CDPL::Descr Namespace Reference

Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors. More...

Classes
class	AtomAutoCorrelation3DVectorCalculator
	AtomAutoCorrelation3DVectorCalculator. More...
class	AtomRDFCodeCalculator
	AtomRDFCodeCalculator. More...
class	AutoCorrelation2DVectorCalculator
	AutoCorrelation2DVectorCalculator. More...
class	AutoCorrelation3DVectorCalculator
	AutoCorrelation3DVectorCalculator. More...
class	BCUTDescriptorCalculator
	BCUTDescriptorCalculator. More...
class	BurdenMatrixGenerator
	BurdenMatrixGenerator. More...
class	CircularFingerprintGenerator
	CircularFingerprintGenerator. More...
class	FeatureAutoCorrelation3DVectorCalculator
	FeatureAutoCorrelation3DVectorCalculator. More...
class	FeatureRDFCodeCalculator
	FeatureRDFCodeCalculator. More...
class	MACCSFingerprintGenerator
	Generation of 166 bit MACCS key fingerprints. More...
class	MolecularComplexityCalculator
	MolecularComplexityCalculator. More...
class	MoleculeAutoCorr2DDescriptorCalculator
	MoleculeAutoCorr2DDescriptorCalculator. More...
class	MoleculeAutoCorr3DDescriptorCalculator
	MoleculeAutoCorr3DDescriptorCalculator. More...
class	MoleculeRDFDescriptorCalculator
	MoleculeRDFDescriptorCalculator. More...
class	NPoint2DPharmacophoreFingerprintGenerator
	NPoint2DPharmacophoreFingerprintGenerator. More...
class	NPoint3DPharmacophoreFingerprintGenerator
	NPoint3DPharmacophoreFingerprintGenerator. More...
class	NPointPharmacophoreFingerprintGenerator
	NPointPharmacophoreFingerprintGenerator. More...
class	PathFingerprintGenerator
	PathFingerprintGenerator. More...
class	PharmacophoreAutoCorr3DDescriptorCalculator
	PharmacophoreAutoCorr3DDescriptorCalculator. More...
class	PharmacophoreRDFDescriptorCalculator
	PharmacophoreRDFDescriptorCalculator. More...
class	PubChemFingerprintGenerator
	Generation of 881 bit PubChem fingerprints. More...
class	RDFCodeCalculator
	RDFCodeCalculator. More...

Functions
CDPL_DESCR_API double	calcGeometricalRadius (const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func)
CDPL_DESCR_API double	calcGeometricalDiameter (const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func)
CDPL_DESCR_API double	calcGeometricalRadius (const Chem::Entity3DContainer &cntnr)
CDPL_DESCR_API double	calcGeometricalDiameter (const Chem::Entity3DContainer &cntnr)
CDPL_DESCR_API std::size_t	calcTopologicalRadius (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API std::size_t	calcTopologicalDiameter (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcRingComplexity (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcMolecularComplexity (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcKierShape1 (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcKierShape2 (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcKierShape3 (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API std::size_t	calcWienerIndex (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcRandicIndex (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API std::size_t	calcZagrebIndex1 (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API std::size_t	calcZagrebIndex2 (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API std::size_t	calcTotalWalkCount (const Chem::MolecularGraph &molgraph)
CDPL_DESCR_API double	calcTanimotoSimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Tanimoto Similarity Measure [CITB] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcCosineSimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Cosine Similarity Measure [WCOS] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcEuclideanSimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Euclidean Similarity Measure [GSIM] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcManhattanSimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Manhattan Similarity Measure [GSIM] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcDiceSimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Dice Similarity Measure [GSIM] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcTverskySimilarity (const Util::BitSet &bs1, const Util::BitSet &bs2, double a, double b)
	Calculates the Tversky Similarity Measure [GSIM] for the given bitsets bs1 and bs2. More...
CDPL_DESCR_API std::size_t	calcHammingDistance (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Hamming Distance [WHAM, CITB] between the bitsets bs1 and bs2. More...
CDPL_DESCR_API double	calcEuclideanDistance (const Util::BitSet &bs1, const Util::BitSet &bs2)
	Calculates the Euclidean Distance [CITB] between the bitsets bs1 and bs2. More...

Detailed Description

Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors.

Function Documentation

calcGeometricalRadius() [1/2]

CDPL_DESCR_API double CDPL::Descr::calcGeometricalRadius	(	const Chem::AtomContainer &	cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func
	)

calcGeometricalDiameter() [1/2]

CDPL_DESCR_API double CDPL::Descr::calcGeometricalDiameter	(	const Chem::AtomContainer &	cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func
	)

calcGeometricalRadius() [2/2]

CDPL_DESCR_API double CDPL::Descr::calcGeometricalRadius

(

const Chem::Entity3DContainer &

cntnr

)

calcGeometricalDiameter() [2/2]

CDPL_DESCR_API double CDPL::Descr::calcGeometricalDiameter

(

const Chem::Entity3DContainer &

cntnr

)

calcTopologicalRadius()

CDPL_DESCR_API std::size_t CDPL::Descr::calcTopologicalRadius

(

const Chem::MolecularGraph &

molgraph

)

calcTopologicalDiameter()

CDPL_DESCR_API std::size_t CDPL::Descr::calcTopologicalDiameter

(

const Chem::MolecularGraph &

molgraph

)

calcRingComplexity()

CDPL_DESCR_API double CDPL::Descr::calcRingComplexity

(

const Chem::MolecularGraph &

molgraph

)

calcMolecularComplexity()

