1 package FingerprintsBitVector;
   2 #
   3 # $RCSfile: FingerprintsBitVector.pm,v $
   4 # $Date: 2008/04/19 16:11:36 $
   5 # $Revision: 1.5 $
   6 #
   7 # Author: Manish Sud <msud@san.rr.com>
   8 #
   9 # Copyright (C) 2004-2008 Manish Sud. All rights reserved.
  10 #
  11 # This file is part of MayaChemTools.
  12 #
  13 # MayaChemTools is free software; you can redistribute it and/or modify it under
  14 # the terms of the GNU Lesser General Public License as published by the Free
  15 # Software Foundation; either version 3 of the License, or (at your option) any
  16 # later version.
  17 #
  18 # MayaChemTools is distributed in the hope that it will be useful, but without
  19 # any warranty; without even the implied warranty of merchantability of fitness
  20 # for a particular purpose.  See the GNU Lesser General Public License for more
  21 # details.
  22 #
  23 # You should have received a copy of the GNU Lesser General Public License
  24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  26 # Boston, MA, 02111-1307, USA.
  27 #
  28 use 5.006;
  29 use strict;
  30 use Carp;
  31 use Exporter;
  32 use ObjectProperty;
  33 use BitVector;
  34 use MathUtil;
  35 use TextUtil ();
  36 
  37 use vars qw($VERSION @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
  38 
  39 $VERSION = '1.00';
  40 @ISA = qw(BitVector Exporter);
  41 
  42 # Similiarity coefficients
  43 my(@SimilarityCoefficients) = qw(BaroniUrbaniSimilarityCoefficient BuserSimilarityCoefficient CosineSimilarityCoefficient DiceSimilarityCoefficient DennisSimilarityCoefficient EuclidSimilarityCoefficient ForbesSimilarityCoefficient FossumSimilarityCoefficient HamannSimilarityCoefficient JacardSimilarityCoefficient Kulczynski1SimilarityCoefficient Kulczynski2SimilarityCoefficient ManhattanSimilarityCoefficient MatchingSimilarityCoefficient McConnaugheySimilarityCoefficient OchiaiSimilarityCoefficient PearsonSimilarityCoefficient RogersTanimotoSimilarityCoefficient RussellRaoSimilarityCoefficient SimpsonSimilarityCoefficient SkoalSneath1SimilarityCoefficient SkoalSneath2SimilarityCoefficient SkoalSneath3SimilarityCoefficient TanimotoSimilarityCoefficient TverskySimilarityCoefficient YuleSimilarityCoefficient WeightedTanimotoSimilarityCoefficient WeightedTverskySimilarityCoefficient);
  44 
  45 # New from string...
  46 my(@NewFromString) = qw(NewFromBinaryString NewFromDecimalString NewFromHexadecimalString NewFromOctalString NewFromRawBinaryString);
  47 
  48 @EXPORT = qw(IsFingerprintsBitVector GetSupportedSimilarityCoefficients);
  49 @EXPORT_OK = (@NewFromString, @SimilarityCoefficients);
  50 
  51 %EXPORT_TAGS = (
  52 		new => [@NewFromString],
  53 		coefficients => [@SimilarityCoefficients],
  54 		all  => [@EXPORT, @EXPORT_OK]
  55 	       );
  56 
  57 # Setup class variables...
  58 my($ClassName);
  59 _InitializeClass();
  60 
  61 use overload '""' => 'StringifyFingerprintsBitVector';
  62 
  63 # Class constructor...
  64 sub new {
  65   my($Class, $Size) = @_;
  66 
  67   # Initialize object...
  68   my $This = $Class->SUPER::new($Size);
  69   bless $This, ref($Class) || $Class;
  70   $This->_InitializeFingerprintsBitVector($Size);
  71 
  72   return $This;
  73 }
  74 
  75 # Initialize object data...
  76 #
  77 # Note:
  78 #  . The class, BitVector, used to derive this class provides all the functionality to
  79 #    manipulate bits.
  80 #  . Irrespective of specified size, Perl functions used to handle bit data data in
  81 #    BitVector class automatically sets the size to the next nearest power of 2.
  82 #    SpecifiedSize is used by this class to process any aribitray size during similarity
  83 #    coefficient calculations.
  84 #
  85 sub _InitializeFingerprintsBitVector {
  86   my($This, $Size) = @_;
  87 
  88   if (!defined $Size) {
  89     croak "Error: ${ClassName}->new: FingerprintsBitVector object instantiated without specifying its size ...";
  90   }
  91   if ($Size <=0) {
  92     croak "Error: ${ClassName}->new: Fingerprints bit vector size, $Size, must be a positive integer...";
  93   }
  94 
  95   # Specified size of fingerprints...
  96   $This->{SpecifiedSize} = $Size;
  97 }
  98 
  99 # Initialize class ...
