CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator Class Reference

N-point pharmacophore fingerprint generator that uses topological feature distances. More...

#include <NPoint2DPharmacophoreFingerprintGenerator.hpp>

Inheritance diagram for CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator:

Public Types
enum	FeatureDistanceType {   MIN_PATH_LENGTH ,   MAX_PATH_LENGTH ,   AVG_PATH_LENGTH }
	Specifies how the topological distance between two features is derived from the topological distances between their underlying atoms. More...
typedef std::shared_ptr< NPoint2DPharmacophoreFingerprintGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated NPoint2DPharmacophoreFingerprintGenerator instances. More...
Public Types inherited from CDPL::Descr::NPointPharmacophoreFingerprintGenerator
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
	NPoint2DPharmacophoreFingerprintGenerator ()
	Constructs the NPoint2DPharmacophoreFingerprintGenerator instance. More...
	NPoint2DPharmacophoreFingerprintGenerator (const NPoint2DPharmacophoreFingerprintGenerator &gen)=default
	Copy constructor. More...
	NPoint2DPharmacophoreFingerprintGenerator (const Chem::MolecularGraph &molgraph, Util::BitSet &fp)
	Constructs the NPoint2DPharmacophoreFingerprintGenerator instance and generates the fingerprint of molgraph. More...
void	setFeatureDistanceType (FeatureDistanceType dist_type)
	Sets the type of feature-pair topological distance to use. More...
FeatureDistanceType	getFeatureDistanceType () const
	Returns the currently configured feature distance type. More...
void	generate (const Chem::MolecularGraph &molgraph, Util::BitSet &fp)
	Generates the fingerprint of the molecular graph molgraph. More...
Public Member Functions inherited from CDPL::Descr::NPointPharmacophoreFingerprintGenerator
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 double	DEF_BIN_SIZE = 2.0
	Default distance bin size. More...
static constexpr FeatureDistanceType	DEF_FEATURE_DISTANCE_TYPE = MIN_PATH_LENGTH
	Default feature distance type. More...
Static Public Attributes inherited from CDPL::Descr::NPointPharmacophoreFingerprintGenerator
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...

Additional Inherited Members
Protected Member Functions inherited from CDPL::Descr::NPointPharmacophoreFingerprintGenerator
	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 inherited from CDPL::Descr::NPointPharmacophoreFingerprintGenerator
static constexpr double	DEF_BIN_SIZE = 2.0
	Default distance bin size. More...

Detailed Description

N-point pharmacophore fingerprint generator that uses topological feature distances.

The fingerprint encodes the binned topological distances between all pairs of features in tuples generated from a molecular graph. The choice of how feature-pair topological distance is computed (min, max or average over the topological distances between the underlying atoms) is configurable via FeatureDistanceType.

Since

1.2

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<NPoint2DPharmacophoreFingerprintGenerator> CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated NPoint2DPharmacophoreFingerprintGenerator instances.

Member Enumeration Documentation

FeatureDistanceType

enum CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::FeatureDistanceType

Specifies how the topological distance between two features is derived from the topological distances between their underlying atoms.

Enumerator
MIN_PATH_LENGTH	Use the minimum topological distance between any two underlying atoms.
MAX_PATH_LENGTH	Use the maximum topological distance between any two underlying atoms.
AVG_PATH_LENGTH	Use the average topological distance between all pairs of underlying atoms.

Constructor & Destructor Documentation

NPoint2DPharmacophoreFingerprintGenerator() [1/3]

CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::NPoint2DPharmacophoreFingerprintGenerator

(

)

Constructs the NPoint2DPharmacophoreFingerprintGenerator instance.

NPoint2DPharmacophoreFingerprintGenerator() [2/3]

CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::NPoint2DPharmacophoreFingerprintGenerator ( const NPoint2DPharmacophoreFingerprintGenerator &  gen )

default

Copy constructor.

NPoint2DPharmacophoreFingerprintGenerator() [3/3]

CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::NPoint2DPharmacophoreFingerprintGenerator	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	fp
	)

Constructs the NPoint2DPharmacophoreFingerprintGenerator instance and generates the fingerprint of molgraph.

Parameters

molgraph	The molecular graph.
fp	The output bitset.

Member Function Documentation

setFeatureDistanceType()

void CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::setFeatureDistanceType

(

FeatureDistanceType

dist_type

)

Sets the type of feature-pair topological distance to use.

Parameters

dist_type

The feature distance type.

getFeatureDistanceType()

FeatureDistanceType CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::getFeatureDistanceType

(

)

const

Returns the currently configured feature distance type.

Returns

The configured feature distance type.

generate()

void CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		Util::BitSet &	fp
	)

Generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
fp	The output bitset.

Member Data Documentation

DEF_BIN_SIZE

constexpr double CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::DEF_BIN_SIZE = 2.0

staticconstexpr

Default distance bin size.

Since

1.3

DEF_FEATURE_DISTANCE_TYPE

constexpr FeatureDistanceType CDPL::Descr::NPoint2DPharmacophoreFingerprintGenerator::DEF_FEATURE_DISTANCE_TYPE = MIN_PATH_LENGTH

staticconstexpr

Default feature distance type.

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

• NPoint2DPharmacophoreFingerprintGenerator.hpp