CDPL::GRAIL::GRAILXDescriptorCalculator Class Reference

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

#include <GRAILXDescriptorCalculator.hpp>

Public Types
enum	ElementIndex {   PI_COUNT ,   NI_COUNT ,   AR_COUNT ,   H_COUNT ,   HBD_COUNT ,   HBA_COUNT ,   XBD_COUNT ,   XBA_COUNT ,   HBD_N3_COUNT ,   HBD_N2_COUNT ,   HBD_Nar_COUNT ,   HBD_Nam_COUNT ,   HBD_Npl3_COUNT ,   HBD_N4_COUNT ,   HBD_O3_COUNT ,   HBD_S3_COUNT ,   HBA_N3_COUNT ,   HBA_N2_COUNT ,   HBA_N1_COUNT ,   HBA_Nar_COUNT ,   HBA_Npl3_COUNT ,   HBA_O3_COUNT ,   HBA_O2_COUNT ,   HBA_Oco2_COUNT ,   HBA_S3_COUNT ,   HBA_S2_COUNT ,   HVY_ATOM_COUNT ,   ROT_BOND_COUNT ,   TOTAL_HYD ,   LOGP ,   TPSA ,   ENV_HBA_N_OCC_SUM ,   ENV_HBA_N_OCC_MAX ,   ENV_HBA_O_OCC_SUM ,   ENV_HBA_O_OCC_MAX ,   ENV_HBA_S_OCC_SUM ,   ENV_HBA_S_OCC_MAX ,   ENV_HBD_N_OCC_SUM ,   ENV_HBD_N_OCC_MAX ,   ENV_HBD_O_OCC_SUM ,   ENV_HBD_O_OCC_MAX ,   ENV_HBD_S_OCC_SUM ,   ENV_HBD_S_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_N_SCORE_SUM ,   HBD_HBA_N_SCORE_MAX ,   HBD_HBA_O_SCORE_SUM ,   HBD_HBA_O_SCORE_MAX ,   HBD_HBA_S_SCORE_SUM ,   HBD_HBA_S_SCORE_MAX ,   HBD_N3_HBA_N_SCORE_SUM ,   HBD_N3_HBA_N_SCORE_MAX ,   HBD_N3_HBA_O_SCORE_SUM ,   HBD_N3_HBA_O_SCORE_MAX ,   HBD_N3_HBA_S_SCORE_SUM ,   HBD_N3_HBA_S_SCORE_MAX ,   HBD_N2_HBA_N_SCORE_SUM ,   HBD_N2_HBA_N_SCORE_MAX ,   HBD_N2_HBA_O_SCORE_SUM ,   HBD_N2_HBA_O_SCORE_MAX ,   HBD_N2_HBA_S_SCORE_SUM ,   HBD_N2_HBA_S_SCORE_MAX ,   HBD_Nar_HBA_N_SCORE_SUM ,   HBD_Nar_HBA_N_SCORE_MAX ,   HBD_Nar_HBA_O_SCORE_SUM ,   HBD_Nar_HBA_O_SCORE_MAX ,   HBD_Nar_HBA_S_SCORE_SUM ,   HBD_Nar_HBA_S_SCORE_MAX ,   HBD_Nam_HBA_N_SCORE_SUM ,   HBD_Nam_HBA_N_SCORE_MAX ,   HBD_Nam_HBA_O_SCORE_SUM ,   HBD_Nam_HBA_O_SCORE_MAX ,   HBD_Nam_HBA_S_SCORE_SUM ,   HBD_Nam_HBA_S_SCORE_MAX ,   HBD_Npl3_HBA_N_SCORE_SUM ,   HBD_Npl3_HBA_N_SCORE_MAX ,   HBD_Npl3_HBA_O_SCORE_SUM ,   HBD_Npl3_HBA_O_SCORE_MAX ,   HBD_Npl3_HBA_S_SCORE_SUM ,   HBD_Npl3_HBA_S_SCORE_MAX ,   HBD_N4_HBA_N_SCORE_SUM ,   HBD_N4_HBA_N_SCORE_MAX ,   HBD_N4_HBA_O_SCORE_SUM ,   HBD_N4_HBA_O_SCORE_MAX ,   HBD_N4_HBA_S_SCORE_SUM ,   HBD_N4_HBA_S_SCORE_MAX ,   HBD_O3_HBA_N_SCORE_SUM ,   HBD_O3_HBA_N_SCORE_MAX ,   HBD_O3_HBA_O_SCORE_SUM ,   HBD_O3_HBA_O_SCORE_MAX ,   