 100 sub _InitializeClass {
 101   #Class name...
 102   $ClassName = __PACKAGE__;
 103 }
 104 
 105 # Create a new fingerprints bit vector using binary string. This functionality can be
 106 # either invoked as a class function or an object method.
 107 #
 108 sub NewFromBinaryString ($;$) {
 109 
 110   return _NewFingerptinsBitVectorFromString(@_, 'Binary');
 111 }
 112 
 113 # Create a new fingerprints bit vector using hexadecimal string. This functionality can be
 114 # either invoked as a class function or an object method.
 115 #
 116 sub NewFromHexadecimalString ($;$) {
 117 
 118   return _NewFingerptinsBitVectorFromString(@_, 'Hexadecimal');
 119 }
 120 
 121 # Create a new fingerprints bit vector using octal string. This functionality can be
 122 # either invoked as a class function or an object method.
 123 #
 124 #
 125 sub NewFromOctalString ($) {
 126   croak "Error: ${ClassName}->NewFromOctalString: Creation of fingerprits bit vector from an octal string is not supported ...";
 127 }
 128 
 129 # Create a new fingerprints bit vector using decimal string. This functionality can be
 130 # either invoked as a class function or an object method.
 131 #
 132 sub NewFromDecimalString ($;$) {
 133   croak "Error: ${ClassName}->NewFromDecimalString: Creation of fingerprits bit vector from a decimal string is not supported ...";
 134 }
 135 
 136 # Create a new fingerprints bit vector using raw binary string. This functionality can be
 137 # either invoked as a class function or an object method.
 138 #
 139 sub NewFromRawBinaryString ($;$) {
 140 
 141   return _NewFingerptinsBitVectorFromString(@_, 'RawBinary');
 142 }
 143 
 144 # Create a new fingerprints bit vector from a string...
 145 #
 146 sub _NewFingerptinsBitVectorFromString ($$;$) {
 147   my($FirstParameter, $SecondParameter, $ThirdParameter) = @_;
 148   my($This, $Format, $String, $Size, $FingerprintsBitVector);
 149 
 150   if (@_ == 3) {
 151     ($This, $String, $Format) = ($FirstParameter, $SecondParameter, $ThirdParameter);
 152   }
 153   else {
 154     ($This, $String, $Format) = (undef, $FirstParameter, $SecondParameter);
 155   }
 156   $Size = BitVector::_CalculateStringSizeInBits($Format, $String);
 157   if (defined $This) {
 158     $FingerprintsBitVector = (ref $This)->new($Size);
 159   }
 160   else {
 161     $FingerprintsBitVector = new FingerprintsBitVector($Size);
 162   }
 163   $FingerprintsBitVector->_SetBitsAsString($Format, $String);
 164 
 165   return $FingerprintsBitVector;
 166 }
 167 
 168 # Get fingerprint bits as a hexadecimal string...
 169 #
 170 sub GetBitsAsHexadecimalString {
 171   my($This) = @_;
 172 
 173   return $This->_GetFingerprintBitsAsString('Hexadecimal');
 174 }
 175 
 176 # Get fingerprint bits as an octal string...
 177 #
 178 sub GetBitsAsOctalString {
 179   my($This) = @_;
 180 
 181   croak "Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as an octal string is not supported ...";
 182 }
 183 
 184 # Get fingerprint bits as an decimal string...
 185 #
 186 sub GetBitsAsDecimalString {
 187   my($This) = @_;
 188 
 189   croak "Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as a decimal string is not supported ...";
 190 }
 191 
 192 # Get fingerprint bits as a binary string conatning 1s and 0s...
 193 #
 194 sub GetBitsAsBinaryString {
 195   my($This) = @_;
 196 
 197   return $This->_GetFingerprintBitsAsString('Binary');
 198 }
 199 
 200 # Get fingerprint bits as a binary string conatning 1s and 0s...
 201 #
 202 sub GetBitsAsRawBinaryString {
 203   my($This) = @_;
 204 
 205   return $This->_GetFingerprintBitsAsString('RawBinary');
 206 }
 207 
 208 # Return fingerprint bits as a string...
 209 #
 210 sub _GetFingerprintBitsAsString {
 211   my($This, $Format) = @_;
 212 
 213   return $This->_GetBitsAsString($Format, 'Descending');
 214 }
 215 
 216 # Is it a fingerprints bit vector object?
 217 sub IsFingerprintsBitVector ($) {
 218   my($Object) = @_;
 219 
 220   return _IsFingerprintsBitVector($Object);
 221 }
 222 
 223 # Is it a fingerprints bit vector object?
 224 sub _IsFingerprintsBitVector {
 225   my($Object) = @_;
 226 
 227   return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
 228 }
 229 
 230 # Return a list of supported similarity coefficients...
