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