } +} + +# Process fingerprints vectors with ordered numerical values for similarity calculations... +# +sub _ProcessOrderedNumericalValuesFingerprintsVectorsForSimilarityCalculation { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + + $FingerprintsVectorA->{OrderedValuesRef} = \@{$FingerprintsVectorA->{Values}}; + $FingerprintsVectorB->{OrderedValuesRef} = \@{$FingerprintsVectorB->{Values}}; +} + +# Process fingerprints vectors with numerical values for similarity calculations... +# +sub _ProcessNumericalValuesFingerprintsVectorsForSimilarityCalculation { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + + # Set up unique IDs and values map for each fingerprint vector... + my($Index, $Value, $ValueID, %UniqueFingerprintsVectorAValueIDValues, %UniqueFingerprintsVectorBValueIDValues, %UniqueFingerprintsVectorsValueIDs); + + %UniqueFingerprintsVectorAValueIDValues = (); + %UniqueFingerprintsVectorBValueIDValues = (); + %UniqueFingerprintsVectorsValueIDs = (); + + # Go over first vector... + for $Index (0 .. $#{$FingerprintsVectorA->{ValueIDs}}) { + $ValueID = $FingerprintsVectorA->{ValueIDs}[$Index]; + $Value = $FingerprintsVectorA->{Values}[$Index]; + if (exists $UniqueFingerprintsVectorAValueIDValues{$ValueID}) { + $UniqueFingerprintsVectorAValueIDValues{$ValueID} += $Value; + } + else { + $UniqueFingerprintsVectorAValueIDValues{$ValueID} = $Value; + } + if (!exists $UniqueFingerprintsVectorsValueIDs{$ValueID}) { + $UniqueFingerprintsVectorsValueIDs{$ValueID} = 1; + } + } + + # Go over second vector... + for $Index (0 .. $#{$FingerprintsVectorB->{ValueIDs}}) { + $ValueID = $FingerprintsVectorB->{ValueIDs}[$Index]; + $Value = $FingerprintsVectorB->{Values}[$Index]; + if (exists $UniqueFingerprintsVectorBValueIDValues{$ValueID}) { + $UniqueFingerprintsVectorBValueIDValues{$ValueID} += $Value; + } + else { + $UniqueFingerprintsVectorBValueIDValues{$ValueID} = $Value; + } + if (!exists $UniqueFingerprintsVectorsValueIDs{$ValueID}) { + $UniqueFingerprintsVectorsValueIDs{$ValueID} = 1; + } + } + + # Setup ordered values... + my(@UniqueOrderedValueIDs, @OrderedValuesA, @OrderedValuesB); + + @UniqueOrderedValueIDs = (); + @UniqueOrderedValueIDs = sort keys %UniqueFingerprintsVectorsValueIDs; + + @OrderedValuesA = (); + @OrderedValuesA = map { exists $UniqueFingerprintsVectorAValueIDValues{$_} ? $UniqueFingerprintsVectorAValueIDValues{$_} : 0 } @UniqueOrderedValueIDs; + + @OrderedValuesB = (); + @OrderedValuesB = map { exists $UniqueFingerprintsVectorBValueIDValues{$_} ? $UniqueFingerprintsVectorBValueIDValues{$_} : 0 } @UniqueOrderedValueIDs; + + $FingerprintsVectorA->{OrderedValuesRef} = \@OrderedValuesA; + $FingerprintsVectorB->{OrderedValuesRef} = \@OrderedValuesB; +} + +# Process fingerprints vectors with allpha numerical values for similarity calculations... +# +sub _ProcessAlphaNumericalValuesFingerprintsVectorsForSimilarityCalculation { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + + # Set up unique IDs and values map for each vector... + my($Index, $Value, $ValueID, %UniqueFingerprintsVectorAValuesCount, %UniqueFingerprintsVectorBValuesCount, %UniqueFingerprintsVectorsValues); + + %UniqueFingerprintsVectorAValuesCount = (); + %UniqueFingerprintsVectorBValuesCount = (); + %UniqueFingerprintsVectorsValues = (); + + # Go over first vector... + for $Value (@{$FingerprintsVectorA->{Values}}) { + if (exists $UniqueFingerprintsVectorAValuesCount{$Value}) { + $UniqueFingerprintsVectorAValuesCount{$Value} += 1; + } + else { + $UniqueFingerprintsVectorAValuesCount{$Value} = 1; + } + if (!exists $UniqueFingerprintsVectorsValues{$Value}) { + $UniqueFingerprintsVectorsValues{$Value} = 1; + } + } + + # Go over second vector... + for $Value (@{$FingerprintsVectorB->{Values}}) { + if (exists $UniqueFingerprintsVectorBValuesCount{$Value}) { + $UniqueFingerprintsVectorBValuesCount{$Value} += 1; + } + else { + $UniqueFingerprintsVectorBValuesCount{$Value} = 1; + } + if (!exists $UniqueFingerprintsVectorsValues{$Value}) { + $UniqueFingerprintsVectorsValues{$Value} = 1; + } + } + + # Setup ordered values... + my(@UniqueOrderedValueIDs, @OrderedValuesA, @OrderedValuesB); + + @UniqueOrderedValueIDs = (); + @UniqueOrderedValueIDs = sort keys %UniqueFingerprintsVectorsValues; + + @OrderedValuesA = (); + @OrderedValuesA = map { exists $UniqueFingerprintsVectorAValuesCount{$_} ? $UniqueFingerprintsVectorAValuesCount{$_} : 0 } @UniqueOrderedValueIDs; + + @OrderedValuesB = (); + @OrderedValuesB = map { exists $UniqueFingerprintsVectorBValuesCount{$_} ? $UniqueFingerprintsVectorBValuesCount{$_} : 0 } @UniqueOrderedValueIDs; + + $FingerprintsVectorA->{OrderedValuesRef} = \@OrderedValuesA; + $FingerprintsVectorB->{OrderedValuesRef} = \@OrderedValuesB; + +} + +# Transform final ordered values array into a BitVector for similarity calculation... +# +sub _TransformFinalOrderedValuesIntoBitVectorsForSimilarityCalculation { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $Size, $BitVectorA, $BitVectorB, $SkipCheck); + + # Create bit vectors... + $Size = scalar @{$FingerprintsVectorA->{OrderedValuesRef}}; + + $FingerprintsVectorA->{BitVector} = new BitVector($Size); + $FingerprintsVectorB->{BitVector} = new BitVector($Size); + + # Set bits... + $SkipCheck = 1; + for $Index (0 .. ($Size - 1)) { + if ($FingerprintsVectorA->{OrderedValuesRef}[$Index]) { + $FingerprintsVectorA->{BitVector}->SetBit($Index, $SkipCheck); + } + if ($FingerprintsVectorB->{OrderedValuesRef}[$Index]) { + $FingerprintsVectorB->{BitVector}->SetBit($Index, $SkipCheck); + } + } +} + +# Return sum of ordered vector values... +# +sub _GetSumOfFingerprintsOrderedValues { + my($FingerprintVector) = @_; + + return StatisticsUtil::Sum($FingerprintVector->{OrderedValuesRef}); +} + +# Return sum of squared ordered vector values... +# +sub _GetSumOfSquaresOfFingerprintsOrderedValues { + my($FingerprintVector) = @_; + + return StatisticsUtil::SumOfSquares($FingerprintVector->{OrderedValuesRef}); +} + +# Return sum of product of correponding ordered vector values... +# +sub _GetSumOfProductOfFingerprintsOrderedValues { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $SumProductXaiXbi); + + $SumProductXaiXbi = 0; + for $Index (0 .. $#{$FingerprintsVectorA->{OrderedValuesRef}}) { + $SumProductXaiXbi += $FingerprintsVectorA->{OrderedValuesRef}[$Index] * $FingerprintsVectorB->{OrderedValuesRef}[$Index]; + } + return $SumProductXaiXbi; +} + +# Return sum of absolute value of subtraction of correponding ordered vector values... +# +sub _GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $SumAbsSubtractionXaiXbi); + + $SumAbsSubtractionXaiXbi = 0; + for $Index (0 .. $#{$FingerprintsVectorA->{OrderedValuesRef}}) { + $SumAbsSubtractionXaiXbi += abs($FingerprintsVectorA->{OrderedValuesRef}[$Index] - $FingerprintsVectorB->{OrderedValuesRef}[$Index]); + } + return $SumAbsSubtractionXaiXbi; +} + +# Return sum of squares of subtraction of correponding ordered vector values... +# +sub _GetSumOfSquaresOfSubtractionOfFingerprintsOrderedValues { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $SumSquaresSubtractionXaiXbi); + + $SumSquaresSubtractionXaiXbi = 0; + for $Index (0 .. $#{$FingerprintsVectorA->{OrderedValuesRef}}) { + $SumSquaresSubtractionXaiXbi += ($FingerprintsVectorA->{OrderedValuesRef}[$Index] - $FingerprintsVectorB->{OrderedValuesRef}[$Index])**2; + } + return $SumSquaresSubtractionXaiXbi; +} + +# Return sum of minimum of correponding ordered vector values... +# +sub _GetSumOfMinimumOfFingerprintsOrderdedValues { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $SumMinXaiXbi); + + $SumMinXaiXbi = 0; + for $Index (0 .. $#{$FingerprintsVectorA->{OrderedValuesRef}}) { + $SumMinXaiXbi += MathUtil::min($FingerprintsVectorA->{OrderedValuesRef}[$Index], $FingerprintsVectorB->{OrderedValuesRef}[$Index]); + } + return $SumMinXaiXbi; +} + +# Return sum of maximum of correponding ordered vector values... +# +sub _GetSumOfMaximumOfFingerprintsOrderdedValues { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Index, $SumMaxXaiXbi); + + $SumMaxXaiXbi = 0; + for $Index (0 .. $#{$FingerprintsVectorA->{OrderedValuesRef}}) { + $SumMaxXaiXbi += MathUtil::max($FingerprintsVectorA->{OrderedValuesRef}[$Index], $FingerprintsVectorB->{OrderedValuesRef}[$Index]); + } + return $SumMaxXaiXbi; +} + +# Get number of Na, Nb and Nc bits in vector A and B for BinaryForm calculation... +# +sub _GetNumOfIndividualAndCommonSetBits ($$) { + my($FingerprintsVectorA, $FingerprintsVectorB) = @_; + my($Na, $Nb, $Nc, $Nd, $FingerprintsBitVectorA, $FingerprintsBitVectorB); + + $FingerprintsBitVectorA = $FingerprintsVectorA->{BitVector}; + $FingerprintsBitVectorB = $FingerprintsVectorB->{BitVector}; + + # Number of bits set to "1" in A + $Na = $FingerprintsBitVectorA->GetNumOfSetBits(); + + # Number of bits set to "1" in B + $Nb = $FingerprintsBitVectorB->GetNumOfSetBits(); + + # Number of bits set to "1" in both A and B + my($NcBitVector); + $NcBitVector = $FingerprintsBitVectorA & $FingerprintsBitVectorB; + $Nc = $NcBitVector->GetNumOfSetBits(); + + return ($Na, $Nb, $Nc); +} + +# Return a list of supported distance coefficients... +# +sub GetSupportedDistanceCoefficients () { + + return @DistanceCoefficients; +} + +# Return a list of supported similarity coefficients... +# +sub GetSupportedSimilarityCoefficients () { + + return @SimilarityCoefficients; +} + +# Return a list of supported distance and similarity coefficients... +# +sub GetSupportedDistanceAndSimilarityCoefficients () { + my(@DistanceAndSimilarityCoefficients); + + @DistanceAndSimilarityCoefficients = (); + push @DistanceAndSimilarityCoefficients, @DistanceCoefficients; + push @DistanceAndSimilarityCoefficients, @SimilarityCoefficients; + + return sort @DistanceAndSimilarityCoefficients; +} + +# Is it a fingerprints vector object? +sub IsFingerprintsVector ($) { + my($Object) = @_; + + return _IsFingerprintsVector($Object); +} + +# Is it a fingerprints vector object? +sub _IsFingerprintsVector { + my($Object) = @_; + + return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0; +} + +# Return a string containing vector values... +sub StringifyFingerprintsVector { + my($This) = @_; + my($FingerprintsVectorString); + + # Set type, values and value IDs... + my($NumOfValues, $ValuesString, $NumOfValueIDs, $ValueIDsString, $MaxValuesToStringify); + + $NumOfValues = $This->GetNumOfValues(); + $MaxValuesToStringify = 500; + + if ($NumOfValues < $MaxValuesToStringify) { + # Append all values... + $ValuesString = $NumOfValues ? join ' ', @{$This->{Values}} : 'None'; + } + else { + # Truncate values... + my($Index, @Values); + for $Index (0 .. ($MaxValuesToStringify - 1)) { + push @Values, $This->{Values}[$Index]; + } + $ValuesString = join(' ', @Values) . " ..."; + } + + $NumOfValueIDs = $This->GetNumOfValueIDs(); + if ($NumOfValueIDs < $MaxValuesToStringify) { + # Append all valueIDs... + $ValueIDsString = $NumOfValueIDs ? join ' ', @{$This->{ValueIDs}} : 'None'; + } + else { + # Truncate value IDs... + my($Index, @ValueIDs); + @ValueIDs = (); + for $Index (0 .. ($MaxValuesToStringify - 1)) { + push @ValueIDs, $This->{ValueIDs}[$Index]; + } + $ValueIDsString = join(' ', @ValueIDs) . " ..."; + } + + $FingerprintsVectorString = "Type: $This->{Type}; NumOfValues: $NumOfValues"; + if ($This->{Type} =~ /^(OrderedNumericalValues|NumericalValues)$/i) { + my($NumOfNonZeroValues); + $NumOfNonZeroValues = $This->GetNumOfNonZeroValues(); + $FingerprintsVectorString .