Classes
struct	CustomFeature

class	ShapeInput

struct	ShapeInputOptions

struct	ShapeOverlayOptions

struct	SingleConformerAlignment

Functions
RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	AlignShape (const ShapeInput &refShape, ShapeInput &fitShape, RDGeom::Transform3D *xform=nullptr, const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions())
	Align a shape onto a reference shape.

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	AlignMolecule (const ShapeInput &refShape, ROMol &fit, const ShapeInputOptions &fitOpts=ShapeInputOptions(), RDGeom::Transform3D *xform=nullptr, const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), int fitConfId=-1)
	Align a molecule to a reference shape.

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	AlignMolecule (const ROMol &ref, ROMol &fit, const ShapeInputOptions &refOpts=ShapeInputOptions(), const ShapeInputOptions &fitOpts=ShapeInputOptions(), RDGeom::Transform3D *xform=nullptr, const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), int refConfId=-1, int fitConfId=-1)
	Align a molecule to a reference molecule.

RDKIT_GAUSSIANSHAPE_EXPORT void	ScoreMoleculeAllConformers (const ROMol &ref, const ROMol &fit, int &refConfId, int &fitConfId, std::vector< std::vector< double > > &combScores, const ShapeInputOptions &refOpts=ShapeInputOptions(), const ShapeInputOptions &fitOpts=ShapeInputOptions(), const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), RDGeom::Transform3D *xform=nullptr)

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	ScoreShape (const ShapeInput &refShape, const ShapeInput &fitShape, const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), std::pair< double, double > *overlapVols=nullptr)
	Score the overlap of a shape to a reference shape without moving.

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	ScoreMolecule (const ShapeInput &refShape, const ROMol &fit, const ShapeInputOptions &fitOpts=ShapeInputOptions(), const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), int fitConfId=-1, std::pair< double, double > *overlapVols=nullptr)
	Score the overlap of a molecule to a reference shape without moving.

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 >	ScoreMolecule (const ROMol &ref, const ROMol &fit, const ShapeInputOptions &refOpts=ShapeInputOptions(), const ShapeInputOptions &fitOpts=ShapeInputOptions(), const ShapeOverlayOptions &overlayOpts=ShapeOverlayOptions(), int refConfId=-1, int fitConfId=-1, std::pair< double, double > *overlapVols=nullptr)
	Score the overlap of a molecule to a reference molecule without moving.

RDKIT_GAUSSIANSHAPE_EXPORT void	findFeatures (const Conformer &conf, std::vector< CustomFeature > &features, const std::optional< std::vector< unsigned int > > &atomSubset=std::nullopt)

RDKIT_GAUSSIANSHAPE_EXPORT RDGeom::Point3D	computeFeaturePos (const Conformer &conf, const std::vector< unsigned int > &ats)

RDKIT_GAUSSIANSHAPE_EXPORT RDGeom::Transform3D	quatTransToTransform (const double quat, const double trans)

RDKIT_GAUSSIANSHAPE_EXPORT void	applyTransformToShape (std::vector< double > &shape, const RDGeom::Transform3D &xform)

RDKIT_GAUSSIANSHAPE_EXPORT void	applyTransformToShape (const double inShape, double outShape, size_t numPoints, const RDGeom::Transform3D &xform)

RDKIT_GAUSSIANSHAPE_EXPORT void	translateShape (std::vector< double > &shape, const RDGeom::Point3D &translation)

RDKIT_GAUSSIANSHAPE_EXPORT void	translateShape (const double inShape, double outShape, size_t numPoints, const RDGeom::Point3D &translation)

RDKIT_GAUSSIANSHAPE_EXPORT double	maxScore (double v1, double v2, double c1, double c2, const ShapeOverlayOptions &overlayOpts)

std::ostream &	operator<< (std::ostream &os, const StartMode &sm)

RDKIT_GAUSSIANSHAPE_EXPORT double	calcVolAndGrads (const double ref, const double refAlphas, int numRefPts, const boost::dynamic_bitset<> refCarbonRadii, const double fit, const double fitAlphas, int numFitPts, const boost::dynamic_bitset<> fitCarbonRadii, std::vector< double > &gradConverters, const bool useCutoff, const double distCutoff2, const double quat=nullptr, double gradients=nullptr)

RDKIT_GAUSSIANSHAPE_EXPORT double	calcVolAndGrads (const double ref, const double refAlphas, int numRefPts, const int refTypes, const double fit, const double fitAlphas, int numFitPts, const int fitTypes, int numFitShape, std::vector< double > &gradConverters, const bool useCutoff, const double distCutoff2, const double quat, double gradients)

Variables
constexpr double	CARBON_RAD = 1.70

constexpr double	DUMMY_RAD = 2.16

constexpr double	P = 2.7

constexpr double	KAPPA = 2.41798793102

Function Documentation

◆ AlignMolecule() [1/2]

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::AlignMolecule	(	const ROMol &	ref,
		ROMol &	fit,
		const ShapeInputOptions &	refOpts = ShapeInputOptions(),
		const ShapeInputOptions &	fitOpts = ShapeInputOptions(),
		RDGeom::Transform3D *	xform = nullptr,
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		int	refConfId = -1,
		int	fitConfId = -1 )

Align a molecule to a reference molecule.