 231 sub GetSupportedSimilarityCoefficients () {
 232 
 233   return @SimilarityCoefficients;
 234 }
 235 
 236 # Get bit density for fingerprints bit vector corresponding to on bits...
 237 #
 238 sub GetFingerprintsBitDensity {
 239   my($This) = @_;
 240   my($BitDensity);
 241 
 242   $BitDensity = $This->GetDensityOfSetBits();
 243 
 244   return round($BitDensity, 2);
 245 }
 246 
 247 # Fold fingerprints bit vector by recursively reducing its size by half untill size is less than or equal to
 248 # specified size...
 249 #
 250 sub FoldFingerprintsBitVectorBySize {
 251   my($This, $Size) = @_;
 252 
 253   if (!($Size > 0 && $Size <= $This->GetSize())) {
 254     croak "Error: ${ClassName}->FoldFingerprintsBitVectorBySize: Specified size, $Size, is not valid:  It must be > 0 && <= ", $This->GetSize()," ...";
 255   }
 256 
 257   if ($This->GetSize() <= $Size) {
 258     return $This;
 259   }
 260   return $This->_FoldFingerprintsBitVector('BySize', $Size);
 261 }
 262 
 263 # Fold fingerprints bit vector by recursively reducing its size by half untill bit density of set bits is greater than
 264 #  or equal to specified density...
 265 #
 266 sub FoldFingerprintsBitVectorByDensity {
 267   my($This, $Density) = @_;
 268 
 269   if (!($Density > 0 && $Density <= 1)) {
 270     croak "Error: ${ClassName}->FoldFingerprintsBitVectorByDensity: Specified bit density, $Density, is not valid:  It must be > 0 && <= 1 ...";
 271   }
 272 
 273   if ($This->GetDensityOfSetBits() >= $Density) {
 274     return $This;
 275   }
 276   return $This->_FoldFingerprintsBitVector('ByDensity', $Density);
 277 }
 278 
 279 # Fold fingerprints bit vector using size or density and return folded fingerprint bit vector...
 280 #
 281 sub _FoldFingerprintsBitVector {
 282   my($This, $Mode, $Value) = @_;
 283 
 284   # Fold upto size of 8 bits...
 285   if ($This->GetSize() <= 8) {
 286     return $This;
 287   }
 288 
 289   # Check size or density....
 290   if ($Mode =~ /^BySize$/i) {
 291     if ($This->GetSize() <= $Value) {
 292       return $This;
 293     }
 294   }
 295   elsif ($Mode =~ /^ByDensity$/i) {
 296     if ($This->GetDensityOfSetBits() >= $Value) {
 297       return $This;
 298     }
 299   }
 300   else {
 301     return $This;
 302   }
 303 
 304   # Recursively reduce its size by half...
 305   my($FirstHalfBinaryString, $SecondHalfBinaryString, $FirstHalfFingerprintsBitVector, $SecondHalfFingerprintsBitVector, $FoldedFingerprintsBitVector, $BinaryString, $StringLength);
 306 
 307   $BinaryString = $This->GetBitsAsBinaryString();
 308   $StringLength = length $BinaryString;
 309 
 310   $FirstHalfBinaryString = substr($BinaryString, 0, $StringLength/2);
 311   $SecondHalfBinaryString = substr($BinaryString, $StringLength/2);
 312 
 313   $FirstHalfFingerprintsBitVector = NewFromBinaryString($FirstHalfBinaryString);
 314   $SecondHalfFingerprintsBitVector = NewFromBinaryString($SecondHalfBinaryString);
 315 
 316   $FoldedFingerprintsBitVector = $FirstHalfFingerprintsBitVector | $SecondHalfFingerprintsBitVector;
 317 
 318   return $FoldedFingerprintsBitVector->_FoldFingerprintsBitVector($Mode, $Value);
 319 }
 320 
 321 # Is first bit vector subset of second bit vector?
 322 #
 323 # For a bit vector to be a subset of another bit vector, both vectors must be of
 324 # the same size and the bit positions set in first vector must also be set in the
 325 # secons bit vector.
 326 #
 327 # This functionality can be either invoked as a class function or an object method.
 328 #
 329 sub IsSubSet ($$) {
 330   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 331 
 332   if ($FingerprintsBitVectorA->GetSize() != $FingerprintsBitVectorB->GetSize()) {
 333     return 0;
 334   }
 335   my($AndFingerprintsBitVector);
 336 
 337   $AndFingerprintsBitVector = $FingerprintsBitVectorA & $FingerprintsBitVectorB;
 338 
 339   return ($FingerprintsBitVectorA->GetNumOfSetBits() == $AndFingerprintsBitVector->GetNumOfSetBits()) ? 1 : 0;
 340 }
 341 
 342 # Return a string containing vector values...
