CDPL.GRAIL.GRAILXDescriptorCalculator Class Reference

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

Inheritance diagram for CDPL.GRAIL.GRAILXDescriptorCalculator:

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

Public Member Functions
None	__init__ ()
	Constructs the GRAILXDescriptorCalculator instance.
None	__init__ (GRAILXDescriptorCalculator calc)
	Constructs a copy of the GRAILXDescriptorCalculator instance calc. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
GRAILXDescriptorCalculator	assign (GRAILXDescriptorCalculator 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 extended GRAIL-X descriptor for the current ligand pose. More...

Static Public Attributes
int	TOTAL_DESCRIPTOR_SIZE = 177
	Total number of elements in the calculated descriptor vector.
int	LIGAND_DESCRIPTOR_SIZE = 31
	Number of ligand-only descriptor elements (the first LIGAND_DESCRIPTOR_SIZE entries of the vector).

Properties
	objectID = property(getObjectID)

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]

Constructor & Destructor Documentation

__init__()

None CDPL.GRAIL.GRAILXDescriptorCalculator.__init__

(

GRAILXDescriptorCalculator

calc

)

Constructs a copy of the GRAILXDescriptorCalculator instance calc.

Parameters

calc	The GRAILXDescriptorCalculator to copy.

Member Function Documentation

getObjectID()

int CDPL.GRAIL.GRAILXDescriptorCalculator.getObjectID

(

)

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

Different Python GRAILXDescriptorCalculator 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 GRAILXDescriptorCalculator 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()

GRAILXDescriptorCalculator CDPL.GRAIL.GRAILXDescriptorCalculator.assign

(

GRAILXDescriptorCalculator

calc

)

Copy assignment operator.

Parameters

calc	The other GRAILXDescriptorCalculator instance.

Returns

self

initTargetData()

None CDPL.GRAIL.GRAILXDescriptorCalculator.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.GRAILXDescriptorCalculator.initLigandData

(

Chem.MolecularGraph

ligand

)

Initializes the calculator with the molecular graph of the ligand.

Parameters

ligand

The ligand molecular graph.

calculate()

None CDPL.GRAIL.GRAILXDescriptorCalculator.calculate	(	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.