Abstract base for N-point pharmacophore fingerprint generators. More...

#include <NPointPharmacophoreFingerprintGenerator.hpp>

Inheritance diagram for CDPL::Descr::NPointPharmacophoreFingerprintGenerator:

Public Types
typedef std::function< bool(const Pharm::Feature &)>	FeatureFilterFunction
	Type of the generic functor used to filter which features participate in the fingerprint. More...

Public Member Functions
virtual	~NPointPharmacophoreFingerprintGenerator ()
	Virtual destructor. More...

void	setMinFeatureTupleSize (std::size_t min_size)
	Sets the minimum size of generated feature tuples. More...

std::size_t	getMinFeatureTupleSize () const
	Returns the currently configured minimum feature tuple size. More...

void	setMaxFeatureTupleSize (std::size_t max_size)
	Sets the maximum size of generated feature tuples. More...

std::size_t	getMaxFeatureTupleSize () const
	Returns the currently configured maximum feature tuple size. More...

void	setBinSize (double bin_size)
	Sets the size of the bins used to discretize feature-pair distances. More...

double	getBinSize () const
	Returns the currently configured distance bin size. More...

Pharm::PharmacophoreGenerator &	getPharmacophoreGenerator ()
	Returns the internal pharmacophore generator used for the input molecular graph. More...

const Pharm::PharmacophoreGenerator &	getPharmacophoreGenerator () const
	Returns the internal pharmacophore generator used for the input molecular graph. More...

void	setFeatureFilterFunction (const FeatureFilterFunction &func)
	Specifies a predicate that selects which features participate in the fingerprint. More...

const FeatureFilterFunction &	getFeatureFilterFunction () const
	Returns the currently configured feature filter function. More...

Static Public Attributes
static constexpr std::size_t	DEF_MIN_FEATURE_TUPLE_SIZE = 1
	Default minimum size of generated feature tuples. More...

static constexpr std::size_t	DEF_MAX_FEATURE_TUPLE_SIZE = 3
	Default maximum size of generated feature tuples. More...

Protected Member Functions
	NPointPharmacophoreFingerprintGenerator ()
	Constructs the `NPointPharmacophoreFingerprintGenerator` instance. More...

	NPointPharmacophoreFingerprintGenerator (const NPointPharmacophoreFingerprintGenerator &gen)=default
	Copy constructor. More...

void	generate (const Chem::MolecularGraph &molgraph, Util::BitSet &fp)
	Generates the fingerprint of the molecular graph molgraph. More...

void	generate (const Pharm::FeatureContainer &cntnr, Util::BitSet &fp)
	Generates the fingerprint of the feature container cntnr. More...

Static Protected Attributes
static constexpr double	DEF_BIN_SIZE = 2.0
	Default distance bin size. More...

Detailed Description

Abstract base for N-point pharmacophore fingerprint generators.

The base class implements the common machinery for enumerating feature tuples of size in [minTupleSize, maxTupleSize], binning the feature-pair distances of each tuple and setting the corresponding bits of the output fingerprint. The concrete distance (topological vs. 3D) is provided by the derived class via the pure virtual getDistance() hook.

Since: 1.2

Member Typedef Documentation

◆ FeatureFilterFunction

typedef std::function<bool(const Pharm::Feature&)> CDPL::Descr::NPointPharmacophoreFingerprintGenerator::FeatureFilterFunction

Type of the generic functor used to filter which features participate in the fingerprint.

Constructor & Destructor Documentation

◆ ~NPointPharmacophoreFingerprintGenerator()

virtual CDPL::Descr::NPointPharmacophoreFingerprintGenerator::~NPointPharmacophoreFingerprintGenerator ( )

inlinevirtual

Virtual destructor.

◆ NPointPharmacophoreFingerprintGenerator() [1/2]

CDPL::Descr::NPointPharmacophoreFingerprintGenerator::NPointPharmacophoreFingerprintGenerator ( )

protected

Constructs the NPointPharmacophoreFingerprintGenerator instance.

◆ NPointPharmacophoreFingerprintGenerator() [2/2]

CDPL::Descr::NPointPharmacophoreFingerprintGenerator::NPointPharmacophoreFingerprintGenerator ( const NPointPharmacophoreFingerprintGenerator & gen )

protecteddefault

Copy constructor.

