class for reading and searching FPB files More...

#include <FPBReader.h>

Public Member Functions
	FPBReader ()

	FPBReader (const char *fname, bool lazyRead=false)
	ctor for reading from a named file

	FPBReader (const std::string &fname, bool lazyRead=false)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

	FPBReader (std::istream *inStream, bool takeOwnership=true, bool lazyRead=false)
	ctor for reading from an open istream

	~FPBReader ()

void	init ()
	Read the data from the file and initialize internal data structures.

void	cleanup ()
	cleanup

boost::shared_ptr< ExplicitBitVect >	getFP (unsigned int idx) const
	returns the requested fingerprint as an `ExplicitBitVect`

boost::shared_array< std::uint8_t >	getBytes (unsigned int idx) const
	returns the requested fingerprint as an array of bytes

std::string	getId (unsigned int idx) const
	returns the id of the requested fingerprint

std::pair< boost::shared_ptr< ExplicitBitVect >, std::string >	operator[] (unsigned int idx) const
	returns the fingerprint and id of the requested fingerprint

std::pair< unsigned int, unsigned int >	getFPIdsInCountRange (unsigned int minCount, unsigned int maxCount)

unsigned int	length () const
	returns the number of fingerprints

unsigned int	nBits () const
	returns the number of bits in our fingerprints

double	getTanimoto (unsigned int idx, const std::uint8_t *bv) const

double	getTanimoto (unsigned int idx, boost::shared_array< std::uint8_t > bv) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

double	getTanimoto (unsigned int idx, const ExplicitBitVect &ebv) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< std::pair< double, unsigned int > >	getTanimotoNeighbors (const std::uint8_t *bv, double threshold=0.7, bool usePopcountScreen=true) const
	returns tanimoto neighbors that are within a similarity threshold

std::vector< std::pair< double, unsigned int > >	getTanimotoNeighbors (boost::shared_array< std::uint8_t > bv, double threshold=0.7, bool usePopcountScreen=true) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< std::pair< double, unsigned int > >	getTanimotoNeighbors (const ExplicitBitVect &ebv, double threshold=0.7, bool usePopcountScreen=true) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

double	getTversky (unsigned int idx, const std::uint8_t *bv, double ca, double cb) const

double	getTversky (unsigned int idx, boost::shared_array< std::uint8_t > bv, double ca, double cb) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

double	getTversky (unsigned int idx, const ExplicitBitVect &ebv, double ca, double cb) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< std::pair< double, unsigned int > >	getTverskyNeighbors (const std::uint8_t *bv, double ca, double cb, double threshold=0.7, bool usePopcountScreen=true) const
	returns Tversky neighbors that are within a similarity threshold

std::vector< std::pair< double, unsigned int > >	getTverskyNeighbors (boost::shared_array< std::uint8_t > bv, double ca, double cb, double threshold=0.7, bool usePopcountScreen=true) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< std::pair< double, unsigned int > >	getTverskyNeighbors (const ExplicitBitVect &ebv, double ca, double cb, double threshold=0.7, bool usePopcountScreen=true) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< unsigned int >	getContainingNeighbors (const std::uint8_t *bv) const
	returns indices of all fingerprints that completely contain this one

std::vector< unsigned int >	getContainingNeighbors (boost::shared_array< std::uint8_t > bv) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

std::vector< unsigned int >	getContainingNeighbors (const ExplicitBitVect &ebv) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Detailed Description

class for reading and searching FPB files

basic usage:

FPBReader reader("foo.fpb");
reader.init();
boost::shared_ptr<ExplicitBitVect> ebv = reader.getFP(95);
std::vector<std::pair<double, unsigned int> > nbrs =
    reader.getTanimotoNeighbors(*ebv.get(), 0.70);

Note: this functionality is experimental and the API may change in future releases.

Note on thread safety Operations that involve reading from the FPB file are not thread safe. This means that the init() method is not thread safe and none of the search operations are thread safe when an FPBReader is initialized in lazyRead mode.

Definition at line 57 of file FPBReader.h.

Constructor & Destructor Documentation

◆ FPBReader() [1/4]

RDKit::FPBReader::FPBReader ( )

inline

Definition at line 59 of file FPBReader.h.

