RDKit: BitOps.h File Reference

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BitOps.h File Reference

Contains general bit-comparison and similarity operations. More...

`#include "BitVects.h"`
`#include <string>`

Go to the source code of this file.

## Functions
template<typename T >
double | SimilarityWrapper (const T &bv1, const T &bv2, double(*metric)(const T &, const T &), bool returnDistance=false)
template<typename T >
double | SimilarityWrapper (const T &bv1, const T &bv2, double a, double b, double(*metric)(const T &, const T &, double, double), bool returnDistance=false)
bool | AllProbeBitsMatch (const char *probe, const char *ref)
bool | AllProbeBitsMatch (const std::string &probe, const std::string &ref)
bool | AllProbeBitsMatch (const ExplicitBitVect &probe, const ExplicitBitVect &ref)
template<typename T1 >
bool | AllProbeBitsMatch (const T1 &probe, const std::string &pkl)
template<typename T1 >
bool | AllProbeBitsMatch (const T1 &probe, const T1 &ref)
template<typename T1 , typename T2 >
int | NumOnBitsInCommon (const T1 &bv1, const T2 &bv2)
| returns the number of on bits in common between two bit vectors More...
int | NumOnBitsInCommon (const ExplicitBitVect &bv1, const ExplicitBitVect &bv2)
template<typename T1 , typename T2 >
double | TanimotoSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Tanimoto similarity between two bit vects More...
template<typename T1 , typename T2 >
double | CosineSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Cosine similarity between two bit vects More...
template<typename T1 , typename T2 >
double | KulczynskiSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Kulczynski similarity between two bit vects More...
template<typename T1 , typename T2 >
double | DiceSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Dice similarity between two bit vects More...
template<typename T1 , typename T2 >
double | TverskySimilarity (const T1 &bv1, const T2 &bv2, double a, double b)
| returns the Tversky similarity between two bit vects More...
template<typename T1 , typename T2 >
double | SokalSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Sokal similarity between two bit vects More...
template<typename T1 , typename T2 >
double | McConnaugheySimilarity (const T1 &bv1, const T2 &bv2)
| returns the McConnaughey similarity between two bit vects More...
template<typename T1 , typename T2 >
double | AsymmetricSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Asymmetric similarity between two bit vects More...
template<typename T1 , typename T2 >
double | BraunBlanquetSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Braun-Blanquet similarity between two bit vects More...
template<typename T1 , typename T2 >
double | RusselSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Russel similarity between two bit vects More...
template<typename T1 , typename T2 >
double | RogotGoldbergSimilarity (const T1 &bv1, const T2 &bv2)
| returns the Rogot-Goldberg similarity between two bit vects More...
template<typename T1 , typename T2 >
double | OnBitSimilarity (const T1 &bv1, const T2 &bv2)
| returns the on bit similarity between two bit vects More...
template<typename T1 , typename T2 >
int | NumBitsInCommon (const T1 &bv1, const T2 &bv2)
| returns the number of common bits (on and off) between two bit vects More...
int | NumBitsInCommon (const ExplicitBitVect &bv1, const ExplicitBitVect &bv2)
template<typename T1 , typename T2 >
double | AllBitSimilarity (const T1 &bv1, const T2 &bv2)
template<typename T1 , typename T2 >
IntVect | OnBitsInCommon (const T1 &bv1, const T2 &bv2)
| returns an IntVect with indices of all on bits in common between two bit More...
template<typename T1 , typename T2 >
IntVect | OffBitsInCommon (const T1 &bv1, const T2 &bv2)
| returns an IntVect with indices of all off bits in common between two bit More...
template<typename T1 , typename T2 >
DoubleVect | OnBitProjSimilarity (const T1 &bv1, const T2 &bv2)
| returns the on-bit projected similarities between two bit vects More...
template<typename T1 , typename T2 >
DoubleVect | OffBitProjSimilarity (const T1 &bv1, const T2 &bv2)
| returns the on-bit projected similarities between two bit vects More...
template<typename T1 >
T1 * | FoldFingerprint (const T1 &bv1, unsigned int factor=2)
| folds a bit vector `factor` times and returns the result More...
template<typename T1 >
std::string | BitVectToText (const T1 &bv1)
| returns a text representation of a bit vector (a string of 0s and 1s) More...
template<typename T1 >
std::string | BitVectToFPSText (const T1 &bv1)
| returns a hex representation of a bit vector compatible with Andrew Dalke's More...
template<typename T1 >
std::string | BitVectToBinaryText (const T1 &bv1)
| returns a binary string representation of a bit vector (an array of bytes) More...
template<typename T1 >
void | UpdateBitVectFromFPSText (T1 &bv1, const std::string &fps)
| updates a bit vector from Andrew Dalke's FPS format More...
template<typename T1 >
void | UpdateBitVectFromBinaryText (T1 &bv1, const std::string &fps)
| updates a bit vector from a binary string representation of a bit vector (an More...
unsigned int | CalcBitmapPopcount (const unsigned char *bv1, unsigned int nBytes)
double | CalcBitmapTanimoto (const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes)
double | CalcBitmapDice (const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes)
double | CalcBitmapTversky (const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes, double ca, double cb)
bool | CalcBitmapAllProbeBitsMatch (const unsigned char *probe, const unsigned char *ref, unsigned int nBytes)