Member Function Documentation

◆ setMinFeatureTupleSize()

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::setMinFeatureTupleSize ( std::size_t min_size )

Sets the minimum size of generated feature tuples.

Parameters

min_size The minimum tuple size.

◆ getMinFeatureTupleSize()

std::size_t CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getMinFeatureTupleSize ( ) const

Returns the currently configured minimum feature tuple size.

Returns: The configured minimum tuple size.

◆ setMaxFeatureTupleSize()

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::setMaxFeatureTupleSize ( std::size_t max_size )

Sets the maximum size of generated feature tuples.

Parameters

max_size The maximum tuple size.

◆ getMaxFeatureTupleSize()

std::size_t CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getMaxFeatureTupleSize ( ) const

Returns the currently configured maximum feature tuple size.

Returns: The configured maximum tuple size.

◆ setBinSize()

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::setBinSize ( double bin_size )

Sets the size of the bins used to discretize feature-pair distances.

Parameters

bin_size The bin size.

◆ getBinSize()

double CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getBinSize ( ) const

Returns the currently configured distance bin size.

Returns: The configured bin size.

◆ getPharmacophoreGenerator() [1/2]

Pharm::PharmacophoreGenerator& CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getPharmacophoreGenerator ( )

Returns the internal pharmacophore generator used for the input molecular graph.

Returns: A reference to the pharmacophore generator.

◆ getPharmacophoreGenerator() [2/2]

const Pharm::PharmacophoreGenerator& CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getPharmacophoreGenerator ( ) const

Returns the internal pharmacophore generator used for the input molecular graph.

Returns: A const reference to the pharmacophore generator.

◆ setFeatureFilterFunction()

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::setFeatureFilterFunction ( const FeatureFilterFunction & func )

Specifies a predicate that selects which features participate in the fingerprint.

Parameters

func	The feature filter function.

Since: 1.3

◆ getFeatureFilterFunction()

const FeatureFilterFunction& CDPL::Descr::NPointPharmacophoreFingerprintGenerator::getFeatureFilterFunction ( ) const

Returns the currently configured feature filter function.

Returns: The configured feature filter function.

Since: 1.3

◆ generate() [1/2]

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	fp
	)

protected

Generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
fp	The output bitset.

◆ generate() [2/2]

void CDPL::Descr::NPointPharmacophoreFingerprintGenerator::generate	(	const Pharm::FeatureContainer &	cntnr,
		Util::BitSet &	fp
	)

protected

Generates the fingerprint of the feature container cntnr.

Parameters

cntnr	The feature container.
fp	The output bitset.

Member Data Documentation

◆ DEF_MIN_FEATURE_TUPLE_SIZE

constexpr std::size_t CDPL::Descr::NPointPharmacophoreFingerprintGenerator::DEF_MIN_FEATURE_TUPLE_SIZE = 1

staticconstexpr

Default minimum size of generated feature tuples.

◆ DEF_MAX_FEATURE_TUPLE_SIZE

constexpr std::size_t CDPL::Descr::NPointPharmacophoreFingerprintGenerator::DEF_MAX_FEATURE_TUPLE_SIZE = 3

staticconstexpr

Default maximum size of generated feature tuples.

◆ DEF_BIN_SIZE

constexpr double CDPL::Descr::NPointPharmacophoreFingerprintGenerator::DEF_BIN_SIZE = 2.0

staticconstexprprotected

Default distance bin size.

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

NPointPharmacophoreFingerprintGenerator.hpp

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ FeatureFilterFunction

Constructor & Destructor Documentation

◆ ~NPointPharmacophoreFingerprintGenerator()

◆ NPointPharmacophoreFingerprintGenerator() [1/2]

◆ NPointPharmacophoreFingerprintGenerator() [2/2]

Member Function Documentation

◆ setMinFeatureTupleSize()

◆ getMinFeatureTupleSize()

◆ setMaxFeatureTupleSize()

◆ getMaxFeatureTupleSize()

◆ setBinSize()

◆ getBinSize()

◆ getPharmacophoreGenerator() [1/2]

◆ getPharmacophoreGenerator() [2/2]

◆ setFeatureFilterFunction()

◆ getFeatureFilterFunction()

◆ generate() [1/2]

◆ generate() [2/2]

Member Data Documentation

◆ DEF_MIN_FEATURE_TUPLE_SIZE

◆ DEF_MAX_FEATURE_TUPLE_SIZE

◆ DEF_BIN_SIZE