 343 sub StringifyFingerprintsBitVector {
 344   my($This) = @_;
 345   my($FingerprintsBitVectorString);
 346 
 347   if ($This->{SpecifiedSize} != $This->GetSize()) {
 348     $FingerprintsBitVectorString = "SpecifiedSize: " . $This->{SpecifiedSize} . "; BitVector: " . $This->StringifyBitVector();
 349   }
 350   else {
 351     $FingerprintsBitVectorString = "BitVector: " . $This->StringifyBitVector();
 352   }
 353   my($NumOfSetBits, $BitDensity);
 354   $NumOfSetBits = $This->GetNumOfSetBits();
 355   $BitDensity = $This->GetFingerprintsBitDensity();
 356 
 357   $FingerprintsBitVectorString .= "; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity";
 358 
 359   return $FingerprintsBitVectorString;
 360 }
 361 
 362 # For two fingerprints bit vectors A and B of same size, let:
 363 #
 364 #  Na = Number of bits set to "1" in A
 365 #  Nb = Number of bits set to "1" in B
 366 #  Nc = Number of bits set to "1" in both A and B
 367 #  Nd = Number of bits set to "0" in both A and B
 368 #
 369 #  Nt = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd
 370 #
 371 #  Na - Nc = Number of bits set to "1" in A but not in B
 372 #  Nb - Nc = Number of bits set to "1" in B but not in A
 373 #
 374 # Various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit vectors A and B are
 375 # defined as follows:
 376 #
 377 # . BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / (  SQRT ( Nc * Nd ) + Nc + ( Na - Nc )  + ( Nb - Nc ) ) ( same as Buser )
 378 #
 379 # . Buser: ( SQRT ( Nc * Nd ) + Nc ) / (  SQRT ( Nc * Nd ) + Nc + ( Na - Nc )  + ( Nb - Nc ) ) ( same as BaroniUrbani )
 380 #
 381 # . Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)
 382 #
 383 # . Dice: (2 * Nc) / ( Na + Nb )
 384 #
 385 # . Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)
 386 #
 387 # . Euclid: SQRT ( ( Nc + Nd ) / Nt )
 388 #
 389 # . Forbes: ( Nt * Nc ) / ( Na * Nb )
 390 #
 391 # . Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )
 392 #
 393 # . Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt
 394 #
 395 # . Jaccard: Nc /  ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)
 396 #
 397 # . Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )
 398 #
 399 # . Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )
 400 #
 401 # . Manhattan: ( ( Na - Nc ) + (Nb - Nc) ) / Nt = ( Na + Nb - 2Nc ) / Nt
 402 #
 403 # . Matching: ( Nc + Nd ) / Nt
 404 #
 405 # . McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / (  Na * Nb )
 406 #
 407 # . Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)
 408 #
 409 # . Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * (  Na - Nc + Nd ) * ( Nb - Nc + Nd ) )
 410 #
 411 # . RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc)  + ( Nb  - Nc) + Nt) = ( Nc + Nd ) / ( Na  + Nb  - 2Nc + Nt)
 412 #
 413 # . RussellRao: Nc / Nt
 414 #
 415 # . Simpson: Nc / MIN ( Na, Nb)
 416 #
 417 # . SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc)  + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )
 418 #
 419 # . SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
 420 #
 421 # . SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc  )
 422 #
 423 # . Tanimoto: Nc /  ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)
 424 #
 425 # . Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb )  + Nb)
 426 #
 427 # . Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) )  )
 428 #
 429 #
 430 # Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
 431 # are set to "1" in both A and B. In order to take into account all bit positions, modified versions
 432 # of Tanimoto [ Ref. 42 ] and Tversky [  Ref. 43 ] have been developed.
 433 #
 434 # Let:
 435 #
 436 #  Na' = Number of bits set to "0" in A
 437 #  Nb' = Number of bits set to "0" in B
 438 #  Nc' = Number of bits set to "0" in both A and B
 439 #
 440 # . Tanimoto': Nc' /  ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )
 441 #
 442 # . Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' )  + Nb')
 443 #
 444 # Then:
 445 #
 446 # . WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto'
 447 #
 448 # . WeightedTversky = beta * Tversky + (1 - beta) * Tversky'
 449 #
 450 #
 451 
 452 # Calculate BaroniUrbani similarity coefficient for two same size bit vectors.
 453 #
 454 # This functionality can be either invoked as a class function or an object method.
 455 #
 456 sub BaroniUrbaniSimilarityCoefficient ($$) {
 457   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 458 
 459   return BuserSimilarityCoefficient($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 460 }
 461 
 462 # Calculate Buser similarity coefficient for two same size bit vectors.
 463 #
 464 # This functionality can be either invoked as a class function or an object method.
