class for reading and searching multiple FPB files More...

#include <MultiFPBReader.h>

Public Types
typedef std::tuple< double, unsigned int, unsigned int >	ResultTuple

Public Member Functions
	MultiFPBReader ()

	MultiFPBReader (bool initOnSearch)

	MultiFPBReader (std::vector< FPBReader * > &readers, bool takeOwnership=false, bool initOnSearch=false)

	~MultiFPBReader ()

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

unsigned int	length () const
	returns the number of readers

unsigned int	nBits () const

FPBReader *	getReader (unsigned int which)
	returns a particular reader

unsigned int	addReader (FPBReader *rdr)
	adds a new FPBReader to our list

std::vector< ResultTuple >	getTanimotoNeighbors (const std::uint8_t *bv, double threshold=0.7, int numThreads=1) const
	returns tanimoto neighbors that are within a similarity threshold

std::vector< ResultTuple >	getTanimotoNeighbors (boost::shared_array< std::uint8_t > bv, double threshold=0.7, int numThreads=1) 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< ResultTuple >	getTanimotoNeighbors (const ExplicitBitVect &ebv, double threshold=0.7, int numThreads=1) 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< ResultTuple >	getTverskyNeighbors (const std::uint8_t *bv, double ca, double cb, double threshold=0.7, int numThreads=1) const
	returns Tversky neighbors that are within a similarity threshold

std::vector< ResultTuple >	getTverskyNeighbors (boost::shared_array< std::uint8_t > bv, double ca, double cb, double threshold=0.7, int numThreads=1) 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< ResultTuple >	getTverskyNeighbors (const ExplicitBitVect &ebv, double ca, double cb, double threshold=0.7, int numThreads=1) 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< unsigned int, unsigned int > >	getContainingNeighbors (const std::uint8_t *bv, int numThreads=1) const
	returns indices of all fingerprints that completely contain this one

std::vector< std::pair< unsigned int, unsigned int > >	getContainingNeighbors (boost::shared_array< std::uint8_t > bv, int numThreads=1) 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< unsigned int, unsigned int > >	getContainingNeighbors (const ExplicitBitVect &ebv, int numThreads=1) 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 multiple FPB files

basic usage:

FPBReader r1("foo1.fpb"),r2("foo2.fpb");
std::vector<FPBReader *> readers;
readers.append(&r1);
readers.append(&r2);
MultiFPBReader fpbs(readers);
fpbs.init();
boost::shared_ptr<ExplicitBitVect> ebv = fpbs.getReader(0)->getFP(95);
std::vector<std::tuple<double,unsigned int, unsigned int> > nbrs =
    fpbs.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 FPB files 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 53 of file MultiFPBReader.h.

Member Typedef Documentation

◆ ResultTuple

typedef std::tuple<double, unsigned int, unsigned int> RDKit::MultiFPBReader::ResultTuple

Definition at line 55 of file MultiFPBReader.h.

Constructor & Destructor Documentation

◆ MultiFPBReader() [1/3]

RDKit::MultiFPBReader::MultiFPBReader ( )

inline

Definition at line 56 of file MultiFPBReader.h.

◆ MultiFPBReader() [2/3]

RDKit::MultiFPBReader::MultiFPBReader ( bool initOnSearch )

inline

Parameters

initOnSearch if this is true, the init() method on child readers will not be called until the first search is done. This is useful with large FPB readers.

Definition at line 63 of file MultiFPBReader.h.

◆ MultiFPBReader() [3/3]

RDKit::MultiFPBReader::MultiFPBReader	(	std::vector< FPBReader * > &	readers,
		bool	takeOwnership = `false`,
		bool	initOnSearch = `false`
	)

Parameters

readers	the set of FPBReader objects to use.
takeOwnership	if true, we own the memory for the FPBReaders
initOnSearch	if this is true, the `init()` method on child readers will not be called until the first search is done. This is useful with large FPB readers.

◆ ~MultiFPBReader()

RDKit::MultiFPBReader::~MultiFPBReader ( )

inline

Definition at line 77 of file MultiFPBReader.h.

Member Function Documentation

◆ addReader()

unsigned int RDKit::MultiFPBReader::addReader ( FPBReader * rdr )

inline

adds a new FPBReader to our list

This does no error checking on the reader, so be careful.