◆ FPBReader() [2/4]

RDKit::FPBReader::FPBReader	(	const char *	fname,
		bool	lazyRead = false )

inline

ctor for reading from a named file

Parameters

fname	the name of the file to reads
lazyRead	if set to `false` all fingerprints from the file will be read into memory when `init()` is called.

Definition at line 67 of file FPBReader.h.

◆ FPBReader() [3/4]

RDKit::FPBReader::FPBReader	(	const std::string &	fname,
		bool	lazyRead = false )

inline

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 71 of file FPBReader.h.

◆ FPBReader() [4/4]

RDKit::FPBReader::FPBReader	(	std::istream *	inStream,
		bool	takeOwnership = true,
		bool	lazyRead = false )

inline

ctor for reading from an open istream

Parameters

inStream	the stream to read from
takeOwnership	if set, we will take over ownership of the stream pointer
lazyRead	if set to `false` all fingerprints from the file will be read into memory when `init()` is called.

Some additional notes:

if lazyRead is set, inStream must support the seekg() and tellg() operations.

Definition at line 86 of file FPBReader.h.

◆ ~FPBReader()

RDKit::FPBReader::~FPBReader ( )

inline

Definition at line 93 of file FPBReader.h.

Member Function Documentation

◆ cleanup()

void RDKit::FPBReader::cleanup ( )

inline

cleanup

Cleans up whatever memory was allocated during init()

Definition at line 118 of file FPBReader.h.

◆ getBytes()

boost::shared_array< std::uint8_t > RDKit::FPBReader::getBytes ( unsigned int idx ) const

returns the requested fingerprint as an array of bytes

◆ getContainingNeighbors() [1/3]

std::vector< unsigned int > RDKit::FPBReader::getContainingNeighbors ( boost::shared_array< std::uint8_t > bv ) const

inline

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 241 of file FPBReader.h.

References getContainingNeighbors().

◆ getContainingNeighbors() [2/3]

std::vector< unsigned int > RDKit::FPBReader::getContainingNeighbors ( const ExplicitBitVect & ebv ) const

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

◆ getContainingNeighbors() [3/3]

std::vector< unsigned int > RDKit::FPBReader::getContainingNeighbors ( const std::uint8_t * bv ) const

returns indices of all fingerprints that completely contain this one

(i.e. where all the bits set in the query are also set in the db molecule)

Referenced by getContainingNeighbors().

◆ getFP()

boost::shared_ptr< ExplicitBitVect > RDKit::FPBReader::getFP ( unsigned int idx ) const

returns the requested fingerprint as an ExplicitBitVect

Referenced by operator[]().

◆ getFPIdsInCountRange()

std::pair< unsigned int, unsigned int > RDKit::FPBReader::getFPIdsInCountRange	(	unsigned int	minCount,
		unsigned int	maxCount )

returns beginning and end indices of fingerprints having on-bit counts within the range (including end points)

◆ getId()

std::string RDKit::FPBReader::getId ( unsigned int idx ) const

returns the id of the requested fingerprint

Referenced by operator[]().

◆ getTanimoto() [1/3]

double RDKit::FPBReader::getTanimoto	(	unsigned int	idx,
		boost::shared_array< std::uint8_t >	bv ) const

inline

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 152 of file FPBReader.h.

References getTanimoto().

◆ getTanimoto() [2/3]

double RDKit::FPBReader::getTanimoto	(	unsigned int	idx,
		const ExplicitBitVect &	ebv ) const

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

◆ getTanimoto() [3/3]

double RDKit::FPBReader::getTanimoto	(	unsigned int	idx,
		const std::uint8_t *	bv ) const

returns the tanimoto similarity between the specified fingerprint and the provided fingerprint

Referenced by getTanimoto().

◆ getTanimotoNeighbors() [1/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTanimotoNeighbors	(	boost::shared_array< std::uint8_t >	bv,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

inline

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 175 of file FPBReader.h.

References getTanimotoNeighbors().

◆ getTanimotoNeighbors() [2/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTanimotoNeighbors	(	const ExplicitBitVect &	ebv,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

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

◆ getTanimotoNeighbors() [3/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTanimotoNeighbors	(	const std::uint8_t *	bv,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

returns tanimoto neighbors that are within a similarity threshold

The result vector of (similarity,index) pairs is sorted in order of decreasing similarity

Parameters

bv	the query fingerprint
threshold	the minimum similarity to return
usePopcountScreen	if this is true (the default) the popcount of the neighbors will be used to reduce the number of calculations that need to be done

Referenced by getTanimotoNeighbors().