## Detailed Description

Contains general bit-comparison and similarity operations.

The notation used to document the similarity metrics is:

- `V1_n:` number of bits in vector 1
- `V1_o:` number of on bits in vector 1
- `(V1&V2)_o`: number of on bits in the intersection of vectors 1 and 2

Definition in file BitOps.h.

## Function Documentation

template<typename T1 , typename T2 >

double AllBitSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the common-bit similarity (on and off) between two bit vects This is also called Manhattan similarity.

Returns
  `[bv1_n - (bv1^bv2)_o] / bv1_n`

Referenced by SimilarityWrapper().

bool AllProbeBitsMatch | ( | const char * | probe,
|  | const char * | ref
| ) |  |

Referenced by RDKit::FPHolderBase::passesFilter(), and SimilarityWrapper().

bool AllProbeBitsMatch | ( | const std::string & | probe,
|  | const std::string & | ref
| ) |  |

bool AllProbeBitsMatch | ( | const ExplicitBitVect & | probe,
|  | const ExplicitBitVect & | ref
| ) |  |

template<typename T1 >

bool AllProbeBitsMatch | ( | const T1 & | probe,
|  | const std::string & | pkl
| ) |  |

template<typename T1 >

bool AllProbeBitsMatch | ( | const T1 & | probe,
|  | const T1 & | ref
| ) |  |

template<typename T1 , typename T2 >

double AsymmetricSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Asymmetric similarity between two bit vects

Returns
  `(bv1&bv2)_o / min(bv1_o,bv2_o)`

Referenced by SimilarityWrapper().

template<typename T1 >

std::string BitVectToBinaryText | ( | const T1 & | bv1 | ) |

returns a binary string representation of a bit vector (an array of bytes)

Parameters

  bv1 | the vector to use

Returns
  an std::string

Referenced by SimilarityWrapper().

template<typename T1 >

std::string BitVectToFPSText | ( | const T1 & | bv1 | ) |

returns a hex representation of a bit vector compatible with Andrew Dalke's

Parameters

  bv1 | the vector to use

Returns
  an std::string

Referenced by SimilarityWrapper().

template<typename T1 >

std::string BitVectToText | ( | const T1 & | bv1 | ) |

returns a text representation of a bit vector (a string of 0s and 1s)

Parameters

  bv1 | the vector to use

Returns
  an std::string

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double BraunBlanquetSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Braun-Blanquet similarity between two bit vects

Returns
  `(bv1&bv2)_o / max(bv1_o,bv2_o)`

Referenced by SimilarityWrapper().

