CDPL.GRAIL.GRAILDescriptorCalculator Class Reference

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

Inheritance diagram for CDPL.GRAIL.GRAILDescriptorCalculator:

Classes
class	ElementIndex
	Indices of the individual elements of the GRAIL descriptor vector. More...

Public Member Functions
None	__init__ ()
	Constructs the GRAILDescriptorCalculator instance.
None	__init__ (GRAILDescriptorCalculator calc)
	Constructs a copy of the GRAILDescriptorCalculator instance calc. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
GRAILDescriptorCalculator	assign (GRAILDescriptorCalculator calc)
	Copy assignment operator. More...
None	initTargetData (Chem.MolecularGraph tgt_env, Chem.Atom3DCoordinatesFunction coords_func, bool tgt_env_changed=True)
	Initializes the calculator with target-environment data for subsequent descriptor calculations. More...
None	initLigandData (Chem.MolecularGraph ligand)
	Initializes the calculator with the molecular graph of the ligand. More...
None	calculate (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
int	TOTAL_DESCRIPTOR_SIZE = 35
	Total number of elements in the calculated descriptor vector.
int	LIGAND_DESCRIPTOR_SIZE = 13
	Number of ligand-only descriptor elements (the first LIGAND_DESCRIPTOR_SIZE entries of the vector).

Properties
	objectID = property(getObjectID)

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]

Constructor & Destructor Documentation

__init__()

None CDPL.GRAIL.GRAILDescriptorCalculator.__init__

(

GRAILDescriptorCalculator

calc

)

Constructs a copy of the GRAILDescriptorCalculator instance calc.

Parameters

calc	The GRAILDescriptorCalculator to copy.

Member Function Documentation

getObjectID()

int CDPL.GRAIL.GRAILDescriptorCalculator.getObjectID

(

)

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python GRAILDescriptorCalculator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two GRAILDescriptorCalculator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns

The numeric ID of the internally referenced C++ class instance.

assign()

GRAILDescriptorCalculator CDPL.GRAIL.GRAILDescriptorCalculator.assign

(

GRAILDescriptorCalculator

calc

)

Copy assignment operator.

Parameters

calc	The other GRAILDescriptorCalculator instance.

Returns

self

initTargetData()

None CDPL.GRAIL.GRAILDescriptorCalculator.initTargetData	(	Chem.MolecularGraph	tgt_env,
		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()

None CDPL.GRAIL.GRAILDescriptorCalculator.initLigandData

(

Chem.MolecularGraph

ligand

)

Initializes the calculator with the molecular graph of the ligand.

Parameters

ligand

The ligand molecular graph.

calculate()

None CDPL.GRAIL.GRAILDescriptorCalculator.calculate	(	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.