 465 #
 466 sub BuserSimilarityCoefficient ($$) {
 467   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 468   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 469 
 470   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 471   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 472   $Nt = $Na + $Nb - $Nc + $Nd;
 473 
 474   $Numerator = sqrt($Nc*$Nd) + $Nc;
 475   $Denominator = sqrt($Nc*$Nd) + ($Na - $Nc)  + ($Nb - $Nc ) + $Nc;
 476 
 477   return  $Denominator ? ($Numerator/$Denominator) : 0;
 478 }
 479 
 480 # Calculate Cosine similarity coefficient for two same size bit vectors.
 481 #
 482 # This functionality can be either invoked as a class function or an object method.
 483 #
 484 sub CosineSimilarityCoefficient ($$) {
 485   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 486   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 487 
 488   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 489 
 490   $Numerator = $Nc;
 491   $Denominator = sqrt($Na*$Nb);
 492 
 493   return  $Denominator ? ($Numerator/$Denominator) : 0;
 494 }
 495 
 496 # Calculate Dice similarity coefficient for two same size bit vectors.
 497 #
 498 # This functionality can be either invoked as a class function or an object method.
 499 #
 500 sub DiceSimilarityCoefficient ($$) {
 501   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 502   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 503 
 504   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 505 
 506   $Numerator = 2*$Nc;
 507   $Denominator = $Na + $Nb;
 508 
 509   return  $Denominator ? ($Numerator/$Denominator) : 0;
 510 }
 511 
 512 # Calculate Dennis similarity coefficient for two same size bit vectors.
 513 #
 514 # This functionality can be either invoked as a class function or an object method.
 515 #
 516 sub DennisSimilarityCoefficient ($$) {
 517   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 518   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 519 
 520   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 521   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 522   $Nt = $Na + $Nb - $Nc + $Nd;
 523 
 524   $Numerator = $Nc*$Nd - (($Na - $Nc)*($Nb - $Nc));
 525   $Denominator = sqrt($Nt*$Na*$Nb);
 526 
 527   return  $Denominator ? ($Numerator/$Denominator) : 0;
 528 }
 529 
 530 # Calculate Euclid similarity coefficient for two same size bit vectors.
 531 #
 532 # This functionality can be either invoked as a class function or an object method.
 533 #
 534 sub EuclidSimilarityCoefficient ($$) {
 535   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 536   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 537 
 538   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 539   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 540   $Nt = $Na + $Nb - $Nc + $Nd;
 541 
 542   $Numerator = $Nc + $Nd;
 543   $Denominator = $Nt;
 544 
 545   return  $Denominator ? (sqrt($Numerator/$Denominator)) : 0;
 546 }
 547 
 548 # Calculate Forbes similarity coefficient for two same size bit vectors.
 549 #
 550 # This functionality can be either invoked as a class function or an object method.
 551 #
 552 sub ForbesSimilarityCoefficient ($$) {
 553   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 554   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 555 
 556   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 557   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 558   $Nt = $Na + $Nb - $Nc + $Nd;
 559 
 560   $Numerator = $Nt*$Nc;
 561   $Denominator = $Na*$Nb;
 562 
 563   return  $Denominator ? ($Numerator/$Denominator) : 0;
 564 }
 565 
 566 # Calculate Fossum similarity coefficient for two same size bit vectors.
 567 #
 568 # This functionality can be either invoked as a class function or an object method.
 569 #
 570 sub FossumSimilarityCoefficient ($$) {
 571   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 572   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 573 
 574   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 575   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 576   $Nt = $Na + $Nb - $Nc + $Nd;
 577 
 578   $Numerator =  $Nt*(($Nc - 0.5)** 2);
 579   $Denominator =  $Na*$Nb ;
 580 
 581   return  $Denominator ? ($Numerator/$Denominator) : 0;
 582 }
 583 
 584 # Calculate Hamann similarity coefficient for two same size bit vectors.
 585 #
 586 # This functionality can be either invoked as a class function or an object method.
 587 #
 588 sub HamannSimilarityCoefficient ($$) {
 589   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 590   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 591 
 592   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 593   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 594   $Nt = $Na + $Nb - $Nc + $Nd;
 595 
 596   $Numerator =  ($Nc + $Nd ) - ($Na - $Nc) - ($Nb - $Nc) ;
 597   $Denominator = $Nt;
 598 
 599   return  $Denominator ? ($Numerator/$Denominator) : 0;
 600 }
 601 
 602 # Calculate Jacard similarity coefficient for two same size bit vectors.
 603 #
 604 # This functionality can be either invoked as a class function or an object method.
 605 #
 606 sub JacardSimilarityCoefficient ($$) {
 607   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 608 
 609   return TanimotoSimilarityCoefficient($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 610 }
 611 
 612 # Calculate Kulczynski1 similarity coefficient for two same size bit vectors.
 613 #
 614 # This functionality can be either invoked as a class function or an object method.