bool CalcBitmapAllProbeBitsMatch | ( | const unsigned char * | probe,
|  | const unsigned char * | ref,
|  | unsigned int | nBytes
| ) |  |

Referenced by SimilarityWrapper().

double CalcBitmapDice | ( | const unsigned char * | bv1,
|  | const unsigned char * | bv2,
|  | unsigned int | nBytes
| ) |  |

Referenced by SimilarityWrapper().

unsigned int CalcBitmapPopcount | ( | const unsigned char * | bv1,
|  | unsigned int | nBytes
| ) |  |

Referenced by SimilarityWrapper().

double CalcBitmapTanimoto | ( | const unsigned char * | bv1,
|  | const unsigned char * | bv2,
|  | unsigned int | nBytes
| ) |  |

Referenced by SimilarityWrapper().

double CalcBitmapTversky | ( | const unsigned char * | bv1,
|  | const unsigned char * | bv2,
|  | unsigned int | nBytes,
|  | double | ca,
|  | double | cb
| ) |  |

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double CosineSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Cosine similarity between two bit vects

Returns
  `(bv1&bv2)_o / sqrt(bv1_o + bv2_o)`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double DiceSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Dice similarity between two bit vects

Returns
  `2*(bv1&bv2)_o / [bv1_o + bv2_o]`

Referenced by SimilarityWrapper().

template<typename T1 >

T1* FoldFingerprint | ( | const T1 & | bv1,
|  | unsigned int | factor = `2`
| ) |  |

folds a bit vector `factor` times and returns the result

Parameters

  bv1 | the vector to be folded
  factor | (optional) the number of times to fold it

Returns
  a pointer to the folded fingerprint, which is `bv1_n/factor` long.

Note: The caller is responsible for `delete`ing the result.

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double KulczynskiSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Kulczynski similarity between two bit vects

Returns
  `(bv1&bv2)_o * [bv1_o + bv2_o] / [2 * bv1_o * bv2_o]`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double McConnaugheySimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the McConnaughey similarity between two bit vects

Returns
  `[(bv1&bv2)_o * (bv1_o + bv2_o) - (bv1_o * bv2_o)] / (bv1_o * bv2_o)`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

int NumBitsInCommon | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the number of common bits (on and off) between two bit vects

Returns
  `bv1_n - (bv1^bv2)_o`

Referenced by SimilarityWrapper().

int NumBitsInCommon | ( | const ExplicitBitVect & | bv1,
|  | const ExplicitBitVect & | bv2
| ) |  |

template<typename T1 , typename T2 >

int NumOnBitsInCommon | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the number of on bits in common between two bit vectors

Returns
  (bv1&bv2)_o

Referenced by SimilarityWrapper().

int NumOnBitsInCommon | ( | const ExplicitBitVect & | bv1,
|  | const ExplicitBitVect & | bv2
| ) |  |

template<typename T1 , typename T2 >

DoubleVect OffBitProjSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the on-bit projected similarities between two bit vects

Returns
  two values, as a DoubleVect:
  - `[bv1_n - (bv1|bv2)_o] / [bv1_n - bv1_o]`
  - `[bv2_n - (bv1|bv2)_o] / [bv2_n - bv2_o]`

Note: `bv1_n = bv2_n`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

IntVect OffBitsInCommon | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns an IntVect with indices of all off bits in common between two bit

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

DoubleVect OnBitProjSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the on-bit projected similarities between two bit vects

Returns
  two values, as a DoubleVect:
  - `(bv1&bv2)_o / bv1_o`
  - `(bv1&bv2)_o / bv2_o`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double OnBitSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the on bit similarity between two bit vects

Returns
  `(bv1&bv2)_o / (bv1|bv2)_o`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

IntVect OnBitsInCommon | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns an IntVect with indices of all on bits in common between two bit

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double RogotGoldbergSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Rogot-Goldberg similarity between two bit vects

Returns
  `(bv1&bv2)_o / (bv1_o + bv2_o)
  - (bv1_n - bv1_o - bv2_o + (bv1&bv2)_o) / (2*bv1_n - bv1_o - bv2_o)
  `