CDPL_DESCR_API double CDPL::Descr::calcMolecularComplexity

(

const Chem::MolecularGraph &

molgraph

)

calcKierShape1()

CDPL_DESCR_API double CDPL::Descr::calcKierShape1

(

const Chem::MolecularGraph &

molgraph

)

calcKierShape2()

CDPL_DESCR_API double CDPL::Descr::calcKierShape2

(

const Chem::MolecularGraph &

molgraph

)

calcKierShape3()

CDPL_DESCR_API double CDPL::Descr::calcKierShape3

(

const Chem::MolecularGraph &

molgraph

)

calcWienerIndex()

CDPL_DESCR_API std::size_t CDPL::Descr::calcWienerIndex

(

const Chem::MolecularGraph &

molgraph

)

calcRandicIndex()

CDPL_DESCR_API double CDPL::Descr::calcRandicIndex

(

const Chem::MolecularGraph &

molgraph

)

calcZagrebIndex1()

CDPL_DESCR_API std::size_t CDPL::Descr::calcZagrebIndex1

(

const Chem::MolecularGraph &

molgraph

)

calcZagrebIndex2()

CDPL_DESCR_API std::size_t CDPL::Descr::calcZagrebIndex2

(

const Chem::MolecularGraph &

molgraph

)

calcTotalWalkCount()

CDPL_DESCR_API std::size_t CDPL::Descr::calcTotalWalkCount

(

const Chem::MolecularGraph &

molgraph

)

calcTanimotoSimilarity()

CDPL_DESCR_API double CDPL::Descr::calcTanimotoSimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Tanimoto Similarity Measure [CITB] for the given bitsets bs1 and bs2.

The Tanimoto Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \frac{N_{ab}}{N_a + N_b - N_{ab}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set in the first bitset and \( N_b \) is the number of bits that are set in the second bitset.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated similarity measure.

calcCosineSimilarity()

CDPL_DESCR_API double CDPL::Descr::calcCosineSimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Cosine Similarity Measure [WCOS] for the given bitsets bs1 and bs2.

The Cosine Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \frac{N_{ab}}{\sqrt{N_a * N_b}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set in the first bitset and \( N_b \) is the number of bits that are set in the second bitset.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated similarity measure.

calcEuclideanSimilarity()

CDPL_DESCR_API double CDPL::Descr::calcEuclideanSimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Euclidean Similarity Measure [GSIM] for the given bitsets bs1 and bs2.

The Euclidean Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \sqrt{\frac{N_{ab} + N_{!ab}}{N_a + N_b + N_{ab} + N_{!ab}}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set only in the first bitset, \( N_b \) is the number of bits that are set only in the second bitset and \( N_{!ab} \) is the number of bits that are not set in both bitsets.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated similarity measure.

calcManhattanSimilarity()

CDPL_DESCR_API double CDPL::Descr::calcManhattanSimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Manhattan Similarity Measure [GSIM] for the given bitsets bs1 and bs2.

The Manhattan Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \frac{N_a + N_b}{N_a + N_b + N_{ab} + N_{!ab}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set only in the first bitset, \( N_b \) is the number of bits that are set only in the second bitset and \( N_{!ab} \) is the number of bits that are not set in both bitsets.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated similarity measure.

calcDiceSimilarity()

CDPL_DESCR_API double CDPL::Descr::calcDiceSimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Dice Similarity Measure [GSIM] for the given bitsets bs1 and bs2.

The Dice Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \frac{2 * N_{ab}}{N_a + N_b + 2 * N_{ab}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are only set in the first bitset and \( N_b \) is the number of bits that are only set in the second bitset.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated similarity measure.

calcTverskySimilarity()

CDPL_DESCR_API double CDPL::Descr::calcTverskySimilarity	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2,
		double	a,
		double	b
	)

Calculates the Tversky Similarity Measure [GSIM] for the given bitsets bs1 and bs2.

The Tversky Similarity Measure \( S_{ab} \) is calculated by:

\[ S_{ab} = \frac{N_{ab}}{a * N_a + b * N_b + N_{ab}} \]

where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are only set in the first bitset and \( N_b \) is the number of bits that are only set in the second bitset. \( a \) and \( b \) are bitset contribution weighting factors.

The Tversky Measure is asymmetric. Setting the parameters \( a = b = 1.0 \) is identical to using the Tanimoto measure.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.
a	Weights the contribution of the first bitset.
b	Weights the contribution of the second bitset.

Returns

The calculated similarity measure.

calcHammingDistance()

CDPL_DESCR_API std::size_t CDPL::Descr::calcHammingDistance	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Hamming Distance [WHAM, CITB] between the bitsets bs1 and bs2.

The Hamming Distance \( D_{ab} \) is calculated by:

\[ D_{ab} = N_a + N_b \]

where \( N_a \) is the number of bits that are set in the first bitset but not in the second bitset and \( N_b \) is the number of bits that are set in the second bitset but not in the first one.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated distance.

calcEuclideanDistance()

CDPL_DESCR_API double CDPL::Descr::calcEuclideanDistance	(	const Util::BitSet &	bs1,
		const Util::BitSet &	bs2
	)

Calculates the Euclidean Distance [CITB] between the bitsets bs1 and bs2.

The Euclidean Distance \( D_{ab} \) is calculated by:

\[ D_{ab} = \sqrt{N_a + N_b} \]

where \( N_a \) is the number of bits that are set in the first bitset but not in the second bitset and \( N_b \) is the number of bits that are set in the second bitset but not in the first one.

If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.

Parameters

bs1	The first bitset.
bs2	The second bitset.

Returns

The calculated distance.