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.
//
#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;
}
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);
//! returns the number of on bits in common between two bit vectors
/*!
\return (bv1&bv2)_o
*/
template <typename T1, typename T2>
int
NumOnBitsInCommon(const T1& bv1,const T2& bv2);
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>
double
TanimotoSimilarity(const T1& bv1,const T2& bv2);
//! returns the Cosine similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / sqrt(bv1_o + bv2_o)</tt>
*/
template <typename T1, typename T2>
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>
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>
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>
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>
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>
double
McConnaugheySimilarity(const T1& bv1,
const T2& bv2);
//! returns the Asymmetric similarity between two bit vects
/*!
\return <tt>(bv1&bv2)_o / min(bv1_o,bv2_o)</tt>
*/
template <typename T1, typename T2>
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>
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>
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>
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>
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>
int
NumBitsInCommon(const T1& bv1,const T2& bv2);
int
NumBitsInCommon(const ExplicitBitVect & bv1,const ExplicitBitVect & bv2);
//! returns the common-bit similarity (on and off) between two bit vects
//! This is also called Manhattan similarity.
/*!
\return <tt>[bv1_n - (bv1^bv2)_o] / bv1_n</tt>
*/
template <typename T1, typename T2>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
void
UpdateBitVectFromBinaryText(T1& bv1,const std::string &fps);
#endif
BitVects.h
Pulls in all the BitVect classes.
DiceSimilarity
double DiceSimilarity(const T1 &bv1, const T2 &bv2)
returns the Dice similarity between two bit vects
FoldFingerprint
T1 * FoldFingerprint(const T1 &bv1, unsigned int factor=2)
folds a bit vector factor times and returns the result
BitVectToFPSText
std::string BitVectToFPSText(const T1 &bv1)
returns a hex representation of a bit vector compatible with Andrew Dalke's FPS format ...
SokalSimilarity
double SokalSimilarity(const T1 &bv1, const T2 &bv2)
returns the Sokal similarity between two bit vects
OffBitProjSimilarity
DoubleVect OffBitProjSimilarity(const T1 &bv1, const T2 &bv2)
returns the on-bit projected similarities between two bit vects
TanimotoSimilarity
double TanimotoSimilarity(const T1 &bv1, const T2 &bv2)
returns the Tanimoto similarity between two bit vects
OnBitSimilarity
double OnBitSimilarity(const T1 &bv1, const T2 &bv2)
returns the on bit similarity between two bit vects
OnBitProjSimilarity
DoubleVect OnBitProjSimilarity(const T1 &bv1, const T2 &bv2)
returns the on-bit projected similarities between two bit vects
NumOnBitsInCommon
int NumOnBitsInCommon(const T1 &bv1, const T2 &bv2)
returns the number of on bits in common between two bit vectors
NumBitsInCommon
int NumBitsInCommon(const T1 &bv1, const T2 &bv2)
returns the number of common bits (on and off) between two bit vects
RogotGoldbergSimilarity
double RogotGoldbergSimilarity(const T1 &bv1, const T2 &bv2)
returns the Rogot-Goldberg similarity between two bit vects
UpdateBitVectFromBinaryText
void UpdateBitVectFromBinaryText(T1 &bv1, const std::string &fps)
updates a bit vector from a binary string representation of a bit vector (an array of bytes) ...
AsymmetricSimilarity
double AsymmetricSimilarity(const T1 &bv1, const T2 &bv2)
returns the Asymmetric similarity between two bit vects
BitVectToBinaryText
std::string BitVectToBinaryText(const T1 &bv1)
returns a binary string representation of a bit vector (an array of bytes)
CosineSimilarity
double CosineSimilarity(const T1 &bv1, const T2 &bv2)
returns the Cosine similarity between two bit vects
DoubleVect
std::vector< double > DoubleVect
Definition: BitVect.h:18
SimilarityWrapper
double SimilarityWrapper(const T &bv1, const T &bv2, double(*metric)(const T &, const T &), bool returnDistance=false)
Definition: BitOps.h:30
OnBitsInCommon
IntVect OnBitsInCommon(const T1 &bv1, const T2 &bv2)
returns an IntVect with indices of all on bits in common between two bit vects
BitVectToText
std::string BitVectToText(const T1 &bv1)
returns a text representation of a bit vector (a string of 0s and 1s)
TverskySimilarity
double TverskySimilarity(const T1 &bv1, const T2 &bv2, double a, double b)
returns the Tversky similarity between two bit vects
McConnaugheySimilarity
double McConnaugheySimilarity(const T1 &bv1, const T2 &bv2)
returns the McConnaughey similarity between two bit vects
AllBitSimilarity
double AllBitSimilarity(const T1 &bv1, const T2 &bv2)
AllProbeBitsMatch
bool AllProbeBitsMatch(const char *probe, const char *ref)
IntVect
std::vector< int > IntVect
Definition: BitVect.h:16
ExplicitBitVect
a class for bit vectors that are densely occupied
Definition: ExplicitBitVect.h:26
OffBitsInCommon
IntVect OffBitsInCommon(const T1 &bv1, const T2 &bv2)
returns an IntVect with indices of all off bits in common between two bit vects
RusselSimilarity
double RusselSimilarity(const T1 &bv1, const T2 &bv2)
returns the Russel similarity between two bit vects
KulczynskiSimilarity
double KulczynskiSimilarity(const T1 &bv1, const T2 &bv2)
returns the Kulczynski similarity between two bit vects
UpdateBitVectFromFPSText
void UpdateBitVectFromFPSText(T1 &bv1, const std::string &fps)
updates a bit vector from Andrew Dalke's FPS format
BraunBlanquetSimilarity
double BraunBlanquetSimilarity(const T1 &bv1, const T2 &bv2)
returns the Braun-Blanquet similarity between two bit vects