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double RusselSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Russel similarity between two bit vects

Returns
  `(bv1&bv2)_o / bv1_o`

Note: that this operation is non-commutative: RusselSimilarity(bv1,bv2) != RusselSimilarity(bv2,bv1)

Referenced by SimilarityWrapper().

template<typename T >

double SimilarityWrapper | ( | const T & | bv1,
|  | const T & | bv2,
|  | double(*)(const T &, const T &) | metric,
|  | bool | returnDistance = `false`
| ) |  |

general purpose wrapper for calculating the similarity between two bvs that may be of unequal size (will automatically fold as appropriate)

Definition at line 30 of file BitOps.h.

References FoldFingerprint().

Referenced by RDDataManip::TanimotoDistanceMetric(), and RDDataManip::TanimotoSimilarityMetric().

template<typename T >

double SimilarityWrapper | ( | const T & | bv1,
|  | const T & | bv2,
|  | double | a,
|  | double | b,
|  | double(*)(const T &, const T &, double, double) | metric,
|  | bool | returnDistance = `false`
| ) |  |

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 50 of file BitOps.h.

References AllBitSimilarity(), AllProbeBitsMatch(), AsymmetricSimilarity(), BitVectToBinaryText(), BitVectToFPSText(), BitVectToText(), BraunBlanquetSimilarity(), CalcBitmapAllProbeBitsMatch(), CalcBitmapDice(), CalcBitmapPopcount(), CalcBitmapTanimoto(), CalcBitmapTversky(), CosineSimilarity(), DiceSimilarity(), FoldFingerprint(), KulczynskiSimilarity(), McConnaugheySimilarity(), NumBitsInCommon(), NumOnBitsInCommon(), OffBitProjSimilarity(), OffBitsInCommon(), OnBitProjSimilarity(), OnBitSimilarity(), OnBitsInCommon(), RogotGoldbergSimilarity(), RusselSimilarity(), SokalSimilarity(), TanimotoSimilarity(), TverskySimilarity(), UpdateBitVectFromBinaryText(), and UpdateBitVectFromFPSText().

template<typename T1 , typename T2 >

double SokalSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Sokal similarity between two bit vects

Returns
  `(bv1&bv2)_o / [2*bv1_o + 2*bv2_o - 3*(bv1&bv2)_o]`

Referenced by SimilarityWrapper().

template<typename T1 , typename T2 >

double TanimotoSimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2
| ) |  |

returns the Tanimoto similarity between two bit vects

Returns
  `(bv1&bv2)_o / [bv1_o + bv2_o - (bv1&bv2)_o]`

Referenced by SimilarityWrapper(), RDDataManip::TanimotoDistanceMetric(), and RDDataManip::TanimotoSimilarityMetric().

template<typename T1 , typename T2 >

double TverskySimilarity | ( | const T1 & | bv1,
|  | const T2 & | bv2,
|  | double | a,
|  | double | b
| ) |  |

returns the Tversky similarity between two bit vects

Returns
  `(bv1&bv2)_o / [a*bv1_o + b*bv2_o + (1 - a - b)*(bv1&bv2)_o]`

Notes:

# 0 <= a,b <= 1

# Tversky(a=1,b=1) = Tanimoto

# Tversky(a=1/2,b=1/2) = Dice

Referenced by SimilarityWrapper().

template<typename T1 >

void UpdateBitVectFromBinaryText | ( | T1 & | bv1,
|  | const std::string & | fps
| ) |  |

updates a bit vector from a binary string representation of a bit vector (an

Parameters

  bv1 | the vector to use
  fps | the binary string

Referenced by SimilarityWrapper().

template<typename T1 >

void UpdateBitVectFromFPSText | ( | T1 & | bv1,
|  | const std::string & | fps
| ) |  |

updates a bit vector from Andrew Dalke's FPS format

Parameters

  bv1 | the vector to use
  fps | the FPS hex string

Referenced by SimilarityWrapper().