Parameters

ref	the reference molecule
fit	the molecule to align
refOpts	the options for creating the ref shape
fitOpts	the options for creating the fit shape
xform	if passed in as non-null, will be populated with the transformation matrix that aligns fit onto ref.
overlayOpts	options for setting up and running the overlay
refConfId	(optional) the conformer to use for the reference molecule
fitConfId	(optional) the conformer to use for the fit molecule

Returns: an array of the combination score of the shape Tversky value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ AlignMolecule() [2/2]

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::AlignMolecule	(	const ShapeInput &	refShape,
		ROMol &	fit,
		const ShapeInputOptions &	fitOpts = ShapeInputOptions(),
		RDGeom::Transform3D *	xform = nullptr,
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		int	fitConfId = -1 )

Align a molecule to a reference shape.

Parameters

refShape	the reference shape
fit	the molecule to align
fitOpts	the options for creating the fit shape
xform	if passed in as non-null, will be populated with the transformation matrix that aligns fit onto ref.
overlayOpts	options for setting up and running the overlay
fitConfId	(optional) the conformer to use for the fit molecule

Returns: an array of the combination score of the shape Tversky value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ AlignShape()

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::AlignShape	(	const ShapeInput &	refShape,
		ShapeInput &	fitShape,
		RDGeom::Transform3D *	xform = nullptr,
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions() )

Align a shape onto a reference shape.

Parameters

refShape	the reference shape
fitShape	the shape to align
xform	if passed in as non-null, will be populated with the transformation matrix that aligns fit onto ref.
overlayOpts	options for the overlay

Returns: an array of the combination score of the shape Tversky value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ applyTransformToShape() [1/2]

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::applyTransformToShape	(	const double *	inShape,
		double *	outShape,
		size_t	numPoints,
		const RDGeom::Transform3D &	xform )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ applyTransformToShape() [2/2]

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::applyTransformToShape	(	std::vector< double > &	shape,
		const RDGeom::Transform3D &	xform )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ calcVolAndGrads() [1/2]

RDKIT_GAUSSIANSHAPE_EXPORT double RDKit::GaussianShape::calcVolAndGrads	(	const double *	ref,
		const double *	refAlphas,
		int	numRefPts,
		const boost::dynamic_bitset<> *	refCarbonRadii,
		const double *	fit,
		const double *	fitAlphas,
		int	numFitPts,
		const boost::dynamic_bitset<> *	fitCarbonRadii,
		std::vector< double > &	gradConverters,
		const bool	useCutoff,
		const double	distCutoff2,
		const double *	quat = nullptr,
		double *	gradients = nullptr )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ calcVolAndGrads() [2/2]

RDKIT_GAUSSIANSHAPE_EXPORT double RDKit::GaussianShape::calcVolAndGrads	(	const double *	ref,
		const double *	refAlphas,
		int	numRefPts,
		const int *	refTypes,
		const double *	fit,
		const double *	fitAlphas,
		int	numFitPts,
		const int *	fitTypes,
		int	numFitShape,
		std::vector< double > &	gradConverters,
		const bool	useCutoff,
		const double	distCutoff2,
		const double *	quat,
		double *	gradients )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ computeFeaturePos()

RDKIT_GAUSSIANSHAPE_EXPORT RDGeom::Point3D RDKit::GaussianShape::computeFeaturePos	(	const Conformer &	conf,
		const std::vector< unsigned int > &	ats )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ findFeatures()

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::findFeatures	(	const Conformer &	conf,
		std::vector< CustomFeature > &	features,
		const std::optional< std::vector< unsigned int > > &	atomSubset = std::nullopt )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ maxScore()

RDKIT_GAUSSIANSHAPE_EXPORT double RDKit::GaussianShape::maxScore	(	double	v1,
		double	v2,
		double	c1,
		double	c2,
		const ShapeOverlayOptions &	overlayOpts )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ operator<<()

std::ostream & RDKit::GaussianShape::operator<<	(	std::ostream &	os,
		const StartMode &	sm )

inline

Definition at line 86 of file ShapeOverlayOptions.h.

◆ quatTransToTransform()

RDKIT_GAUSSIANSHAPE_EXPORT RDGeom::Transform3D RDKit::GaussianShape::quatTransToTransform	(	const double *	quat,
		const double *	trans )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ ScoreMolecule() [1/2]

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::ScoreMolecule	(	const ROMol &	ref,
		const ROMol &	fit,
		const ShapeInputOptions &	refOpts = ShapeInputOptions(),
		const ShapeInputOptions &	fitOpts = ShapeInputOptions(),
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		int	refConfId = -1,
		int	fitConfId = -1,
		std::pair< double, double > *	overlapVols = nullptr )

Score the overlap of a molecule to a reference molecule without moving.

