Generator that pre-computes the per-cell interaction-score grids and the atom-density grid used by GRAIL scoring of ligand poses against a target environment. More...

#include <GRAILDataSetGenerator.hpp>

Public Types
typedef std::shared_ptr< GRAILDataSetGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `GRAILDataSetGenerator` instances. More...

typedef FeatureInteractionScoreGridCalculator::ScoringFunction	ScoringFunction
	Re-export of the scoring-function type used by the underlying score-grid calculator. More...

typedef FeatureInteractionScoreGridCalculator::ScoreCombinationFunction	ScoreCombinationFunction
	Re-export of the score-combination function type used by the underlying score-grid calculator. More...

typedef std::function< void(CDPL::Pharm::Pharmacophore &)>	PharmacophoreProcessingFunction
	Type of the generic functor used to post-process a generated pharmacophore prior to grid calculation. More...

Public Member Functions
	GRAILDataSetGenerator ()
	Constructs the `GRAILDataSetGenerator` instance. More...

virtual	~GRAILDataSetGenerator ()
	Virtual destructor. More...

void	enableInteraction (unsigned int ftr_type, unsigned int tgt_ftr_type, bool enable)
	Enables or disables interaction-grid generation for the given (ligand feature type, target feature type) pair. More...

bool	isInteractionEnabled (unsigned int ftr_type, unsigned int tgt_ftr_type) const
	Tells whether interaction-grid generation is enabled for the given (ligand feature type, target feature type) pair. More...

void	clearEnabledInteractions ()
	Disables interaction-grid generation for all feature-type pairs. More...

void	setScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type, const ScoringFunction &func)
	Sets the scoring function for the given (ligand feature type, target feature type) pair. More...

const ScoringFunction &	getScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type) const
	Returns the scoring function configured for the given (ligand feature type, target feature type) pair. More...

void	removeScoringFunction (unsigned int ftr_type, unsigned int tgt_ftr_type)
	Removes the scoring function configured for the given (ligand feature type, target feature type) pair. More...

void	setGridName (unsigned int ftr_type, unsigned int tgt_ftr_type, const std::string &name)
	Sets the grid name associated with the given (ligand feature type, target feature type) pair. More...

const std::string &	getGridName (unsigned int ftr_type, unsigned int tgt_ftr_type) const
	Returns the grid name associated with the given (ligand feature type, target feature type) pair. More...

void	removeGridName (unsigned int ftr_type, unsigned int tgt_ftr_type)
	Removes the grid name associated with the given (ligand feature type, target feature type) pair. More...

void	setScoreCombinationFunction (const ScoreCombinationFunction &func)
	Sets the function used to combine per-feature scores into a single grid cell value. More...

const ScoreCombinationFunction &	getScoreCombinationFunction () const
	Returns the currently configured score-combination function. More...

void	normalizeScores (bool normalize)
	Enables or disables normalization of the combined per-cell scores to the range [0, 1]. More...

bool	scoresNormalized () const
	Tells whether the combined per-cell scores are normalized. More...

void	diminishScoresByAtomDensity (bool diminish)
	Enables or disables multiplicative diminishing of interaction scores by the (normalized) atom density of the target environment. More...

bool	scoresDiminishedByAtomDensity () const
	Tells whether the interaction scores are diminished by the atom density of the target environment. More...

void	storeEnvironmentAtomDensityGrid (bool store)
	Specifies whether the target environment atom-density grid shall be added to the produced grid set. More...

bool	environmentAtomDensityGridStored () const
	Tells whether the target environment atom-density grid is stored in the produced grid set. More...

void	setEnvironmentAtomDensityGridName (const std::string &name)
	Sets the name to assign to the target environment atom-density grid in the produced grid set. More...

const std::string &	getEnvironmentAtomDensityGridName () const
	Returns the name assigned to the target environment atom-density grid. More...

const Math::Matrix4D &	getGridTransform () const
	Returns the affine transformation matrix that places the grids in the target coordinate frame. More...

template<typename T >
void	setGridTransform (const T &xform)
	Sets the affine transformation matrix that places the grids in the target coordinate frame. More...

double	getGridStepSize () const
	Returns the currently configured grid spacing. More...

void	setGridStepSize (double size)
	Sets the grid spacing (isotropic). More...

std::size_t	getGridXSize () const
	Returns the grid size in the x direction. More...

void	setGridXSize (std::size_t size)
	Sets the grid size in the x direction. More...

std::size_t	getGridYSize () const
	Returns the grid size in the y direction. More...

void	setGridYSize (std::size_t size)
	Sets the grid size in the y direction. More...

std::size_t	getGridZSize () const
	Returns the grid size in the z direction. More...

void	setGridZSize (std::size_t size)
	Sets the grid size in the z direction. More...

void	setGridParamsForBoundingBox (const Math::Vector3D &bbox_min, const Math::Vector3D &bbox_max, double step_size=DEF_GRID_STEP_SIZE)
	Convenience method that configures grid size, spacing and transformation so that the grid covers the given axis-aligned bounding box. More...

const Pharm::DefaultPharmacophoreGenerator &	getPharmacophoreGenerator () const
	Returns the internal pharmacophore generator used for the target environment. More...

