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BitOps.h
Go to the documentation of this file.
//
// Copyright (C) 2003-2012 greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_BITOPS_H__
#define __RD_BITOPS_H__
/*! \file BitOps.h
\brief Contains general bit-comparison and similarity operations.
The notation used to document the similarity metrics is:
- \c V1_n: number of bits in vector 1
- \c V1_o: number of on bits in vector 1
- <tt>(V1&V2)_o</tt>: number of on bits in the intersection of vectors 1 and
2
*/
#include "BitVects.h"
#include <string>
//! general purpose wrapper for calculating the similarity between two bvs
//! that may be of unequal size (will automatically fold as appropriate)
template <typename T>
double SimilarityWrapper(const T &bv1, const T &bv2,
double (*metric)(const T &, const T &),
bool returnDistance = false) {
double res = 0.0;
if (bv1.getNumBits() > bv2.getNumBits()) {
T *bv1tmp = FoldFingerprint(bv1, bv1.getNumBits() / bv2.getNumBits());
res = metric(*bv1tmp, bv2);
delete bv1tmp;
} else if (bv2.getNumBits() > bv1.getNumBits()) {
T *bv2tmp = FoldFingerprint(bv2, bv2.getNumBits() / bv1.getNumBits());
res = metric(bv1, *bv2tmp);
delete bv2tmp;
} else {
res = metric(bv1, bv2);
}
if (returnDistance) {
res = 1.0 - res;
}
return res;
}
//! \overload
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) {
double res = 0.0;
if (bv1.getNumBits() > bv2.getNumBits()) {
T *bv1tmp = FoldFingerprint(bv1, bv1.getNumBits() / bv2.getNumBits());
res = metric(*bv1tmp, bv2, a, b);
delete bv1tmp;
} else if (bv2.getNumBits() > bv1.getNumBits()) {
T *bv2tmp = FoldFingerprint(bv2, bv2.getNumBits() / bv1.getNumBits());
res = metric(bv1, *bv2tmp, a, b);
delete bv2tmp;
} else {
res = metric(bv1, bv2, a, b);
}
if (returnDistance) {
res = 1.0 - res;
}
return res;
}
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const char *probe,
const char *ref);
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const std::string &probe,
const std::string &ref);
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const ExplicitBitVect &probe,
const ExplicitBitVect &ref);
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const T1 &probe,
const std::string &pkl);
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const T1 &probe, const T1 &ref);
//! returns the number of on bits in common between two bit vectors
/*!
\return (bv1&bv2)_o
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT int NumOnBitsInCommon(const T1 &bv1, const T2 &bv2);
RDKIT_DATASTRUCTS_EXPORT int NumOnBitsInCommon(const ExplicitBitVect &bv1,
const ExplicitBitVect &bv2);
//! returns the Tanimoto similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / [bv1_o + bv2_o - (bv1&bv2)_o]</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double TanimotoSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the Cosine similarity between two bit vects
/*!
Also known as the Ochiai coefficient.
\return <tt>(bv1&bv2)_o / sqrt(bv1_o * bv2_o)</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double CosineSimilarity(const T1 &bv1, const T2 &bv2);
//! returns the Kulczynski similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o * [bv1_o + bv2_o] / [2 * bv1_o * bv2_o]</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double KulczynskiSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the Dice similarity between two bit vects
/*!
\return <tt>2*(bv1&bv2)_o / [bv1_o + bv2_o]</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double DiceSimilarity(const T1 &bv1, const T2 &bv2);
//! returns the Tversky similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / [a*bv1_o + b*bv2_o + (1 - a - b)*(bv1&bv2)_o]</tt>
Notes:
# 0 <= a,b <= 1
# Tversky(a=1,b=1) = Tanimoto
# Tversky(a=1/2,b=1/2) = Dice
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double TverskySimilarity(const T1 &bv1, const T2 &bv2,
double a, double b);
//! returns the Sokal similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / [2*bv1_o + 2*bv2_o - 3*(bv1&bv2)_o]</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double SokalSimilarity(const T1 &bv1, const T2 &bv2);
//! returns the McConnaughey similarity between two bit vects
/*!
