Contains classes and functions related to the GRAIL method [GRAIL, GRADE]. More...

Namespaces
	AttributedGridProperty
	Provides keys for built-in Grid::AttributedGrid properties.

	AttributedGridPropertyDefault
	Provides default values for built-in Grid::AttributedGrid properties.

	FeatureType
	Provides constants for the specification of GRAIL-specific extended pharmacophore feature types that refine H-bond donor and acceptor categories by the chemical environment (atom element + SYBYL-like type) of the participating heavy atom.

Classes
class	AtomDensityGridCalculator
	Calculator that fills a spatial grid with combined per-atom density contributions. More...

class	BindingAffinityCalculator
	Predicts the binding affinity of a ligand pose from its GRAIL descriptor vector. More...

class	BuriednessGridCalculator
	Calculator that fills a spatial grid with per-cell buriedness scores derived from GRAIL::BuriednessScore. More...

class	BuriednessScore
	Functor for the calculation of the buriedness of a 3D query position with respect to the surrounding atoms. More...

class	FeatureInteractionScoreGridCalculator
	Calculator that fills a spatial grid with per-cell feature-interaction scores against a set of target pharmacophore features. More...

class	GeneralizedBellAtomDensity
	Functor for the evaluation of the generalized-bell atom density contribution of an atom at a query position. More...

class	GRAILDataSetGenerator
	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...

class	GRAILDescriptorCalculator
	Calculation of GRAIL descriptors for protein-ligand complexes. More...

class	GRAILXDescriptorCalculator
	Calculation of the extended GRAIL-X descriptor for protein-ligand complexes. More...

Functions
CDPL_GRAIL_API unsigned int	getFeatureType (const Grid::AttributedGrid &grid)
	Returns the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid. More...

CDPL_GRAIL_API void	setFeatureType (Grid::AttributedGrid &grid, unsigned int type)
	Sets the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid to type. More...

CDPL_GRAIL_API void	clearFeatureType (Grid::AttributedGrid &grid)
	Clears the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid. More...

CDPL_GRAIL_API bool	hasFeatureType (const Grid::AttributedGrid &grid)
	Tells whether the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid is set. More...

CDPL_GRAIL_API unsigned int	getTargetFeatureType (const Grid::AttributedGrid &grid)
	Returns the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid. More...

CDPL_GRAIL_API void	setTargetFeatureType (Grid::AttributedGrid &grid, unsigned int type)
	Sets the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid to type. More...

CDPL_GRAIL_API void	clearTargetFeatureType (Grid::AttributedGrid &grid)
	Clears the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid. More...

CDPL_GRAIL_API bool	hasTargetFeatureType (const Grid::AttributedGrid &grid)
	Tells whether the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid is set. More...

CDPL_GRAIL_API unsigned int	perceiveExtendedType (const Pharm::Feature &feature, bool lig_side)
	Perceives the GRAIL extended pharmacophore feature type of the given Pharm::Feature instance. More...

CDPL_GRAIL_API void	prepareForGRAILDescriptorCalculation (Chem::Molecule &mol, bool std_prot_state=false)
	Prepares the molecule mol for GRAIL descriptor calculation. More...

Detailed Description

Contains classes and functions related to the GRAIL method [GRAIL, GRADE].

Function Documentation

◆ getFeatureType()

CDPL_GRAIL_API unsigned int CDPL::GRAIL::getFeatureType ( const Grid::AttributedGrid & grid )

Returns the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to return the property value.

Returns: The feature type value.

◆ setFeatureType()

CDPL_GRAIL_API void CDPL::GRAIL::setFeatureType	(	Grid::AttributedGrid &	grid,
		unsigned int	type
	)

Sets the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid to type.

Parameters

grid	The grid for which to set the property value.
type	The new feature type value.

◆ clearFeatureType()

CDPL_GRAIL_API void CDPL::GRAIL::clearFeatureType ( Grid::AttributedGrid & grid )

Clears the value of the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to clear the property value.

◆ hasFeatureType()

CDPL_GRAIL_API bool CDPL::GRAIL::hasFeatureType ( const Grid::AttributedGrid & grid )

Tells whether the GRAIL::AttributedGridProperty::FEATURE_TYPE property of the grid grid is set.

Parameters

grid	The grid for which to query the property value.

Returns: true if the property is set, and false otherwise.

◆ getTargetFeatureType()

CDPL_GRAIL_API unsigned int CDPL::GRAIL::getTargetFeatureType ( const Grid::AttributedGrid & grid )

Returns the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to return the property value.

Returns: The target feature type value.

◆ setTargetFeatureType()

CDPL_GRAIL_API void CDPL::GRAIL::setTargetFeatureType	(	Grid::AttributedGrid &	grid,
		unsigned int	type
	)

Sets the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid to type.

Parameters

grid	The grid for which to set the property value.
type	The new target feature type value.

◆ clearTargetFeatureType()

CDPL_GRAIL_API void CDPL::GRAIL::clearTargetFeatureType ( Grid::AttributedGrid & grid )

Clears the value of the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to clear the property value.

◆ hasTargetFeatureType()

CDPL_GRAIL_API bool CDPL::GRAIL::hasTargetFeatureType ( const Grid::AttributedGrid & grid )

Tells whether the GRAIL::AttributedGridProperty::TARGET_FEATURE_TYPE property of the grid grid is set.

Parameters

grid	The grid for which to query the property value.

Returns: true if the property is set, and false otherwise.

◆ perceiveExtendedType()

CDPL_GRAIL_API unsigned int CDPL::GRAIL::perceiveExtendedType	(	const Pharm::Feature &	feature,
		bool	lig_side
	)

Perceives the GRAIL extended pharmacophore feature type of the given Pharm::Feature instance.

Parameters

feature	The feature for which to perceive the extended type.
lig_side	If `true`, the perception is performed assuming the feature is part of a ligand. Otherwise, it is assumed to be part of a target structure.

Returns: The perceived extended feature type (see namespace GRAIL::FeatureType).

◆ prepareForGRAILDescriptorCalculation()

CDPL_GRAIL_API void CDPL::GRAIL::prepareForGRAILDescriptorCalculation	(	Chem::Molecule &	mol,
		bool	std_prot_state = `false`
	)

Prepares the molecule mol for GRAIL descriptor calculation.

Performs all molecular structure preprocessing steps (e.g. ring perception, atom typing, hydrogen handling) required by the descriptor calculation procedure (implemented by GRAIL::GRAILDescriptorCalculator).

Parameters

mol	The molecule to prepare. The molecule is modified in place.
std_prot_state	If `true`, the standard protonation state of the molecule is assigned prior to the GRAIL-specific preprocessing.

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ getFeatureType()

◆ setFeatureType()

◆ clearFeatureType()

◆ hasFeatureType()

◆ getTargetFeatureType()

◆ setTargetFeatureType()

◆ clearTargetFeatureType()

◆ hasTargetFeatureType()

◆ perceiveExtendedType()

◆ prepareForGRAILDescriptorCalculation()