If takeOwnership is true then we will take ownership of the memory.

Parameters

rdr	the reader to add. If we have already been initialized, the reader's `init()` method will be called

Returns: a count of the current number of readers

Definition at line 121 of file MultiFPBReader.h.

References RDKit::FPBReader::init(), and PRECONDITION.

◆ getContainingNeighbors() [1/3]

std::vector< std::pair< unsigned int, unsigned int > > RDKit::MultiFPBReader::getContainingNeighbors	(	boost::shared_array< std::uint8_t >	bv,
		int	numThreads = `1`
	)		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 193 of file MultiFPBReader.h.

◆ getContainingNeighbors() [2/3]

std::vector< std::pair< unsigned int, unsigned int > > RDKit::MultiFPBReader::getContainingNeighbors	(	const ExplicitBitVect &	ebv,
		int	numThreads = `1`
	)		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< std::pair< unsigned int, unsigned int > > RDKit::MultiFPBReader::getContainingNeighbors	(	const std::uint8_t *	bv,
		int	numThreads = `1`
	)		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)

◆ getReader()

FPBReader * RDKit::MultiFPBReader::getReader ( unsigned int which )

returns a particular reader

Parameters

which the reader to return

◆ getTanimotoNeighbors() [1/3]

std::vector< ResultTuple > RDKit::MultiFPBReader::getTanimotoNeighbors	(	boost::shared_array< std::uint8_t >	bv,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		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 146 of file MultiFPBReader.h.

◆ getTanimotoNeighbors() [2/3]

std::vector< ResultTuple > RDKit::MultiFPBReader::getTanimotoNeighbors	(	const ExplicitBitVect &	ebv,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		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< ResultTuple > RDKit::MultiFPBReader::getTanimotoNeighbors	(	const std::uint8_t *	bv,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		const

returns tanimoto neighbors that are within a similarity threshold

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

Parameters

bv	the query fingerprint
threshold	the minimum similarity to return
numThreads	Sets the number of threads to use (more than one thread will only be used if the RDKit was build with multithread support) If set to zero, the max supported by the system will be used.

◆ getTverskyNeighbors() [1/3]

std::vector< ResultTuple > RDKit::MultiFPBReader::getTverskyNeighbors	(	boost::shared_array< std::uint8_t >	bv,
		double	ca,
		double	cb,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		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 MultiFPBReader.h.

◆ getTverskyNeighbors() [2/3]

std::vector< ResultTuple > RDKit::MultiFPBReader::getTverskyNeighbors	(	const ExplicitBitVect &	ebv,
		double	ca,
		double	cb,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		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< ResultTuple > RDKit::MultiFPBReader::getTverskyNeighbors	(	const std::uint8_t *	bv,
		double	ca,
		double	cb,
		double	threshold = `0.7`,
		int	numThreads = `1`
	)		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
numThreads	Sets the number of threads to use (more than one thread will only be used if the RDKit was build with multithread support) If set to zero, the max supported by the system will be used.

◆ init()

void RDKit::MultiFPBReader::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. It calls the init() method on each of the child FPBReaders

◆ length()

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

inline

returns the number of readers

Definition at line 96 of file MultiFPBReader.h.

◆ nBits()

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

returns the number of bits in our fingerprints (all readers are expected to have the same length)

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

MultiFPBReader.h

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ResultTuple

Constructor & Destructor Documentation

◆ MultiFPBReader() [1/3]

◆ MultiFPBReader() [2/3]

◆ MultiFPBReader() [3/3]

◆ ~MultiFPBReader()

Member Function Documentation

◆ addReader()

◆ getContainingNeighbors() [1/3]

◆ getContainingNeighbors() [2/3]

◆ getContainingNeighbors() [3/3]

◆ getReader()

◆ getTanimotoNeighbors() [1/3]

◆ getTanimotoNeighbors() [2/3]

◆ getTanimotoNeighbors() [3/3]

◆ getTverskyNeighbors() [1/3]

◆ getTverskyNeighbors() [2/3]

◆ getTverskyNeighbors() [3/3]

◆ init()

◆ length()

◆ nBits()