\return <tt>[(bv1&bv2)_o * (bv1_o + bv2_o) - (bv1_o * bv2_o)] / (bv1_o *
bv2_o)</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double McConnaugheySimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the Asymmetric similarity between two bit vects
/*!
Also known as the **Simpson similarity** or **Overlap coefficient**.
\return <tt>(bv1&bv2)_o / min(bv1_o,bv2_o)</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double AsymmetricSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the Braun-Blanquet similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / max(bv1_o,bv2_o)</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double BraunBlanquetSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the Russel similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / bv1_o</tt>
<b>Note:</b> that this operation is non-commutative:
RusselSimilarity(bv1,bv2) != RusselSimilarity(bv2,bv1)
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double RusselSimilarity(const T1 &bv1, const T2 &bv2);
//! returns the Rogot-Goldberg similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / (bv1_o + bv2_o)
+ (bv1_n - bv1_o - bv2_o + (bv1&bv2)_o) / (2*bv1_n - bv1_o - bv2_o) </tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double RogotGoldbergSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the on bit similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / (bv1|bv2)_o </tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double OnBitSimilarity(const T1 &bv1, const T2 &bv2);
//! returns the number of common bits (on and off) between two bit vects
/*!
\return <tt>bv1_n - (bv1^bv2)_o</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT int NumBitsInCommon(const T1 &bv1, const T2 &bv2);
RDKIT_DATASTRUCTS_EXPORT int NumBitsInCommon(const ExplicitBitVect &bv1,
const ExplicitBitVect &bv2);
//! returns the common-bit similarity (on and off) between two bit vects
/*!
Also known as:
- **Simple Matching Coefficient**
- **Rand similarity**
- **Sokal–Michener similarity**
\return <tt>[bv1_n - (bv1^bv2)_o] / bv1_n</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT double AllBitSimilarity(const T1 &bv1, const T2 &bv2);
//! returns an IntVect with indices of all on bits in common between two bit
/// vects
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT IntVect OnBitsInCommon(const T1 &bv1, const T2 &bv2);
//! returns an IntVect with indices of all off bits in common between two bit
/// vects
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT IntVect OffBitsInCommon(const T1 &bv1, const T2 &bv2);
//! returns the on-bit projected similarities between two bit vects
/*!
\return two values, as a DoubleVect:
- <tt>(bv1&bv2)_o / bv1_o</tt>
- <tt>(bv1&bv2)_o / bv2_o</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT DoubleVect OnBitProjSimilarity(const T1 &bv1,
const T2 &bv2);
//! returns the on-bit projected similarities between two bit vects
/*!
\return two values, as a DoubleVect:
- <tt>[bv1_n - (bv1|bv2)_o] / [bv1_n - bv1_o]</tt>
- <tt>[bv2_n - (bv1|bv2)_o] / [bv2_n - bv2_o]</tt>
<b>Note:</b> <tt>bv1_n = bv2_n</tt>
*/
template <typename T1, typename T2>
RDKIT_DATASTRUCTS_EXPORT DoubleVect OffBitProjSimilarity(const T1 &bv1,
const T2 &bv2);
//! folds a bit vector \c factor times and returns the result
/*!
\param bv1 the vector to be folded
\param factor (optional) the number of times to fold it
\return a pointer to the folded fingerprint, which is
<tt>bv1_n/factor</tt> long.
<b>Note:</b> The caller is responsible for <tt>delete</tt>ing the result.
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT T1 *FoldFingerprint(const T1 &bv1,
unsigned int factor = 2);
//! returns a text representation of a bit vector (a string of 0s and 1s)
/*!
\param bv1 the vector to use
\return an std::string
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToText(const T1 &bv1);
//! returns a hex representation of a bit vector compatible with Andrew Dalke's
/// FPS format
/*!