HBD_O3_HBA_S_SCORE_SUM ,   HBD_O3_HBA_S_SCORE_MAX ,   HBD_S3_HBA_N_SCORE_SUM ,   HBD_S3_HBA_N_SCORE_MAX ,   HBD_S3_HBA_O_SCORE_SUM ,   HBD_S3_HBA_O_SCORE_MAX ,   HBD_S3_HBA_S_SCORE_SUM ,   HBD_S3_HBA_S_SCORE_MAX ,   HBA_HBD_N_SCORE_SUM ,   HBA_HBD_N_SCORE_MAX ,   HBA_HBD_O_SCORE_SUM ,   HBA_HBD_O_SCORE_MAX ,   HBA_HBD_S_SCORE_SUM ,   HBA_HBD_S_SCORE_MAX ,   HBA_N3_HBD_N_SCORE_SUM ,   HBA_N3_HBD_N_SCORE_MAX ,   HBA_N3_HBD_O_SCORE_SUM ,   HBA_N3_HBD_O_SCORE_MAX ,   HBA_N3_HBD_S_SCORE_SUM ,   HBA_N3_HBD_S_SCORE_MAX ,   HBA_N2_HBD_N_SCORE_SUM ,   HBA_N2_HBD_N_SCORE_MAX ,   HBA_N2_HBD_O_SCORE_SUM ,   HBA_N2_HBD_O_SCORE_MAX ,   HBA_N2_HBD_S_SCORE_SUM ,   HBA_N2_HBD_S_SCORE_MAX ,   HBA_N1_HBD_N_SCORE_SUM ,   HBA_N1_HBD_N_SCORE_MAX ,   HBA_N1_HBD_O_SCORE_SUM ,   HBA_N1_HBD_O_SCORE_MAX ,   HBA_N1_HBD_S_SCORE_SUM ,   HBA_N1_HBD_S_SCORE_MAX ,   HBA_Nar_HBD_N_SCORE_SUM ,   HBA_Nar_HBD_N_SCORE_MAX ,   HBA_Nar_HBD_O_SCORE_SUM ,   HBA_Nar_HBD_O_SCORE_MAX ,   HBA_Nar_HBD_S_SCORE_SUM ,   HBA_Nar_HBD_S_SCORE_MAX ,   HBA_Npl3_HBD_N_SCORE_SUM ,   HBA_Npl3_HBD_N_SCORE_MAX ,   HBA_Npl3_HBD_O_SCORE_SUM ,   HBA_Npl3_HBD_O_SCORE_MAX ,   HBA_Npl3_HBD_S_SCORE_SUM ,   HBA_Npl3_HBD_S_SCORE_MAX ,   HBA_O3_HBD_N_SCORE_SUM ,   HBA_O3_HBD_N_SCORE_MAX ,   HBA_O3_HBD_O_SCORE_SUM ,   HBA_O3_HBD_O_SCORE_MAX ,   HBA_O3_HBD_S_SCORE_SUM ,   HBA_O3_HBD_S_SCORE_MAX ,   HBA_O2_HBD_N_SCORE_SUM ,   HBA_O2_HBD_N_SCORE_MAX ,   HBA_O2_HBD_O_SCORE_SUM ,   HBA_O2_HBD_O_SCORE_MAX ,   HBA_O2_HBD_S_SCORE_SUM ,   HBA_O2_HBD_S_SCORE_MAX ,   HBA_Oco2_HBD_N_SCORE_SUM ,   HBA_Oco2_HBD_N_SCORE_MAX ,   HBA_Oco2_HBD_O_SCORE_SUM ,   HBA_Oco2_HBD_O_SCORE_MAX ,   HBA_Oco2_HBD_S_SCORE_SUM ,   HBA_Oco2_HBD_S_SCORE_MAX ,   HBA_S3_HBD_N_SCORE_SUM ,   HBA_S3_HBD_N_SCORE_MAX ,   HBA_S3_HBD_O_SCORE_SUM ,   HBA_S3_HBD_O_SCORE_MAX ,   HBA_S3_HBD_S_SCORE_SUM ,   HBA_S3_HBD_S_SCORE_MAX ,   HBA_S2_HBD_N_SCORE_SUM ,   HBA_S2_HBD_N_SCORE_MAX ,   HBA_S2_HBD_O_SCORE_SUM ,   HBA_S2_HBD_O_SCORE_MAX ,   HBA_S2_HBD_S_SCORE_SUM ,   HBA_S2_HBD_S_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 extended GRAIL-X descriptor vector. More...
typedef std::shared_ptr< GRAILXDescriptorCalculator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated GRAILXDescriptorCalculator instances. More...