 615 #
 616 sub Kulczynski1SimilarityCoefficient ($$) {
 617   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 618   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 619 
 620   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 621 
 622   $Numerator = $Nc;
 623   $Denominator =  $Na + $Nb - 2*$Nc;
 624 
 625   return  $Denominator ? ($Numerator/$Denominator) : 0;
 626 }
 627 
 628 # Calculate Kulczynski2 similarity coefficient for two same size bit vectors.
 629 #
 630 # This functionality can be either invoked as a class function or an object method.
 631 #
 632 sub Kulczynski2SimilarityCoefficient ($$) {
 633   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 634   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 635 
 636   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 637 
 638   $Numerator = 0.5*($Na*$Nc + $Nb*$Nc);
 639   $Denominator = $Na*$Nb;
 640 
 641   return  $Denominator ? ($Numerator/$Denominator) : 0;
 642 }
 643 
 644 # Calculate Manhattan similarity coefficient for two same size bit vectors.
 645 #
 646 # This functionality can be either invoked as a class function or an object method.
 647 #
 648 sub ManhattanSimilarityCoefficient ($$) {
 649   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 650   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 651 
 652   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 653   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 654   $Nt = $Na + $Nb - $Nc + $Nd;
 655 
 656   $Numerator =  ($Na - $Nc) + ($Nb - $Nc);
 657   $Denominator = $Nt;
 658 
 659   return  $Denominator ? ($Numerator/$Denominator) : 0;
 660 }
 661 
 662 # Calculate Matching similarity coefficient for two same size bit vectors.
 663 #
 664 # This functionality can be either invoked as a class function or an object method.
 665 #
 666 sub MatchingSimilarityCoefficient ($$) {
 667   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 668   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 669 
 670   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 671   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 672   $Nt = $Na + $Nb - $Nc + $Nd;
 673 
 674   $Numerator =  $Nc + $Nd;
 675   $Denominator = $Nt;
 676 
 677   return  $Denominator ? ($Numerator/$Denominator) : 0;
 678 }
 679 
 680 # Calculate McConnaughey similarity coefficient for two same size bit vectors.
 681 #
 682 # This functionality can be either invoked as a class function or an object method.
 683 #
 684 sub McConnaugheySimilarityCoefficient ($$) {
 685   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 686   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 687 
 688   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 689 
 690   $Numerator =  $Nc**2 - (($Na - $Nc)*($Nb - $Nc));
 691   $Denominator = $Na*$Nb ;
 692 
 693   return  $Denominator ? ($Numerator/$Denominator) : 0;
 694 }
 695 
 696 # Calculate Ochiai similarity coefficient for two same size bit vectors.
 697 #
 698 # This functionality can be either invoked as a class function or an object method.
 699 #
 700 sub OchiaiSimilarityCoefficient ($$) {
 701   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 702 
 703   return CosineSimilarityCoefficient($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 704 }
 705 
 706 # Calculate Pearson similarity coefficient for two same size bit vectors.
 707 #
 708 # This functionality can be either invoked as a class function or an object method.
 709 #
 710 sub PearsonSimilarityCoefficient ($$) {
 711   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 712   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 713 
 714   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 715   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 716   $Nt = $Na + $Nb - $Nc + $Nd;
 717 
 718   $Numerator = ($Nc*$Nd ) - (($Na - $Nc)*($Nb - $Nc));
 719   $Denominator =  sqrt($Na*$Nb*($Na - $Nc + $Nd )*($Nb - $Nc + $Nd));
 720 
 721   return  $Denominator ? ($Numerator/$Denominator) : 0;
 722 }
 723 
 724 # Calculate RogersTanimoto similarity coefficient for two same size bit vectors.
 725 #
 726 # This functionality can be either invoked as a class function or an object method.
 727 #
 728 sub RogersTanimotoSimilarityCoefficient ($$) {
 729   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 730   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 731 
 732   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 733   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 734   $Nt = $Na + $Nb - $Nc + $Nd;
 735 
 736   $Numerator = $Nc + $Nd;
 737   $Denominator =  ($Na - $Nc)  + ($Nb  - $Nc) + $Nt;
 738 
 739   return  $Denominator ? ($Numerator/$Denominator) : 0;
 740 }
 741 
 742 # Calculate RussellRao similarity coefficient for two same size bit vectors.
 743 #
 744 # This functionality can be either invoked as a class function or an object method.
 745 #
 746 sub RussellRaoSimilarityCoefficient ($$) {
 747   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 748   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 749 
 750   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 751   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 752   $Nt = $Na + $Nb - $Nc + $Nd;
 753 
 754   $Numerator = $Nc;
 755   $Denominator = $Nt;
 756 
 757   return  $Denominator ? ($Numerator/$Denominator) : 0;
 758 }
 759 
 760 # Calculate Simpson similarity coefficient for two same size bit vectors.
 761 #
 762 # This functionality can be either invoked as a class function or an object method.