\param bv1 the vector to use
\return an std::string
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToFPSText(const T1 &bv1);
//! returns a binary string representation of a bit vector (an array of bytes)
/*!
\param bv1 the vector to use
\return an std::string
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToBinaryText(const T1 &bv1);
//! updates a bit vector from Andrew Dalke's FPS format
/*!
\param bv1 the vector to use
\param fps the FPS hex string
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT void UpdateBitVectFromFPSText(T1 &bv1,
const std::string &fps);
//! updates a bit vector from a binary string representation of a bit vector (an
/// array of bytes)
/*!
\param bv1 the vector to use
\param fps the binary string
*/
template <typename T1>
RDKIT_DATASTRUCTS_EXPORT void UpdateBitVectFromBinaryText(
T1 &bv1, const std::string &fps);
// FIX: docs and tests please
RDKIT_DATASTRUCTS_EXPORT unsigned int CalcBitmapPopcount(
const unsigned char *bv1, unsigned int nBytes);
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapTanimoto(const unsigned char *bv1,
const unsigned char *bv2,
unsigned int nBytes);
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapDice(const unsigned char *bv1,
const unsigned char *bv2,
unsigned int nBytes);
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapTversky(const unsigned char *bv1,
const unsigned char *bv2,
unsigned int nBytes,
double ca, double cb);
RDKIT_DATASTRUCTS_EXPORT bool CalcBitmapAllProbeBitsMatch(
const unsigned char *probe, const unsigned char *ref, unsigned int nBytes);
#endif
BitVectToBinaryText
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToBinaryText(const T1 &bv1)
returns a binary string representation of a bit vector (an array of bytes)
McConnaugheySimilarity
RDKIT_DATASTRUCTS_EXPORT double McConnaugheySimilarity(const T1 &bv1, const T2 &bv2)
returns the McConnaughey similarity between two bit vects
NumBitsInCommon
RDKIT_DATASTRUCTS_EXPORT int NumBitsInCommon(const T1 &bv1, const T2 &bv2)
returns the number of common bits (on and off) between two bit vects
AsymmetricSimilarity
RDKIT_DATASTRUCTS_EXPORT double AsymmetricSimilarity(const T1 &bv1, const T2 &bv2)
returns the Asymmetric similarity between two bit vects
AllProbeBitsMatch
RDKIT_DATASTRUCTS_EXPORT bool AllProbeBitsMatch(const char *probe, const char *ref)
CalcBitmapPopcount
RDKIT_DATASTRUCTS_EXPORT unsigned int CalcBitmapPopcount(const unsigned char *bv1, unsigned int nBytes)
SimilarityWrapper
double SimilarityWrapper(const T &bv1, const T &bv2, double(*metric)(const T &, const T &), bool returnDistance=false)
Definition BitOps.h:31
BitVectToFPSText
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToFPSText(const T1 &bv1)
TverskySimilarity
RDKIT_DATASTRUCTS_EXPORT double TverskySimilarity(const T1 &bv1, const T2 &bv2, double a, double b)
returns the Tversky similarity between two bit vects
RusselSimilarity
RDKIT_DATASTRUCTS_EXPORT double RusselSimilarity(const T1 &bv1, const T2 &bv2)
returns the Russel similarity between two bit vects
AllBitSimilarity
RDKIT_DATASTRUCTS_EXPORT double AllBitSimilarity(const T1 &bv1, const T2 &bv2)
returns the common-bit similarity (on and off) between two bit vects
BitVectToText
RDKIT_DATASTRUCTS_EXPORT std::string BitVectToText(const T1 &bv1)
returns a text representation of a bit vector (a string of 0s and 1s)