Public Member Functions
	GRAILXDescriptorCalculator ()
	Constructs the GRAILXDescriptorCalculator instance. More...
	GRAILXDescriptorCalculator (const GRAILXDescriptorCalculator &calc)
	Constructs a copy of the GRAILXDescriptorCalculator instance calc. More...
	~GRAILXDescriptorCalculator ()
	Destructor. More...
GRAILXDescriptorCalculator &	operator= (const GRAILXDescriptorCalculator &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 extended GRAIL-X descriptor for the current ligand pose. More...

Static Public Attributes
static constexpr std::size_t	TOTAL_DESCRIPTOR_SIZE = 177
	Total number of elements in the calculated descriptor vector. More...
static constexpr std::size_t	LIGAND_DESCRIPTOR_SIZE = 31
	Number of ligand-only descriptor elements (the first LIGAND_DESCRIPTOR_SIZE entries of the vector). More...

Detailed Description

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

GRAILXDescriptorCalculator is the SYBYL-atom-type-aware variant of GRAIL::GRAILDescriptorCalculator. The resulting 177-element descriptor refines the generic hydrogen-bond donor/acceptor terms by also resolving the chemical environment (N3, N2, Nar, Nam, Npl3, N4, O3, O2, Oco2, S3, S2) of the participating heavy atom. The full element layout is given by ElementIndex.

See also

[GRADE]

Member Typedef Documentation

SharedPointer

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

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

Member Enumeration Documentation

ElementIndex

enum CDPL::GRAIL::GRAILXDescriptorCalculator::ElementIndex

Indices of the individual elements of the extended GRAIL-X descriptor vector.

The layout consists of six sections (in this order):

1. Feature/atom/bond counts of the ligand (positions [0, 8) and [26, 31)).
2. HBD / HBA counts of the ligand resolved by heavy atom SYBYL type (positions [8, 26)).
3. Target-environment H-bond occupancy SUM/MAX values resolved by ligand-feature heavy atom element ([31, 43)).
4. Generic interaction scores SUM/MAX (PI-AR, AR-PI, H-H, AR-AR) ([43, 51)).
5. Hydrogen-bond interaction SUM/MAX scores between ligand HBD/HBA subtype and target HBA/HBD by heavy atom element ([51, 171)).
6. Halogen-bond and energy terms ([171, 177)).