 763 #
 764 sub SimpsonSimilarityCoefficient ($$) {
 765   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 766   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 767 
 768   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 769 
 770   $Numerator = $Nc;
 771   $Denominator =  min($Na, $Nb);
 772 
 773   return  $Denominator ? ($Numerator/$Denominator) : 0;
 774 }
 775 
 776 # Calculate SkoalSneath1 similarity coefficient for two same size bit vectors.
 777 #
 778 # This functionality can be either invoked as a class function or an object method.
 779 #
 780 sub SkoalSneath1SimilarityCoefficient ($$) {
 781   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 782   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 783 
 784   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 785 
 786   $Numerator = $Nc;
 787   $Denominator = $Nc + 2*($Na - $Nc)  + 2*($Nb - $Nc);
 788 
 789   return  $Denominator ? ($Numerator/$Denominator) : 0;
 790 }
 791 
 792 # Calculate SkoalSneath2 similarity coefficient for two same size bit vectors.
 793 #
 794 # This functionality can be either invoked as a class function or an object method.
 795 #
 796 sub SkoalSneath2SimilarityCoefficient ($$) {
 797   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 798   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 799 
 800   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 801   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 802   $Nt = $Na + $Nb - $Nc + $Nd;
 803 
 804   $Numerator = 2*$Nc + 2*$Nd  ;
 805   $Denominator = $Nc + $Nd + $Nt ;
 806 
 807   return  $Denominator ? ($Numerator/$Denominator) : 0;
 808 }
 809 
 810 # Calculate SkoalSneath3 similarity coefficient for two same size bit vectors.
 811 #
 812 # This functionality can be either invoked as a class function or an object method.
 813 #
 814 sub SkoalSneath3SimilarityCoefficient ($$) {
 815   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 816   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 817 
 818   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 819   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 820   $Nt = $Na + $Nb - $Nc + $Nd;
 821 
 822   $Numerator =  $Nc + $Nd;
 823   $Denominator = ($Na - $Nc) + ($Nb - $Nc ) ;
 824 
 825   return  $Denominator ? ($Numerator/$Denominator) : 0;
 826 }
 827 
 828 # Calculate Tanimoto similarity coefficient for two same size bit vectors.
 829 #
 830 # This functionality can be either invoked as a class function or an object method.
 831 #
 832 sub TanimotoSimilarityCoefficient ($$) {
 833   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 834   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 835 
 836   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 837 
 838   $Numerator = $Nc;
 839   $Denominator = $Na + $Nb - $Nc;
 840 
 841   return  $Denominator ? ($Numerator/$Denominator) : 0;
 842 }
 843 
 844 # Calculate Tversky similarity coefficient for two same size bit vectors.
 845 #
 846 # This functionality can be either invoked as a class function or an object method.
 847 #
 848 sub TverskySimilarityCoefficient ($$$) {
 849   my($FingerprintsBitVectorA, $FingerprintsBitVectorB, $Alpha) = @_;
 850   my($Na, $Nb, $Nc, $Numerator, $Denominator);
 851 
 852   if (!(defined($Alpha) && ($Alpha >= 0 && $Alpha <= 1))) {
 853     croak "Error: ${ClassName}->TverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ...";
 854   }
 855 
 856   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 857 
 858   $Numerator = $Nc;
 859   $Denominator =  $Alpha*($Na - $Nb )  + $Nb;
 860 
 861   return  $Denominator ? ($Numerator/$Denominator) : 0;
 862 }
 863 
 864 # Calculate Yule similarity coefficient for two same size bit vectors.
 865 #
 866 # This functionality can be either invoked as a class function or an object method.
 867 #
 868 sub YuleSimilarityCoefficient ($$) {
 869   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 870   my($Na, $Nb, $Nc, $Nd, $Nt, $Numerator, $Denominator);
 871 
 872   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 873   $Nd = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 874   $Nt = $Na + $Nb - $Nc + $Nd;
 875 
 876   $Numerator = ($Nc*$Nd) - (($Na - $Nc)*($Nb - $Nc)) ;
 877   $Denominator = ($Nc*$Nd) + (($Na - $Nc)*($Nb - $Nc))  ;
 878 
 879   return  $Denominator ? ($Numerator/$Denominator) : 0;
 880 }
 881 
 882 # Calculate WeightedTanimoto similarity coefficient for two same size bit vectors.
 883 #
 884 # This functionality can be either invoked as a class function or an object method.
 885 #
 886 sub WeightedTanimotoSimilarityCoefficient ($$$) {
 887   my($FingerprintsBitVectorA, $FingerprintsBitVectorB, $Beta) = @_;
 888   my($Na, $Nb, $Nc, $TanimotoForSetBits, $TanimotoForClearBits, $Numerator, $Denominator, $WeightedTanimoto);
 889 
 890   if (!(defined($Beta) && ($Beta >= 0 && $Beta <= 1))) {
 891     croak "Error: ${ClassName}->WeightedTanimotoSimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ...";
 892   }
 893 
 894   # Get Tanimoto for set bits...