BraunBlanquetSimilarity
RDKIT_DATASTRUCTS_EXPORT double BraunBlanquetSimilarity(const T1 &bv1, const T2 &bv2)
returns the Braun-Blanquet similarity between two bit vects
OnBitSimilarity
RDKIT_DATASTRUCTS_EXPORT double OnBitSimilarity(const T1 &bv1, const T2 &bv2)
returns the on bit similarity between two bit vects
CalcBitmapAllProbeBitsMatch
RDKIT_DATASTRUCTS_EXPORT bool CalcBitmapAllProbeBitsMatch(const unsigned char *probe, const unsigned char *ref, unsigned int nBytes)
OnBitsInCommon
RDKIT_DATASTRUCTS_EXPORT IntVect OnBitsInCommon(const T1 &bv1, const T2 &bv2)
FoldFingerprint
RDKIT_DATASTRUCTS_EXPORT T1 * FoldFingerprint(const T1 &bv1, unsigned int factor=2)
folds a bit vector factor times and returns the result
SokalSimilarity
RDKIT_DATASTRUCTS_EXPORT double SokalSimilarity(const T1 &bv1, const T2 &bv2)
returns the Sokal similarity between two bit vects
CosineSimilarity
RDKIT_DATASTRUCTS_EXPORT double CosineSimilarity(const T1 &bv1, const T2 &bv2)
returns the Cosine similarity between two bit vects
DiceSimilarity
RDKIT_DATASTRUCTS_EXPORT double DiceSimilarity(const T1 &bv1, const T2 &bv2)
returns the Dice similarity between two bit vects
KulczynskiSimilarity
RDKIT_DATASTRUCTS_EXPORT double KulczynskiSimilarity(const T1 &bv1, const T2 &bv2)
returns the Kulczynski similarity between two bit vects
RogotGoldbergSimilarity
RDKIT_DATASTRUCTS_EXPORT double RogotGoldbergSimilarity(const T1 &bv1, const T2 &bv2)
returns the Rogot-Goldberg similarity between two bit vects
OffBitsInCommon
RDKIT_DATASTRUCTS_EXPORT IntVect OffBitsInCommon(const T1 &bv1, const T2 &bv2)
CalcBitmapDice
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapDice(const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes)
TanimotoSimilarity
RDKIT_DATASTRUCTS_EXPORT double TanimotoSimilarity(const T1 &bv1, const T2 &bv2)
returns the Tanimoto similarity between two bit vects
UpdateBitVectFromBinaryText
RDKIT_DATASTRUCTS_EXPORT void UpdateBitVectFromBinaryText(T1 &bv1, const std::string &fps)
CalcBitmapTversky
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapTversky(const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes, double ca, double cb)
UpdateBitVectFromFPSText
RDKIT_DATASTRUCTS_EXPORT void UpdateBitVectFromFPSText(T1 &bv1, const std::string &fps)
updates a bit vector from Andrew Dalke's FPS format
CalcBitmapTanimoto
RDKIT_DATASTRUCTS_EXPORT double CalcBitmapTanimoto(const unsigned char *bv1, const unsigned char *bv2, unsigned int nBytes)
OffBitProjSimilarity
RDKIT_DATASTRUCTS_EXPORT DoubleVect OffBitProjSimilarity(const T1 &bv1, const T2 &bv2)
returns the on-bit projected similarities between two bit vects
NumOnBitsInCommon
RDKIT_DATASTRUCTS_EXPORT int NumOnBitsInCommon(const T1 &bv1, const T2 &bv2)
returns the number of on bits in common between two bit vectors
OnBitProjSimilarity
RDKIT_DATASTRUCTS_EXPORT DoubleVect OnBitProjSimilarity(const T1 &bv1, const T2 &bv2)
returns the on-bit projected similarities between two bit vects
IntVect
std::vector< int > IntVect
Definition BitVect.h:17
DoubleVect
std::vector< double > DoubleVect
Definition BitVect.h:19
BitVects.h
Pulls in all the BitVect classes.
ExplicitBitVect
a class for bit vectors that are densely occupied
Definition ExplicitBitVect.h:29
export.h
RDKIT_DATASTRUCTS_EXPORT
#define RDKIT_DATASTRUCTS_EXPORT
Definition export.h:89