CDPL::GRAIL::GRAILDescriptorCalculator Class Reference

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

#include <GRAILDescriptorCalculator.hpp>

Public Types
enum	ElementIndex {   PI_COUNT ,   NI_COUNT ,   AR_COUNT ,   H_COUNT ,   HBD_COUNT ,   HBA_COUNT ,   XBD_COUNT ,   XBA_COUNT ,   HVY_ATOM_COUNT ,   ROT_BOND_COUNT ,   TOTAL_HYD ,   LOGP ,   TPSA ,   ENV_HBA_OCC_SUM ,   ENV_HBA_OCC_MAX ,   ENV_HBD_OCC_SUM ,   ENV_HBD_OCC_MAX ,   PI_AR_SCORE_SUM ,   PI_AR_SCORE_MAX ,   AR_PI_SCORE_SUM ,   AR_PI_SCORE_MAX ,   H_H_SCORE_SUM ,   H_H_SCORE_MAX ,   AR_AR_SCORE_SUM ,   AR_AR_SCORE_MAX ,   HBD_HBA_SCORE_SUM ,   HBD_HBA_SCORE_MAX ,   HBA_HBD_SCORE_SUM ,   HBA_HBD_SCORE_MAX ,   XBD_XBA_SCORE_SUM ,   XBD_XBA_SCORE_MAX ,   ES_ENERGY ,   ES_ENERGY_SQRD_DIST ,   VDW_ENERGY_ATT ,   VDW_ENERGY_REP }
	Indices of the individual elements of the GRAIL descriptor vector. More...
typedef std::shared_ptr< GRAILDescriptorCalculator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated GRAILDescriptorCalculator instances. More...

Public Member Functions
	GRAILDescriptorCalculator ()
	Constructs the GRAILDescriptorCalculator instance. More...
	GRAILDescriptorCalculator (const GRAILDescriptorCalculator &calc)
	Constructs a copy of the GRAILDescriptorCalculator instance calc. More...
	~GRAILDescriptorCalculator ()
	Destructor. More...
GRAILDescriptorCalculator &	operator= (const GRAILDescriptorCalculator &calc)
	Copy assignment operator. More...
void	initTargetData (const Chem::MolecularGraph &tgt_env, const Chem::Atom3DCoordinatesFunction &coords_func, bool tgt_env_changed=true)
	Initializes the calculator with target-environment data for subsequent descriptor calculations. More...
void	initLigandData (const Chem::MolecularGraph &ligand)
	Initializes the calculator with the molecular graph of the ligand. More...
void	calculate (const Math::Vector3DArray &atom_coords, Math::DVector &descr, bool update_lig_part=true)
	Calculates the GRAIL descriptor for the current ligand pose. More...

Static Public Attributes
static constexpr std::size_t	TOTAL_DESCRIPTOR_SIZE = 35
	Total number of elements in the calculated descriptor vector. More...
static constexpr std::size_t	LIGAND_DESCRIPTOR_SIZE = 13
	Number of ligand-only descriptor elements (the first LIGAND_DESCRIPTOR_SIZE entries of the vector). More...

Detailed Description

Calculation of GRAIL descriptors for protein-ligand complexes.

The descriptor is a vector of 35 elements that captures ligand-only properties (counts of pharmacophore features, heavy atoms, rotatable bonds, \( \log P \), \( TPSA \), etc.) and target-environment-specific scores (HBA/HBD occupancy sums and maxima, pi/aromatic/hydrophobic/halogen-bonding interaction scores, and electrostatic

• Van der Waals energy contributions). See ElementIndex for the layout.

See also

[GRADE]

Member Typedef Documentation

SharedPointer

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

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

Member Enumeration Documentation

ElementIndex

enum CDPL::GRAIL::GRAILDescriptorCalculator::ElementIndex

Indices of the individual elements of the GRAIL descriptor vector.