 895   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 896 
 897   $Numerator = $Nc;
 898   $Denominator = $Na + $Nb - $Nc;
 899   $TanimotoForSetBits = $Denominator ? ($Numerator/$Denominator) : 0;
 900 
 901   # Get Tanimoto for clear bits...
 902   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 903 
 904   $Numerator = $Nc;
 905   $Denominator = $Na + $Nb - $Nc;
 906   $TanimotoForClearBits = $Denominator ? ($Numerator/$Denominator) : 0;
 907 
 908   $WeightedTanimoto = $Beta*$TanimotoForSetBits + (1 - $Beta)*$TanimotoForClearBits;
 909 
 910   return  $WeightedTanimoto;
 911 }
 912 
 913 # Calculate WeightedTversky similarity coefficient for two same size bit vectors.
 914 #
 915 # This functionality can be either invoked as a class function or an object method.
 916 #
 917 sub WeightedTverskySimilarityCoefficient ($$$) {
 918   my($FingerprintsBitVectorA, $FingerprintsBitVectorB, $Alpha, $Beta) = @_;
 919   my($Na, $Nb, $Nc, $TverskyForSetBits, $TverskyForClearBits, $Numerator, $Denominator, $WeightedTversky);
 920 
 921   if (!(defined($Alpha) && ($Alpha >= 0 && $Alpha <= 1))) {
 922     croak "Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ...";
 923   }
 924   if (!(defined($Beta) && ($Beta >= 0 && $Beta <= 1))) {
 925     croak "Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ...";
 926   }
 927 
 928   # Get Tversky for set bits...
 929   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonSetBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 930 
 931   $Numerator = $Nc;
 932   $Denominator =  $Alpha*($Na - $Nb )  + $Nb;
 933   $TverskyForSetBits =  $Denominator ? ($Numerator/$Denominator) : 0;
 934 
 935   # Get Tversky for clear bits...
 936   ($Na, $Nb, $Nc) = _GetNumOfIndividualAndCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 937 
 938   $Numerator = $Nc;
 939   $Denominator =  $Alpha*($Na - $Nb )  + $Nb;
 940   $TverskyForClearBits =  $Denominator ? ($Numerator/$Denominator) : 0;
 941 
 942   $WeightedTversky = $Beta*$TverskyForSetBits + (1 - $Beta)*$TverskyForClearBits;
 943 
 944   return  $WeightedTversky;
 945 }
 946 
 947 # Get number of Na, Nb and Nc bits in bit vector A and B to be used for similarity coefficient calculations...
 948 #
 949 sub _GetNumOfIndividualAndCommonSetBits ($$) {
 950   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 951   my($Na, $Nb, $Nc, $Nd);
 952 
 953   # Number of bits set to "1" in A
 954   $Na = $FingerprintsBitVectorA->GetNumOfSetBits();
 955 
 956   # Number of bits set to "1" in B
 957   $Nb = $FingerprintsBitVectorB->GetNumOfSetBits();
 958 
 959   # Number of bits set to "1" in both A and B
 960   my($NcBitVector);
 961   $NcBitVector = $FingerprintsBitVectorA & $FingerprintsBitVectorB;
 962   $Nc = $NcBitVector->GetNumOfSetBits();
 963 
 964   return ($Na, $Nb, $Nc);
 965 }
 966 
 967 # Get number of Nd bits in bit vector A and B to be used for similarity coefficient calculations...
 968 #
 969 sub _GetNumOfCommonClearBits ($$) {
 970   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 971   my($Nd, $NdBitVector);
 972 
 973   #  Number of bits set to "0" in both A and B
 974   $NdBitVector = ~$FingerprintsBitVectorA & ~$FingerprintsBitVectorB;
 975   $Nd = $NdBitVector->GetNumOfSetBits();
 976 
 977   return $Nd;
 978 }
 979 
 980 
 981 # Get number of Na, Nb and Nc bits in bit vector A and B to be used for similarity coefficient calculations...
 982 #
 983 sub _GetNumOfIndividualAndCommonClearBits ($$) {
 984   my($FingerprintsBitVectorA, $FingerprintsBitVectorB) = @_;
 985   my($Na, $Nb, $Nc, $Nd);
 986 
 987   # Number of bits set to "0" in A
 988   $Na = $FingerprintsBitVectorA->GetNumOfClearBits();
 989 
 990   # Number of bits set to "0" in B
 991   $Nb = $FingerprintsBitVectorB->GetNumOfClearBits();
 992 
 993   # Number of bits set to "0" in both A and B
 994   $Nc = _GetNumOfCommonClearBits($FingerprintsBitVectorA, $FingerprintsBitVectorB);
 995 
 996   return ($Na, $Nb, $Nc);
 997 }
 998