Pharm::DefaultPharmacophoreGenerator &	getPharmacophoreGenerator ()
	Returns the internal pharmacophore generator used for the target environment. More...

void	setPharmacophoreProcessingFunction (const PharmacophoreProcessingFunction &func)
	Sets the function applied to the generated target pharmacophore before grid calculation (e.g. for filtering or modification). More...

const PharmacophoreProcessingFunction &	getPharmacophoreProcessingFunction () const
	Returns the currently configured pharmacophore processing function. More...

void	calcInteractionGrids (const Chem::MolecularGraph &tgt_env, const Chem::Atom3DCoordinatesFunction &coords_func, Grid::DRegularGridSet &grid_set, bool append=false)
	Calculates the interaction-score grids for all enabled feature-type pairs and stores them in grid_set. More...

Grid::DRegularGrid::SharedPointer	calcAtomDensityGrid (const Chem::AtomContainer &atoms, const Chem::Atom3DCoordinatesFunction &coords_func, const std::string &grid_name)
	Calculates an atom-density grid for the given atoms. More...

Static Public Attributes
static constexpr double	DEF_GRID_STEP_SIZE = 0.5
	Default grid spacing (isotropic). More...

Detailed Description

Generator that pre-computes the per-cell interaction-score grids and the atom-density grid used by GRAIL scoring of ligand poses against a target environment.

For every enabled (ligand feature type, target feature type) pair the generator runs a GRAIL::FeatureInteractionScoreGridCalculator and stores the resulting grid in a Grid::DRegularGridSet. Optionally the generator also produces an atom-density grid of the target environment (e.g. for use as a buriedness or accessibility weight).

See also: [GRAIL]

Since: 1.1

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<GRAILDataSetGenerator> CDPL::GRAIL::GRAILDataSetGenerator::SharedPointer

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

◆ ScoringFunction

typedef FeatureInteractionScoreGridCalculator::ScoringFunction CDPL::GRAIL::GRAILDataSetGenerator::ScoringFunction

Re-export of the scoring-function type used by the underlying score-grid calculator.

◆ ScoreCombinationFunction

typedef FeatureInteractionScoreGridCalculator::ScoreCombinationFunction CDPL::GRAIL::GRAILDataSetGenerator::ScoreCombinationFunction

Re-export of the score-combination function type used by the underlying score-grid calculator.

◆ PharmacophoreProcessingFunction

typedef std::function<void(CDPL::Pharm::Pharmacophore&)> CDPL::GRAIL::GRAILDataSetGenerator::PharmacophoreProcessingFunction

Type of the generic functor used to post-process a generated pharmacophore prior to grid calculation.

Constructor & Destructor Documentation

◆ GRAILDataSetGenerator()

CDPL::GRAIL::GRAILDataSetGenerator::GRAILDataSetGenerator ( )

Constructs the GRAILDataSetGenerator instance.

◆ ~GRAILDataSetGenerator()

virtual CDPL::GRAIL::GRAILDataSetGenerator::~GRAILDataSetGenerator ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ enableInteraction()

void CDPL::GRAIL::GRAILDataSetGenerator::enableInteraction	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type,
		bool	enable
	)

Enables or disables interaction-grid generation for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
enable	If `true`, the interaction is enabled.

◆ isInteractionEnabled()

bool CDPL::GRAIL::GRAILDataSetGenerator::isInteractionEnabled	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type
	)		const

Tells whether interaction-grid generation is enabled for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: true if the interaction is enabled, and false otherwise.

◆ clearEnabledInteractions()

void CDPL::GRAIL::GRAILDataSetGenerator::clearEnabledInteractions ( )

Disables interaction-grid generation for all feature-type pairs.

◆ setScoringFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setScoringFunction	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type,
		const ScoringFunction &	func
	)

Sets the scoring function for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
func	The scoring function.

◆ getScoringFunction()

const ScoringFunction& CDPL::GRAIL::GRAILDataSetGenerator::getScoringFunction	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type
	)		const

Returns the scoring function configured for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: The configured scoring function (or an empty function if no entry is registered).

◆ removeScoringFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::removeScoringFunction	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type
	)

Removes the scoring function configured for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

◆ setGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridName	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type,
		const std::string &	name
	)

Sets the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
name	The grid name.