Parameters

ref	the reference molecule
fit	the molecule to score
refOpts	the options for creating the ref shape
fitOpts	the options for creating the fit shape
overlayOpts	options for controlling the volume calculation
refConfId	(optional) the conformer to use for the reference molecule
fitConfId	(optional) the conformer to use for the fit molecule
overlapVols	if not-null, is filled with the raw overlap volumes

Returns: an array of the combination score of the shape Tverksy value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ ScoreMolecule() [2/2]

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::ScoreMolecule	(	const ShapeInput &	refShape,
		const ROMol &	fit,
		const ShapeInputOptions &	fitOpts = ShapeInputOptions(),
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		int	fitConfId = -1,
		std::pair< double, double > *	overlapVols = nullptr )

Score the overlap of a molecule to a reference shape without moving.

Parameters

refShape	the reference shape
fit	the molecule to score
fitOpts	the options for creating the fit shape
overlayOpts	options for controlling the volume calculation
fitConfId	(optional) the conformer to use for the fit molecule
overlapVols	if not-null, is filled with the raw overlap volumes

Returns: an array of the combination score of the shape Tversky value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ ScoreMoleculeAllConformers()

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::ScoreMoleculeAllConformers	(	const ROMol &	ref,
		const ROMol &	fit,
		int &	refConfId,
		int &	fitConfId,
		std::vector< std::vector< double > > &	combScores,
		const ShapeInputOptions &	refOpts = ShapeInputOptions(),
		const ShapeInputOptions &	fitOpts = ShapeInputOptions(),
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		RDGeom::Transform3D *	xform = nullptr )

Calculate scores for the alignment of all conformers of one molecule onto another. Returns a matrix of the combination scores, the conformer numbers of the two molecules that gave the best overlay and the transformation matrix for that overlay if requested. The molecules themselves are not altered. scores[0][1] is the score of aligning fit conformer 1 onto ref conformer 0

Parameters

ref	the reference molecule
fit	the molecule to align
refConfId	returns the reference conformer for the best scoring overlay
fitConfId	returns the fit conformer for the best scoring overlay
combScores	the scores for all the overlays. Will be returned sized by the number of conformers of the ref and fit molecules. combScores[i][j] will be the score for the jth fit conformer onto the ith ref conformer.
refOpts	the options for creating the ref shape
fitOpts	the options for creating the fit shape
overlayOpts	options for setting up and running the overlay
xform	if passed in as non-null, will be populated with the transformation matrix that gives the best-scoring overlay.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ ScoreShape()

RDKIT_GAUSSIANSHAPE_EXPORT std::array< double, 3 > RDKit::GaussianShape::ScoreShape	(	const ShapeInput &	refShape,
		const ShapeInput &	fitShape,
		const ShapeOverlayOptions &	overlayOpts = ShapeOverlayOptions(),
		std::pair< double, double > *	overlapVols = nullptr )

Score the overlap of a shape to a reference shape without moving.

Parameters

refShape	the reference shape
fitShape	the shape to score
overlayOpts	options for controlling the volume calculation
overlapVols	if not-null, is filled with the raw overlap volumes

Returns: an array of the combination score of the shape Tversky value and the color Tversky value (zero if colors not used) and the individual values. If using color features, defaults to RDKit pharmacophore types for the features.

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ translateShape() [1/2]

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::translateShape	(	const double *	inShape,
		double *	outShape,
		size_t	numPoints,
		const RDGeom::Point3D &	translation )

References RDKIT_GAUSSIANSHAPE_EXPORT.

◆ translateShape() [2/2]

RDKIT_GAUSSIANSHAPE_EXPORT void RDKit::GaussianShape::translateShape	(	std::vector< double > &	shape,
		const RDGeom::Point3D &	translation )

References RDKIT_GAUSSIANSHAPE_EXPORT.

Variable Documentation

◆ CARBON_RAD

double RDKit::GaussianShape::CARBON_RAD = 1.70

constexpr

Definition at line 71 of file ShapeInput.h.

◆ DUMMY_RAD

double RDKit::GaussianShape::DUMMY_RAD = 2.16

constexpr

Definition at line 72 of file ShapeInput.h.

◆ KAPPA

double RDKit::GaussianShape::KAPPA = 2.41798793102

constexpr

Definition at line 75 of file ShapeInput.h.

◆ P

double RDKit::GaussianShape::P = 2.7

constexpr

Definition at line 74 of file ShapeInput.h.

Classes

Functions

Variables

Function Documentation

◆ AlignMolecule() [1/2]

◆ AlignMolecule() [2/2]

◆ AlignShape()

◆ applyTransformToShape() [1/2]

◆ applyTransformToShape() [2/2]

◆ calcVolAndGrads() [1/2]

◆ calcVolAndGrads() [2/2]

◆ computeFeaturePos()

◆ findFeatures()

◆ maxScore()

◆ operator<<()

◆ quatTransToTransform()

◆ ScoreMolecule() [1/2]

◆ ScoreMolecule() [2/2]

◆ ScoreMoleculeAllConformers()

◆ ScoreShape()

◆ translateShape() [1/2]

◆ translateShape() [2/2]

Variable Documentation

◆ CARBON_RAD

◆ DUMMY_RAD

◆ KAPPA

◆ P