◆ getTversky() [1/3]

double RDKit::FPBReader::getTversky	(	unsigned int	idx,
		boost::shared_array< std::uint8_t >	bv,
		double	ca,
		double	cb ) const

inline

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 198 of file FPBReader.h.

References getTversky().

◆ getTversky() [2/3]

double RDKit::FPBReader::getTversky	(	unsigned int	idx,
		const ExplicitBitVect &	ebv,
		double	ca,
		double	cb ) const

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

◆ getTversky() [3/3]

double RDKit::FPBReader::getTversky	(	unsigned int	idx,
		const std::uint8_t *	bv,
		double	ca,
		double	cb ) const

returns the Tversky similarity between the specified fingerprint and the provided fingerprint

Parameters

idx	the fingerprint to compare to
bv	the query fingerprint
ca	the Tversky a coefficient
cb	the Tversky a coefficient

Referenced by getTversky().

◆ getTverskyNeighbors() [1/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTverskyNeighbors	(	boost::shared_array< std::uint8_t >	bv,
		double	ca,
		double	cb,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

inline

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 224 of file FPBReader.h.

References getTverskyNeighbors().

◆ getTverskyNeighbors() [2/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTverskyNeighbors	(	const ExplicitBitVect &	ebv,
		double	ca,
		double	cb,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

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

◆ getTverskyNeighbors() [3/3]

std::vector< std::pair< double, unsigned int > > RDKit::FPBReader::getTverskyNeighbors	(	const std::uint8_t *	bv,
		double	ca,
		double	cb,
		double	threshold = 0.7,
		bool	usePopcountScreen = true ) const

returns Tversky neighbors that are within a similarity threshold

The result vector of (similarity,index) pairs is sorted in order of decreasing similarity

Parameters

bv	the query fingerprint
ca	the Tversky a coefficient
cb	the Tversky a coefficient
threshold	the minimum similarity to return
usePopcountScreen	if this is true (the default) the popcount of the neighbors will be used to reduce the number of calculations that need to be done

Referenced by getTverskyNeighbors().

◆ init()

void RDKit::FPBReader::init ( )

Read the data from the file and initialize internal data structures.

This must be called before most of the other methods of this class.

Some notes:

if lazyRead is not set, all fingerprints will be read into memory. This can require substantial amounts of memory for large files.
For large files, this can take a long time.
If lazyRead and takeOwnership are both false it is safe to close and delete inStream after calling init()

Referenced by RDKit::MultiFPBReader::addReader().

◆ length()

unsigned int RDKit::FPBReader::length ( ) const

returns the number of fingerprints

◆ nBits()

unsigned int RDKit::FPBReader::nBits ( ) const

returns the number of bits in our fingerprints

◆ operator[]()

std::pair< boost::shared_ptr< ExplicitBitVect >, std::string > RDKit::FPBReader::operator[] ( unsigned int idx ) const

inline

returns the fingerprint and id of the requested fingerprint

Definition at line 133 of file FPBReader.h.

References getFP(), and getId().

The documentation for this class was generated from the following file:

FPBReader.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ FPBReader() [1/4]

◆ FPBReader() [2/4]

◆ FPBReader() [3/4]

◆ FPBReader() [4/4]

◆ ~FPBReader()

Member Function Documentation

◆ cleanup()

◆ getBytes()

◆ getContainingNeighbors() [1/3]

◆ getContainingNeighbors() [2/3]

◆ getContainingNeighbors() [3/3]

◆ getFP()

◆ getFPIdsInCountRange()

◆ getId()

◆ getTanimoto() [1/3]

◆ getTanimoto() [2/3]

◆ getTanimoto() [3/3]

◆ getTanimotoNeighbors() [1/3]

◆ getTanimotoNeighbors() [2/3]

◆ getTanimotoNeighbors() [3/3]

◆ getTversky() [1/3]

◆ getTversky() [2/3]

◆ getTversky() [3/3]

◆ getTverskyNeighbors() [1/3]

◆ getTverskyNeighbors() [2/3]

◆ getTverskyNeighbors() [3/3]

◆ init()

◆ length()

◆ nBits()

◆ operator[]()