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).
HBD_N3_COUNT	Ligand HBD feature count with N3 heavy atom.
HBD_N2_COUNT	Ligand HBD feature count with N2 heavy atom.
HBD_Nar_COUNT	Ligand HBD feature count with Nar heavy atom.
HBD_Nam_COUNT	Ligand HBD feature count with Nam heavy atom.
HBD_Npl3_COUNT	Ligand HBD feature count with Npl3 heavy atom.
HBD_N4_COUNT	Ligand HBD feature count with N4 heavy atom.
HBD_O3_COUNT	Ligand HBD feature count with O3 heavy atom.
HBD_S3_COUNT	Ligand HBD feature count with S3 heavy atom.
HBA_N3_COUNT	Ligand HBA feature count with N3 heavy atom.
HBA_N2_COUNT	Ligand HBA feature count with N2 heavy atom.
HBA_N1_COUNT	Ligand HBA feature count with N1 heavy atom.
HBA_Nar_COUNT	Ligand HBA feature count with Nar heavy atom.
HBA_Npl3_COUNT	Ligand HBA feature count with Npl3 heavy atom.
HBA_O3_COUNT	Ligand HBA feature count with O3 heavy atom.
HBA_O2_COUNT	Ligand HBA feature count with O2 heavy atom.
HBA_Oco2_COUNT	Ligand HBA feature count with Oco2 heavy atom.
HBA_S3_COUNT	Ligand HBA feature count with S3 heavy atom.
HBA_S2_COUNT	Ligand HBA feature count with S2 heavy atom.
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_N_OCC_SUM	Sum of environment HBA occupancy scores against ligand HBD-N atoms.
ENV_HBA_N_OCC_MAX	Maximum environment HBA occupancy score against ligand HBD-N atoms.
ENV_HBA_O_OCC_SUM	Sum of environment HBA occupancy scores against ligand HBD-O atoms.
ENV_HBA_O_OCC_MAX	Maximum environment HBA occupancy score against ligand HBD-O atoms.
ENV_HBA_S_OCC_SUM	Sum of environment HBA occupancy scores against ligand HBD-S atoms.
ENV_HBA_S_OCC_MAX	Maximum environment HBA occupancy score against ligand HBD-S atoms.
ENV_HBD_N_OCC_SUM	Sum of environment HBD occupancy scores against ligand HBA-N atoms.
ENV_HBD_N_OCC_MAX	Maximum environment HBD occupancy score against ligand HBA-N atoms.
ENV_HBD_O_OCC_SUM	Sum of environment HBD occupancy scores against ligand HBA-O atoms.
ENV_HBD_O_OCC_MAX	Maximum environment HBD occupancy score against ligand HBA-O atoms.
ENV_HBD_S_OCC_SUM	Sum of environment HBD occupancy scores against ligand HBA-S atoms.
ENV_HBD_S_OCC_MAX	Maximum environment HBD occupancy score against ligand HBA-S atoms.
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_N_SCORE_SUM	Sum of (any ligand HBD → target HBA-N) interaction scores.
HBD_HBA_N_SCORE_MAX	Maximum (any ligand HBD → target HBA-N) interaction score.
HBD_HBA_O_SCORE_SUM	Sum of (any ligand HBD → target HBA-O) interaction scores.
HBD_HBA_O_SCORE_MAX	Maximum (any ligand HBD → target HBA-O) interaction score.
HBD_HBA_S_SCORE_SUM	Sum of (any ligand HBD → target HBA-S) interaction scores.
HBD_HBA_S_SCORE_MAX	Maximum (any ligand HBD → target HBA-S) interaction score.
HBD_N3_HBA_N_SCORE_SUM	Sum of (ligand HBD-N3 → target HBA-N) interaction scores.
HBD_N3_HBA_N_SCORE_MAX	Maximum (ligand HBD-N3 → target HBA-N) interaction score.
HBD_N3_HBA_O_SCORE_SUM	Sum of (ligand HBD-N3 → target HBA-O) interaction scores.
HBD_N3_HBA_O_SCORE_MAX	Maximum (ligand HBD-N3 → target HBA-O) interaction score.