◆ getGridName()

const std::string& CDPL::GRAIL::GRAILDataSetGenerator::getGridName	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type
	)		const

Returns the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: The grid name.

◆ removeGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::removeGridName	(	unsigned int	ftr_type,
		unsigned int	tgt_ftr_type
	)

Removes the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

◆ setScoreCombinationFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setScoreCombinationFunction ( const ScoreCombinationFunction & func )

Sets the function used to combine per-feature scores into a single grid cell value.

Parameters

func	The score-combination function.

◆ getScoreCombinationFunction()

const ScoreCombinationFunction& CDPL::GRAIL::GRAILDataSetGenerator::getScoreCombinationFunction ( ) const

Returns the currently configured score-combination function.

Returns: The configured score-combination function.

◆ normalizeScores()

void CDPL::GRAIL::GRAILDataSetGenerator::normalizeScores ( bool normalize )

Enables or disables normalization of the combined per-cell scores to the range [0, 1].

Parameters

normalize If true, the combined scores are normalized.

◆ scoresNormalized()

bool CDPL::GRAIL::GRAILDataSetGenerator::scoresNormalized ( ) const

Tells whether the combined per-cell scores are normalized.

Returns: true if the combined scores are normalized, and false otherwise.

◆ diminishScoresByAtomDensity()

void CDPL::GRAIL::GRAILDataSetGenerator::diminishScoresByAtomDensity ( bool diminish )

Enables or disables multiplicative diminishing of interaction scores by the (normalized) atom density of the target environment.

Parameters

diminish If true, scores are diminished by atom density.

◆ scoresDiminishedByAtomDensity()

bool CDPL::GRAIL::GRAILDataSetGenerator::scoresDiminishedByAtomDensity ( ) const

Tells whether the interaction scores are diminished by the atom density of the target environment.

Returns: true if scores are diminished by atom density, and false otherwise.

◆ storeEnvironmentAtomDensityGrid()

void CDPL::GRAIL::GRAILDataSetGenerator::storeEnvironmentAtomDensityGrid ( bool store )

Specifies whether the target environment atom-density grid shall be added to the produced grid set.

Parameters

store If true, the atom-density grid is stored.

◆ environmentAtomDensityGridStored()

bool CDPL::GRAIL::GRAILDataSetGenerator::environmentAtomDensityGridStored ( ) const

Tells whether the target environment atom-density grid is stored in the produced grid set.

Returns: true if the atom-density grid is stored, and false otherwise.

◆ setEnvironmentAtomDensityGridName()

void CDPL::GRAIL::GRAILDataSetGenerator::setEnvironmentAtomDensityGridName ( const std::string & name )

Sets the name to assign to the target environment atom-density grid in the produced grid set.

Parameters

name	The grid name.

◆ getEnvironmentAtomDensityGridName()

const std::string& CDPL::GRAIL::GRAILDataSetGenerator::getEnvironmentAtomDensityGridName ( ) const

Returns the name assigned to the target environment atom-density grid.

Returns: The grid name.

◆ getGridTransform()

const Math::Matrix4D& CDPL::GRAIL::GRAILDataSetGenerator::getGridTransform ( ) const

Returns the affine transformation matrix that places the grids in the target coordinate frame.

Returns: The grid transformation matrix.

◆ setGridTransform()

template<typename T >

void CDPL::GRAIL::GRAILDataSetGenerator::setGridTransform ( const T & xform )

inline

Sets the affine transformation matrix that places the grids in the target coordinate frame.

Template Parameters

T	The transformation matrix expression type.

Parameters

xform The transformation matrix.

◆ getGridStepSize()

double CDPL::GRAIL::GRAILDataSetGenerator::getGridStepSize ( ) const

Returns the currently configured grid spacing.

Returns: The configured grid spacing.

◆ setGridStepSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridStepSize ( double size )

Sets the grid spacing (isotropic).

Parameters

size	The grid spacing.

◆ getGridXSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridXSize ( ) const

Returns the grid size in the x direction.

Returns: The grid size in the x direction.

◆ setGridXSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridXSize ( std::size_t size )

Sets the grid size in the x direction.

Parameters

size	The grid size.

◆ getGridYSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridYSize ( ) const

Returns the grid size in the y direction.

Returns: The grid size in the y direction.

◆ setGridYSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridYSize ( std::size_t size )

Sets the grid size in the y direction.

Parameters

size	The grid size.

◆ getGridZSize()

std::size_t CDPL::GRAIL::GRAILDataSetGenerator::getGridZSize ( ) const

Returns the grid size in the z direction.

Returns: The grid size in the z direction.

◆ setGridZSize()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridZSize ( std::size_t size )

Sets the grid size in the z direction.

Parameters

size	The grid size.