Enumerator
PI_COUNT	Positive-ionizable feature count (ligand).
NI_COUNT	Negative-ionizable feature count (ligand).
AR_COUNT	Aromatic feature count (ligand).
H_COUNT	Hydrophobic feature count (ligand).
HBD_COUNT	Hydrogen-bond donor feature count (ligand).
HBA_COUNT	Hydrogen-bond acceptor feature count (ligand).
XBD_COUNT	Halogen-bond donor feature count (ligand).
XBA_COUNT	Halogen-bond acceptor feature count (ligand).
HVY_ATOM_COUNT	Heavy atom count (ligand).
ROT_BOND_COUNT	Rotatable bond count (ligand).
TOTAL_HYD	Total computed hydrophobicity (ligand).
LOGP	Computed \( \log P \) (ligand).
TPSA	Computed topological polar surface area (ligand).
ENV_HBA_OCC_SUM	Sum of HBA occupancy scores against the target environment.
ENV_HBA_OCC_MAX	Maximum HBA occupancy score against the target environment.
ENV_HBD_OCC_SUM	Sum of HBD occupancy scores against the target environment.
ENV_HBD_OCC_MAX	Maximum HBD occupancy score against the target environment.
PI_AR_SCORE_SUM	Sum of (ligand positive-ionizable → target aromatic) interaction scores.
PI_AR_SCORE_MAX	Maximum (ligand positive-ionizable → target aromatic) interaction score.
AR_PI_SCORE_SUM	Sum of (ligand aromatic → target positive-ionizable) interaction scores.
AR_PI_SCORE_MAX	Maximum (ligand aromatic → target positive-ionizable) interaction score.
H_H_SCORE_SUM	Sum of hydrophobic-hydrophobic interaction scores.
H_H_SCORE_MAX	Maximum hydrophobic-hydrophobic interaction score.
AR_AR_SCORE_SUM	Sum of aromatic-aromatic interaction scores.
AR_AR_SCORE_MAX	Maximum aromatic-aromatic interaction score.
HBD_HBA_SCORE_SUM	Sum of (ligand HBD → target HBA) interaction scores.
HBD_HBA_SCORE_MAX	Maximum (ligand HBD → target HBA) interaction score.
HBA_HBD_SCORE_SUM	Sum of (ligand HBA → target HBD) interaction scores.
HBA_HBD_SCORE_MAX	Maximum (ligand HBA → target HBD) interaction score.
XBD_XBA_SCORE_SUM	Sum of (ligand XBD → target XBA) interaction scores.
XBD_XBA_SCORE_MAX	Maximum (ligand XBD → target XBA) interaction score.
ES_ENERGY	Electrostatic interaction energy.
ES_ENERGY_SQRD_DIST	Electrostatic interaction energy with squared atom-pair distance dependency.
VDW_ENERGY_ATT	Attractive part of the Van der Waals interaction energy.
VDW_ENERGY_REP	Repulsive part of the Van der Waals interaction energy.

Constructor & Destructor Documentation

GRAILDescriptorCalculator() [1/2]

CDPL::GRAIL::GRAILDescriptorCalculator::GRAILDescriptorCalculator

(

)

Constructs the GRAILDescriptorCalculator instance.

GRAILDescriptorCalculator() [2/2]

CDPL::GRAIL::GRAILDescriptorCalculator::GRAILDescriptorCalculator

(

const GRAILDescriptorCalculator &

calc

)

Constructs a copy of the GRAILDescriptorCalculator instance calc.

Parameters

calc	The GRAILDescriptorCalculator to copy.

~GRAILDescriptorCalculator()

CDPL::GRAIL::GRAILDescriptorCalculator::~GRAILDescriptorCalculator

(

)

Destructor.

Member Function Documentation

operator=()

GRAILDescriptorCalculator& CDPL::GRAIL::GRAILDescriptorCalculator::operator=

(

const GRAILDescriptorCalculator &

calc

)

Copy assignment operator.

Parameters

calc	The other GRAILDescriptorCalculator instance.

Returns

A reference to itself.

initTargetData()

void CDPL::GRAIL::GRAILDescriptorCalculator::initTargetData	(	const Chem::MolecularGraph &	tgt_env,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		bool	tgt_env_changed = true
	)

Initializes the calculator with target-environment data for subsequent descriptor calculations.

Parameters

tgt_env	The target environment (e.g. binding-site residues).
coords_func	The function used to retrieve atom 3D-coordinates from tgt_env.
tgt_env_changed	If true, the target environment is reinitialized even if the same target was supplied previously.

initLigandData()

void CDPL::GRAIL::GRAILDescriptorCalculator::initLigandData

(

const Chem::MolecularGraph &

ligand

)

Initializes the calculator with the molecular graph of the ligand.

Parameters

ligand

The ligand molecular graph.

calculate()

void CDPL::GRAIL::GRAILDescriptorCalculator::calculate	(	const Math::Vector3DArray &	atom_coords,
		Math::DVector &	descr,
		bool	update_lig_part = true
	)

Calculates the GRAIL descriptor for the current ligand pose.

The pose is supplied via per-atom 3D coordinates in atom_coords (same order as the atoms of the molecular graph passed to initLigandData()). The result is written to descr.

Parameters

atom_coords	The 3D coordinates of the ligand atoms.
descr	The output descriptor vector (resized to TOTAL_DESCRIPTOR_SIZE).
update_lig_part	If true, the ligand-only part of the descriptor is recomputed.

Member Data Documentation

TOTAL_DESCRIPTOR_SIZE

constexpr std::size_t CDPL::GRAIL::GRAILDescriptorCalculator::TOTAL_DESCRIPTOR_SIZE = 35

staticconstexpr

Total number of elements in the calculated descriptor vector.

LIGAND_DESCRIPTOR_SIZE

constexpr std::size_t CDPL::GRAIL::GRAILDescriptorCalculator::LIGAND_DESCRIPTOR_SIZE = 13

staticconstexpr

Number of ligand-only descriptor elements (the first LIGAND_DESCRIPTOR_SIZE entries of the vector).

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

• GRAILDescriptorCalculator.hpp