HBD_N3_HBA_S_SCORE_SUM	Sum of (ligand HBD-N3 → target HBA-S) interaction scores.
HBD_N3_HBA_S_SCORE_MAX	Maximum (ligand HBD-N3 → target HBA-S) interaction score.
HBD_N2_HBA_N_SCORE_SUM	Sum of (ligand HBD-N2 → target HBA-N) interaction scores.
HBD_N2_HBA_N_SCORE_MAX	Maximum (ligand HBD-N2 → target HBA-N) interaction score.
HBD_N2_HBA_O_SCORE_SUM	Sum of (ligand HBD-N2 → target HBA-O) interaction scores.
HBD_N2_HBA_O_SCORE_MAX	Maximum (ligand HBD-N2 → target HBA-O) interaction score.
HBD_N2_HBA_S_SCORE_SUM	Sum of (ligand HBD-N2 → target HBA-S) interaction scores.
HBD_N2_HBA_S_SCORE_MAX	Maximum (ligand HBD-N2 → target HBA-S) interaction score.
HBD_Nar_HBA_N_SCORE_SUM	Sum of (ligand HBD-Nar → target HBA-N) interaction scores.
HBD_Nar_HBA_N_SCORE_MAX	Maximum (ligand HBD-Nar → target HBA-N) interaction score.
HBD_Nar_HBA_O_SCORE_SUM	Sum of (ligand HBD-Nar → target HBA-O) interaction scores.
HBD_Nar_HBA_O_SCORE_MAX	Maximum (ligand HBD-Nar → target HBA-O) interaction score.
HBD_Nar_HBA_S_SCORE_SUM	Sum of (ligand HBD-Nar → target HBA-S) interaction scores.
HBD_Nar_HBA_S_SCORE_MAX	Maximum (ligand HBD-Nar → target HBA-S) interaction score.
HBD_Nam_HBA_N_SCORE_SUM	Sum of (ligand HBD-Nam → target HBA-N) interaction scores.
HBD_Nam_HBA_N_SCORE_MAX	Maximum (ligand HBD-Nam → target HBA-N) interaction score.
HBD_Nam_HBA_O_SCORE_SUM	Sum of (ligand HBD-Nam → target HBA-O) interaction scores.
HBD_Nam_HBA_O_SCORE_MAX	Maximum (ligand HBD-Nam → target HBA-O) interaction score.
HBD_Nam_HBA_S_SCORE_SUM	Sum of (ligand HBD-Nam → target HBA-S) interaction scores.
HBD_Nam_HBA_S_SCORE_MAX	Maximum (ligand HBD-Nam → target HBA-S) interaction score.
HBD_Npl3_HBA_N_SCORE_SUM	Sum of (ligand HBD-Npl3 → target HBA-N) interaction scores.
HBD_Npl3_HBA_N_SCORE_MAX	Maximum (ligand HBD-Npl3 → target HBA-N) interaction score.
HBD_Npl3_HBA_O_SCORE_SUM	Sum of (ligand HBD-Npl3 → target HBA-O) interaction scores.
HBD_Npl3_HBA_O_SCORE_MAX	Maximum (ligand HBD-Npl3 → target HBA-O) interaction score.
HBD_Npl3_HBA_S_SCORE_SUM	Sum of (ligand HBD-Npl3 → target HBA-S) interaction scores.
HBD_Npl3_HBA_S_SCORE_MAX	Maximum (ligand HBD-Npl3 → target HBA-S) interaction score.
HBD_N4_HBA_N_SCORE_SUM	Sum of (ligand HBD-N4 → target HBA-N) interaction scores.
HBD_N4_HBA_N_SCORE_MAX	Maximum (ligand HBD-N4 → target HBA-N) interaction score.
HBD_N4_HBA_O_SCORE_SUM	Sum of (ligand HBD-N4 → target HBA-O) interaction scores.
HBD_N4_HBA_O_SCORE_MAX	Maximum (ligand HBD-N4 → target HBA-O) interaction score.
HBD_N4_HBA_S_SCORE_SUM	Sum of (ligand HBD-N4 → target HBA-S) interaction scores.
HBD_N4_HBA_S_SCORE_MAX	Maximum (ligand HBD-N4 → target HBA-S) interaction score.
HBD_O3_HBA_N_SCORE_SUM	Sum of (ligand HBD-O3 → target HBA-N) interaction scores.
HBD_O3_HBA_N_SCORE_MAX	Maximum (ligand HBD-O3 → target HBA-N) interaction score.
HBD_O3_HBA_O_SCORE_SUM	Sum of (ligand HBD-O3 → target HBA-O) interaction scores.
HBD_O3_HBA_O_SCORE_MAX	Maximum (ligand HBD-O3 → target HBA-O) interaction score.