◆ setGridParamsForBoundingBox()

void CDPL::GRAIL::GRAILDataSetGenerator::setGridParamsForBoundingBox	(	const Math::Vector3D &	bbox_min,
		const Math::Vector3D &	bbox_max,
		double	step_size = `DEF_GRID_STEP_SIZE`
	)

Convenience method that configures grid size, spacing and transformation so that the grid covers the given axis-aligned bounding box.

Parameters

bbox_min	The bounding box minimum-corner coordinates.
bbox_max	The bounding box maximum-corner coordinates.
step_size	The grid spacing.

◆ getPharmacophoreGenerator() [1/2]

const Pharm::DefaultPharmacophoreGenerator& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreGenerator ( ) const

Returns the internal pharmacophore generator used for the target environment.

Returns: A const reference to the pharmacophore generator.

◆ getPharmacophoreGenerator() [2/2]

Pharm::DefaultPharmacophoreGenerator& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreGenerator ( )

Returns the internal pharmacophore generator used for the target environment.

Returns: A reference to the pharmacophore generator.

◆ setPharmacophoreProcessingFunction()

void CDPL::GRAIL::GRAILDataSetGenerator::setPharmacophoreProcessingFunction ( const PharmacophoreProcessingFunction & func )

Sets the function applied to the generated target pharmacophore before grid calculation (e.g. for filtering or modification).

Parameters

func	The pharmacophore processing function.

◆ getPharmacophoreProcessingFunction()

const PharmacophoreProcessingFunction& CDPL::GRAIL::GRAILDataSetGenerator::getPharmacophoreProcessingFunction ( ) const

Returns the currently configured pharmacophore processing function.

Returns: The configured pharmacophore processing function.

◆ calcInteractionGrids()

void CDPL::GRAIL::GRAILDataSetGenerator::calcInteractionGrids	(	const Chem::MolecularGraph &	tgt_env,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		Grid::DRegularGridSet &	grid_set,
		bool	append = `false`
	)

Calculates the interaction-score grids for all enabled feature-type pairs and stores them in grid_set.

Parameters

tgt_env	The target environment.
coords_func	The function used to retrieve atom 3D-coordinates from tgt_env.
grid_set	The output grid set.
append	If `true`, the new grids are appended to grid_set; otherwise grid_set is cleared first.

◆ calcAtomDensityGrid()

Grid::DRegularGrid::SharedPointer CDPL::GRAIL::GRAILDataSetGenerator::calcAtomDensityGrid	(	const Chem::AtomContainer &	atoms,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		const std::string &	grid_name
	)

Calculates an atom-density grid for the given atoms.

Parameters

atoms	The atoms contributing to the density.
coords_func	The function used to retrieve atom 3D-coordinates.
grid_name	The name to assign to the resulting grid.

Returns: A smart pointer to the calculated atom-density grid.

Member Data Documentation

◆ DEF_GRID_STEP_SIZE

constexpr double CDPL::GRAIL::GRAILDataSetGenerator::DEF_GRID_STEP_SIZE = 0.5

staticconstexpr

Default grid spacing (isotropic).

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

GRAILDataSetGenerator.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ScoringFunction

◆ ScoreCombinationFunction

◆ PharmacophoreProcessingFunction

Constructor & Destructor Documentation

◆ GRAILDataSetGenerator()

◆ ~GRAILDataSetGenerator()

Member Function Documentation

◆ enableInteraction()

◆ isInteractionEnabled()

◆ clearEnabledInteractions()

◆ setScoringFunction()

◆ getScoringFunction()

◆ removeScoringFunction()

◆ setGridName()

◆ getGridName()

◆ removeGridName()

◆ setScoreCombinationFunction()

◆ getScoreCombinationFunction()

◆ normalizeScores()

◆ scoresNormalized()

◆ diminishScoresByAtomDensity()

◆ scoresDiminishedByAtomDensity()

◆ storeEnvironmentAtomDensityGrid()

◆ environmentAtomDensityGridStored()

◆ setEnvironmentAtomDensityGridName()

◆ getEnvironmentAtomDensityGridName()

◆ getGridTransform()

◆ setGridTransform()

◆ getGridStepSize()

◆ setGridStepSize()

◆ getGridXSize()

◆ setGridXSize()

◆ getGridYSize()

◆ setGridYSize()

◆ getGridZSize()

◆ setGridZSize()

◆ setGridParamsForBoundingBox()

◆ getPharmacophoreGenerator() [1/2]

◆ getPharmacophoreGenerator() [2/2]

◆ setPharmacophoreProcessingFunction()

◆ getPharmacophoreProcessingFunction()

◆ calcInteractionGrids()

◆ calcAtomDensityGrid()

Member Data Documentation

◆ DEF_GRID_STEP_SIZE