= "; NumOfNonZeroValues: $NumOfNonZeroValues"; + } + + # Append all the values and value IDs... + if ($NumOfValues < $MaxValuesToStringify) { + $FingerprintsVectorString .= "; Values: <$ValuesString>; NumOfValueIDs: $NumOfValueIDs; ValueIDs: <$ValueIDsString>"; + } + else { + $FingerprintsVectorString .= "; Values (Truncated after $MaxValuesToStringify): <$ValuesString>; NumOfValueIDs: $NumOfValueIDs; ValueIDs (Truncated after $MaxValuesToStringify): <$ValueIDsString>"; + } + + return $FingerprintsVectorString; +} + +1; + +__END__ + +=head1 NAME + +FingerprintsVector + +=head1 SYNOPSIS + +use Fingerprints::FingerprintsVector; + +use Fingerprints::FingerprintsVector qw(:all); + +=head1 DESCRIPTION + +B<FingerprintsVector> class provides the following methods: + +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 + +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. + +B<FingerprintsVector> class provides support to perform comparison between vectors +containing three different types of values: + +Type I: OrderedNumericalValues + + 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. + +Type II: UnorderedNumericalValues + + 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 + +Type III: AlphaNumericalValues + + o Size of two vectors might not be same + o Vectors contain unordered alphanumerical values. For example: Extended + connectivity fingerprints, atom neighborhood fingerprints. + +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. + +Three forms of similarity and distance calculation between two vectors, specified using B<CalculationMode> +option, are supported: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. + +For I<BinaryForm>, 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. + +For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: + + 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 + +For SetTheoreticForm of calculation between two vectors, let: + + SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) + SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) + +For BinaryForm of calculation between two vectors, let: + + 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 + +Additionally, for BinaryForm various values also correspond to: + + Na = | Xa | + Nb = | Xb | + Nc = | SetIntersectionXaXb | + Nd = N - | SetDifferenceXaXb | + + | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc + = | Xa | + | Xb | - | SetIntersectionXaXb | + +Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B +in I<AlgebraicForm, BinaryForm and SetTheoreticForm> are defined as follows: + +B<CityBlockDistance>: ( same as HammingDistance and ManhattanDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<CosineSimilarity>: ( same as OchiaiSimilarityCoefficient) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) + +I<BinaryForm>: Nc / SQRT ( Na * Nb) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) + +B<CzekanowskiSimilarity>: ( same as DiceSimilarity and SorensonSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<DiceSimilarity>: ( same as CzekanowskiSimilarity and SorensonSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<EuclideanDistance>: + +I<AlgebraicForm>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) ) + +I<BinaryForm>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc ) + +I<SetTheoreticForm>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) + +B<HammingDistance>: ( same as CityBlockDistance and ManhattanDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<JaccardSimilarity>: ( same as TanimotoSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) + +I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +B<ManhattanDistance>: ( same as