HBD_O3_HBA_S_SCORE_SUM	Sum of (ligand HBD-O3 → target HBA-S) interaction scores.
HBD_O3_HBA_S_SCORE_MAX	Maximum (ligand HBD-O3 → target HBA-S) interaction score.
HBD_S3_HBA_N_SCORE_SUM	Sum of (ligand HBD-S3 → target HBA-N) interaction scores.
HBD_S3_HBA_N_SCORE_MAX	Maximum (ligand HBD-S3 → target HBA-N) interaction score.
HBD_S3_HBA_O_SCORE_SUM	Sum of (ligand HBD-S3 → target HBA-O) interaction scores.
HBD_S3_HBA_O_SCORE_MAX	Maximum (ligand HBD-S3 → target HBA-O) interaction score.
HBD_S3_HBA_S_SCORE_SUM	Sum of (ligand HBD-S3 → target HBA-S) interaction scores.
HBD_S3_HBA_S_SCORE_MAX	Maximum (ligand HBD-S3 → target HBA-S) interaction score.
HBA_HBD_N_SCORE_SUM	Sum of (any ligand HBA → target HBD-N) interaction scores.
HBA_HBD_N_SCORE_MAX	Maximum (any ligand HBA → target HBD-N) interaction score.
HBA_HBD_O_SCORE_SUM	Sum of (any ligand HBA → target HBD-O) interaction scores.
HBA_HBD_O_SCORE_MAX	Maximum (any ligand HBA → target HBD-O) interaction score.
HBA_HBD_S_SCORE_SUM	Sum of (any ligand HBA → target HBD-S) interaction scores.
HBA_HBD_S_SCORE_MAX	Maximum (any ligand HBA → target HBD-S) interaction score.
HBA_N3_HBD_N_SCORE_SUM	Sum of (ligand HBA-N3 → target HBD-N) interaction scores.
HBA_N3_HBD_N_SCORE_MAX	Maximum (ligand HBA-N3 → target HBD-N) interaction score.
HBA_N3_HBD_O_SCORE_SUM	Sum of (ligand HBA-N3 → target HBD-O) interaction scores.
HBA_N3_HBD_O_SCORE_MAX	Maximum (ligand HBA-N3 → target HBD-O) interaction score.
HBA_N3_HBD_S_SCORE_SUM	Sum of (ligand HBA-N3 → target HBD-S) interaction scores.
HBA_N3_HBD_S_SCORE_MAX	Maximum (ligand HBA-N3 → target HBD-S) interaction score.
HBA_N2_HBD_N_SCORE_SUM	Sum of (ligand HBA-N2 → target HBD-N) interaction scores.
HBA_N2_HBD_N_SCORE_MAX	Maximum (ligand HBA-N2 → target HBD-N) interaction score.
HBA_N2_HBD_O_SCORE_SUM	Sum of (ligand HBA-N2 → target HBD-O) interaction scores.
HBA_N2_HBD_O_SCORE_MAX	Maximum (ligand HBA-N2 → target HBD-O) interaction score.
HBA_N2_HBD_S_SCORE_SUM	Sum of (ligand HBA-N2 → target HBD-S) interaction scores.
HBA_N2_HBD_S_SCORE_MAX	Maximum (ligand HBA-N2 → target HBD-S) interaction score.
HBA_N1_HBD_N_SCORE_SUM	Sum of (ligand HBA-N1 → target HBD-N) interaction scores.
HBA_N1_HBD_N_SCORE_MAX	Maximum (ligand HBA-N1 → target HBD-N) interaction score.
HBA_N1_HBD_O_SCORE_SUM	Sum of (ligand HBA-N1 → target HBD-O) interaction scores.
HBA_N1_HBD_O_SCORE_MAX	Maximum (ligand HBA-N1 → target HBD-O) interaction score.
HBA_N1_HBD_S_SCORE_SUM	Sum of (ligand HBA-N1 → target HBD-S) interaction scores.
HBA_N1_HBD_S_SCORE_MAX	Maximum (ligand HBA-N1 → target HBD-S) interaction score.
HBA_Nar_HBD_N_SCORE_SUM	Sum of (ligand HBA-Nar → target HBD-N) interaction scores.
HBA_Nar_HBD_N_SCORE_MAX	Maximum (ligand HBA-Nar → target HBD-N) interaction score.
HBA_Nar_HBD_O_SCORE_SUM	Sum of (ligand HBA-Nar → target HBD-O) interaction scores.
HBA_Nar_HBD_O_SCORE_MAX	Maximum (ligand HBA-Nar → target HBD-O) interaction score.
HBA_Nar_HBD_S_SCORE_SUM	Sum of (ligand HBA-Nar → target HBD-S) interaction scores.
HBA_Nar_HBD_S_SCORE_MAX	Maximum (ligand HBA-Nar → target HBD-S) interaction score.
HBA_Npl3_HBD_N_SCORE_SUM	Sum of (ligand HBA-Npl3 → target HBD-N) interaction scores.
HBA_Npl3_HBD_N_SCORE_MAX	Maximum (ligand HBA-Npl3 → target HBD-N) interaction score.
HBA_Npl3_HBD_O_SCORE_SUM	Sum of (ligand HBA-Npl3 → target HBD-O) interaction scores.
HBA_Npl3_HBD_O_SCORE_MAX	Maximum (ligand HBA-Npl3 → target HBD-O) interaction score.
HBA_Npl3_HBD_S_SCORE_SUM	Sum of (ligand HBA-Npl3 → target HBD-S) interaction scores.
HBA_Npl3_HBD_S_SCORE_MAX	Maximum (ligand HBA-Npl3 → target HBD-S) interaction score.
HBA_O3_HBD_N_SCORE_SUM	Sum of (ligand HBA-O3 → target HBD-N) interaction scores.
HBA_O3_HBD_N_SCORE_MAX	Maximum (ligand HBA-O3 → target HBD-N) interaction score.
HBA_O3_HBD_O_SCORE_SUM	Sum of (ligand HBA-O3 → target HBD-O) interaction scores.
HBA_O3_HBD_O_SCORE_MAX	Maximum (ligand HBA-O3 → target HBD-O) interaction score.
HBA_O3_HBD_S_SCORE_SUM	Sum of (ligand HBA-O3 → target HBD-S) interaction scores.
HBA_O3_HBD_S_SCORE_MAX	Maximum (ligand HBA-O3 → target HBD-S) interaction score.
HBA_O2_HBD_N_SCORE_SUM	Sum of (ligand HBA-O2 → target HBD-N) interaction scores.
HBA_O2_HBD_N_SCORE_MAX	Maximum (ligand HBA-O2 → target HBD-N) interaction score.
HBA_O2_HBD_O_SCORE_SUM	Sum of (ligand HBA-O2 → target HBD-O) interaction scores.
HBA_O2_HBD_O_SCORE_MAX	Maximum (ligand HBA-O2 → target HBD-O) interaction score.
HBA_O2_HBD_S_SCORE_SUM	Sum of (ligand HBA-O2 → target HBD-S) interaction scores.
HBA_O2_HBD_S_SCORE_MAX	Maximum (ligand HBA-O2 → target HBD-S) interaction score.
HBA_Oco2_HBD_N_SCORE_SUM	Sum of (ligand HBA-Oco2 → target HBD-N) interaction scores.
HBA_Oco2_HBD_N_SCORE_MAX	Maximum (ligand HBA-Oco2 → target HBD-N) interaction score.
HBA_Oco2_HBD_O_SCORE_SUM	Sum of (ligand HBA-Oco2 → target HBD-O) interaction scores.
HBA_Oco2_HBD_O_SCORE_MAX	Maximum (ligand HBA-Oco2 → target HBD-O) interaction score.
HBA_Oco2_HBD_S_SCORE_SUM	Sum of (ligand HBA-Oco2 → target HBD-S) interaction scores.
HBA_Oco2_HBD_S_SCORE_MAX	Maximum (ligand HBA-Oco2 → target HBD-S) interaction score.
HBA_S3_HBD_N_SCORE_SUM	Sum of (ligand HBA-S3 → target HBD-N) interaction scores.
HBA_S3_HBD_N_SCORE_MAX	Maximum (ligand HBA-S3 → target HBD-N) interaction score.
HBA_S3_HBD_O_SCORE_SUM	Sum of (ligand HBA-S3 → target HBD-O) interaction scores.
HBA_S3_HBD_O_SCORE_MAX	Maximum (ligand HBA-S3 → target HBD-O) interaction score.
HBA_S3_HBD_S_SCORE_SUM	Sum of (ligand HBA-S3 → target HBD-S) interaction scores.
HBA_S3_HBD_S_SCORE_MAX	Maximum (ligand HBA-S3 → target HBD-S) interaction score.
HBA_S2_HBD_N_SCORE_SUM	Sum of (ligand HBA-S2 → target HBD-N) interaction scores.
HBA_S2_HBD_N_SCORE_MAX	Maximum (ligand HBA-S2 → target HBD-N) interaction score.
HBA_S2_HBD_O_SCORE_SUM	Sum of (ligand HBA-S2 → target HBD-O) interaction scores.
HBA_S2_HBD_O_SCORE_MAX	Maximum (ligand HBA-S2 → target HBD-O) interaction score.
HBA_S2_HBD_S_SCORE_SUM	Sum of (ligand HBA-S2 → target HBD-S) interaction scores.
HBA_S2_HBD_S_SCORE_MAX	Maximum (ligand HBA-S2 → target HBD-S) 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