CityBlockDistance and HammingDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<OchiaiSimilarity>: ( same as CosineSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) + +I<BinaryForm>: Nc / SQRT ( Na * Nb) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) + +B<SorensonSimilarity>: ( same as CzekanowskiSimilarity and DiceSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<SoergelDistance>: + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) ) + +I<BinaryForm>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +B<TanimotoSimilarity>: ( same as JaccardSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) + +I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +=head2 METHODS + +=over 4 + +=item B<new> + + $FPVector = new Fingerprints::FingerprintsVector(%NamesAndValues); + +Using specified I<FingerprintsVector> property names and values hash, B<new> method creates +a new object and returns a reference to newly created B<FingerprintsVectorsVector> +object. By default, the following properties are initialized: + + Type = '' + @{Values} = () + @{ValuesIDs} = () + +Examples: + + $FPVector = new Fingerprints::FingerprintsVector('Type' => 'OrderedNumericalValues', + 'Values' => [1, 2, 3, 4]); + $FPVector = new Fingerprints::FingerprintsVector('Type' => 'NumericalValues', + 'Values' => [10, 22, 33, 44], + 'ValueIDs' => ['ID1', 'ID2', 'ID3', 'ID4']); + $FPVector = new Fingerprints::FingerprintsVector('Type' => 'AlphaNumericalValues', + 'Values' => ['a1', 2, 'a3', 4]); + +=item B<AddValueIDs> + + $FingerprintsVector->AddValueIDs($ValueIDsRef); + $FingerprintsVector->AddValueIDs(@ValueIDs); + +Adds specified I<ValueIDs> to I<FingerprintsVector> and returns I<FingerprintsVector>. + +=item B<AddValues> + + $FingerprintsVector->AddValues($ValuesRef); + $FingerprintsVector->AddValues(@Values); + $FingerprintsVector->AddValues($Vector); + +Adds specified I<Values> to I<FingerprintsVector> and returns I<FingerprintsVector>. + +=item B<CityBlockDistanceCoefficient> + + $Value = $FingerprintsVector->CityBlockDistanceCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::CityBlockDistanceCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<CityBlock> distance coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<CosineSimilarityCoefficient> + + $Value = $FingerprintsVector->CosineSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::CosineSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Cosine> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<CzekanowskiSimilarityCoefficient> + + $Value = $FingerprintsVector->CzekanowskiSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::CzekanowskiSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Czekanowski> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<DiceSimilarityCoefficient> + + $Value = $FingerprintsVector->DiceSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::DiceSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Dice> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<EuclideanDistanceCoefficient> + + $Value = $FingerprintsVector->EuclideanDistanceCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::EuclideanDistanceCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Euclidean> distance coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<GetDescription> + + $Description = $FingerprintsVector->GetDescription(); + +Returns a string containing description of fingerprints vector. + +=item B<GetFingerprintsVectorString> + + $FPString = $FingerprintsVector->GetFingerprintsVectorString($Format); + +Returns a B<FingerprintsString> containing vector values and/or IDs in I<FingerprintsVector> +corresponding to specified I<Format>. + +Possible I<Format> values: I<IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, +IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, +ValueIDsString, ValueIDs, ValuesString, or Values>. + +=item B<GetID> + + $ID = $FingerprintsVector->GetID(); + +Returns I<ID> of I<FingerprintsVector>. + +=item B<GetVectorType> + + $VectorType = $FingerprintsVector->GetVectorType(); + +Returns I<VectorType> of I<FingerprintsVector>. + +=item B<GetIDsAndValuesPairsString> + + $IDsValuesPairsString = $FingerprintsVector->GetIDsAndValuesPairsString(); + +Returns I<FingerprintsVector> value IDs and values as space delimited ID/value pair +string. + +=item B<GetIDsAndValuesString> + + $IDsValuesString = $FingerprintsVector->GetIDsAndValuesString(); + +Returns I<FingerprintsVector> value IDs and values as string containing space delimited IDs followed by +values with semicolon as IDs and values delimiter. + +=item B<GetNumOfNonZeroValues> + + $NumOfNonZeroValues = $FingerprintsVector->GetNumOfNonZeroValues(); + +Returns number of non-zero values in I<FingerprintsVector>. + +=item B<GetNumOfValueIDs> + + $NumOfValueIDs = $FingerprintsVector->GetNumOfValueIDs(); + +Returns number of value IDs I<FingerprintsVector>. + +=item B<GetNumOfValues> + + $NumOfValues = $FingerprintsVector->GetNumOfValues(); + +Returns number of values I<FingerprintsVector>. + +=item B<GetSupportedDistanceAndSimilarityCoefficients> + + @SupportedDistanceAndSimilarityCoefficientsReturn = + Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients(); + +Returns an array containing names of supported distance and similarity coefficients. + +=item B<GetSupportedDistanceCoefficients> + + @SupportedDistanceCoefficientsReturn = + Fingerprints::FingerprintsVector::GetSupportedDistanceCoefficients(); + +Returns an array containing names of supported disyance coefficients. + +=item B<GetSupportedSimilarityCoefficients> + + @SupportedSimilarityCoefficientsReturn = + Fingerprints::FingerprintsVector::GetSupportedSimilarityCoefficients(); + +Returns an array containing names of supported similarity coefficients. + +=item B<GetType> + + $VectorType = $FingerprintsVector->GetType(); + +Returns I<FingerprintsVector> vector type. + +=item B<GetValue> + + $Value = $FingerprintsVector->GetValue($Index); + +Returns fingerprints vector B<Value> specified using I<Index> starting at 0. + +=item B<GetValueID> + + $ValueID = $FingerprintsVector->GetValueID(); + +Returns fingerprints vector B<ValueID> specified using I<Index> starting at 0. + +=item B<GetValueIDs> + + $ValueIDs = $FingerprintsVector->GetValueIDs(); + @ValueIDs = $FingerprintsVector->GetValueIDs(); + +Returns fingerprints vector B<ValueIDs> as an array or reference to an array. + +=item B<GetValueIDsString> + + $ValueIDsString = $FingerprintsVector->GetValueIDsString(); + +Returns fingerprints vector B<ValueIDsString> with value IDs delimited by space. + +=item B<GetValues> + + $ValuesRef = $FingerprintsVector->GetValues(); + @Values = $FingerprintsVector->GetValues(); + +Returns fingerprints vector B<Values> as an array or reference to an array. + +=item B<GetValuesAndIDsPairsString> + + $ValuesIDsPairsString = $FingerprintsVector->GetValuesAndIDsPairsString(); + +Returns I<FingerprintsVector> value and value IDs as space delimited ID/value pair +string. + +=item B<GetValuesAndIDsString> + + $ValuesIDsString = $FingerprintsVector->GetValuesAndIDsString(); + +Returns I<FingerprintsVector> values and value IDs as string containing space delimited IDs followed by +values with semicolon as IDs and values delimiter. + +=item B<GetValuesString> + + $Return = $FingerprintsVector->GetValuesString(); + +Returns I<FingerprintsVector> values as space delimited string. + +=item B<HammingDistanceCoefficient> + + $Value = $FingerprintsVector->HammingDistanceCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::HammingDistanceCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Hamming> distance coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<IsFingerprintsVector> + + $Status = Fingerprints::FingerprintsVector::IsFingerprintsVector($Object); + +Returns 1 or 0 based on whether I<Object> is a I<FingerprintsVector>. + +=item B<JaccardSimilarityCoefficient> + + $Value = $FingerprintsVector->JaccardSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::JaccardSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Jaccard> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<ManhattanDistanceCoefficient> + + $Value = $FingerprintsVector->ManhattanDistanceCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::ManhattanDistanceCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Manhattan> distance coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<NewFromIDsAndValuesPairsString> + + $FingerprintsVector = $FingerprintsVector->NewFromIDsAndValuesPairsString( + $ValuesType, $IDsAndValuesPairsString); + $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesPairsString( + $ValuesType, $IDsAndValuesPairsString); + +Creates a new I<FingerprintsVector> of I<ValuesType> using I<IDsAndValuesPairsString> containing +space delimited value IDs and values pairs and returns new B<FingerprintsVector> object. +Possible I<ValuesType> values: I<OrderedNumericalValues, NumericalValues, or AlphaNumericalValues>. + +=item B<NewFromIDsAndValuesString> + + $FingerprintsVector = $FingerprintsVector->NewFromIDsAndValuesString( + $ValuesType, $IDsAndValuesString); + $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromIDsAndValuesString( + $ValuesType, $IDsAndValuesString); + +Creates a new I<FingerprintsVector> of I<ValuesType> using I<IDsAndValuesString> containing +semicolon delimited value IDs string followed by values strings and returns new B<FingerprintsVector> +object. The values within value and value IDs tring are delimited by spaces. Possible I<ValuesType> +values: I<OrderedNumericalValues, NumericalValues, or AlphaNumericalValues>. + +=item B<NewFromValuesAndIDsPairsString> + + $FingerprintsVector = $FingerprintsVector->NewFromValuesAndIDsPairsString( + $ValuesType, $ValuesAndIDsPairsString); + $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsPairsString( + $ValuesType, $ValuesAndIDsPairsString); + +Creates a new I<FingerprintsVector> of I<ValuesType> using I<ValuesAndIDsPairsString> containing +space delimited value and value IDs pairs and returns new B<FingerprintsVector> object. +Possible I<ValuesType> values: I<OrderedNumericalValues, NumericalValues, or AlphaNumericalValues>. + +=item B<NewFromValuesAndIDsString> + + $FingerprintsVector = $FingerprintsVector->NewFromValuesAndIDsString( + $ValuesType, $IDsAndValuesString); + $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesAndIDsString( + $ValuesType, $IDsAndValuesString); + +Creates a new I<FingerprintsVector> of I<ValuesType> using I<ValuesAndIDsString> containing +semicolon delimited values string followed by value IDs strings and returns new B<FingerprintsVector> +object. The values within values and value IDs tring are delimited by spaces. Possible I<ValuesType> +values: I<OrderedNumericalValues, NumericalValues, or AlphaNumericalValues>. + +=item B<NewFromValuesString> + + $FingerprintsVector = $FingerprintsVector->NewFromValuesString( + $ValuesType, $ValuesString); + $FingerprintsVector = Fingerprints::FingerprintsVector::NewFromValuesString( + $ValuesType, $ValuesString); + +Creates a new I<FingerprintsVector> of I<ValuesType> using I<ValuesString> containing space +delimited values string and returns new B<FingerprintsVector> object. The values within values +and value IDs tring are delimited by spaces. Possible I<ValuesType> values: I<OrderedNumericalValues, +NumericalValues, or AlphaNumericalValues>. + +=item B<OchiaiSimilarityCoefficient> + + $Value = $FingerprintsVector->OchiaiSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::OchiaiSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Ochiai> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<SetDescription> + + $FingerprintsVector->SetDescription($Description); + +Sets I<Description> of fingerprints vector and returns I<FingerprintsVector>. + +=item B<SetID> + + $FingerprintsVector->SetID($ID); + +Sets I<ID> of fingerprints vector and returns I<FingerprintsVector>. + +=item B<SetVectorType> + + $FingerprintsVector->SetVectorType($VectorType); + +Sets I<VectorType> of fingerprints vector and returns I<FingerprintsVector>. + +=item B<SetType> + + $FingerprintsVector->SetType($Type); + +Sets I<FingerprintsVector> values I<Type> and returns I<FingerprintsVector>. Possible I<Type> +values: I<OrderedNumericalValues, NumericalValues, or AlphaNumericalValues>. + +During calculation of similarity and distance coefficients between two I<FingerprintsVectors>, the +following conditions apply to vector type, size, value and value IDs: + + 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. + +=item B<SetValue> + + $FingerprintsVector->SetValue($Index, $Value, [$SkipIndexCheck]); + +Sets a I<FingerprintsVector> value specified by I<Index> starting at 0 to I<Value> along with +optional index range check and returns I<FingerprintsVector>. + +=item B<SetValueID> + + $FingerprintsVector->SetValueID($Index, $ValueID, [$SkipIndexCheck]); + +Sets a I<FingerprintsVector> value ID specified by I<Index> starting at 0 to I<ValueID> along with +optional index range check and returns I<FingerprintsVector>. + +=item B<SetValueIDs> + + $FingerprintsVector->SetValueIDs($ValueIDsRef); + $FingerprintsVector->SetValueIDs(@ValueIDs); + +Sets I<FingerprintsVector> value IDs to specified I<ValueIDs> and returns I<FingerprintsVector>. + +=item B<SetValues> + + $FingerprintsVector->SetValues($ValuesRef); + $FingerprintsVector->SetValues(@Values); + +Sets I<FingerprintsVector> value to specified I<Values> and returns I<FingerprintsVector>. + +=item B<SoergelDistanceCoefficient> + + $Value = $FingerprintsVector->SoergelDistanceCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::SoergelDistanceCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Soergel> distance coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<SorensonSimilarityCoefficient> + + $Value = $FingerprintsVector->SorensonSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::SorensonSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Sorenson> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<TanimotoSimilarityCoefficient> + + $Value = $FingerprintsVector->TanimotoSimilarityCoefficient( + $OtherFingerprintVector, [$CalculationMode, $SkipValuesCheck]); + $Value = Fingerprints::FingerprintsVector::TanimotoSimilarityCoefficient( + $FingerprintsVectorA, $FingerprintVectorB, + [$CalculationMode, $SkipValuesCheck]); + +Returns value of I<Tanimoto> similarity coefficient between two I<FingerprintsVectors> using +optionally specified I<CalculationMode> and optional checking of vector values. + +Possible I<CalculationMode> values: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. Default +I<CalculationMode> value: I<AlgebraicForm>. Default I<SkipValuesCheck> value: I<0>. + +=item B<StringifyFingerprintsVector> + + $String = $FingerprintsVector->StringifyFingerprintsVector(); + +Returns a string containing information about I<FingerprintsVector> object. + +=back + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +BitVector.pm, FingerprintsStringUtil.pm, FingerprintsBitVector.pm, Vector.pm + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version. + +=cut