GRAILXDescriptorCalculator() [1/2]

CDPL::GRAIL::GRAILXDescriptorCalculator::GRAILXDescriptorCalculator

(

)

Constructs the GRAILXDescriptorCalculator instance.

GRAILXDescriptorCalculator() [2/2]

CDPL::GRAIL::GRAILXDescriptorCalculator::GRAILXDescriptorCalculator

(

const GRAILXDescriptorCalculator &

calc

)

Constructs a copy of the GRAILXDescriptorCalculator instance calc.

Parameters

calc	The GRAILXDescriptorCalculator to copy.

~GRAILXDescriptorCalculator()

CDPL::GRAIL::GRAILXDescriptorCalculator::~GRAILXDescriptorCalculator

(

)

Destructor.

Member Function Documentation

operator=()

GRAILXDescriptorCalculator& CDPL::GRAIL::GRAILXDescriptorCalculator::operator=

(

const GRAILXDescriptorCalculator &

calc

)

Copy assignment operator.

Parameters

calc	The other GRAILXDescriptorCalculator instance.

Returns

A reference to itself.

initTargetData()

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

Calculates the extended GRAIL-X 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::GRAILXDescriptorCalculator::TOTAL_DESCRIPTOR_SIZE = 177

staticconstexpr

Total number of elements in the calculated descriptor vector.

LIGAND_DESCRIPTOR_SIZE

constexpr std::size_t CDPL::GRAIL::GRAILXDescriptorCalculator::LIGAND_DESCRIPTOR_SIZE = 31

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:

• GRAILXDescriptorCalculator.hpp