CDPL.GRAIL.AtomDensityGridCalculator Class Reference

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

Inheritance diagram for CDPL.GRAIL.AtomDensityGridCalculator:

Public Member Functions
None	__init__ ()
	Constructs the AtomDensityGridCalculator instance.
None	__init__ (Chem.DoubleVector3D2AtomFunctor func)
	Constructs the AtomDensityGridCalculator instance with the given density function. More...
None	__init__ (Chem.DoubleVector3D2AtomFunctor density_func, Math.DoubleDVectorFunctor comb_func)
	Constructs the AtomDensityGridCalculator instance with the given density and density-combination functions. More...
None	__init__ (AtomDensityGridCalculator calc)
	Constructs a copy of the AtomDensityGridCalculator instance calc. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
AtomDensityGridCalculator	assign (AtomDensityGridCalculator calc)
	Copy assignment operator. More...
None	setDistanceCutoff (float dist)
	Sets the distance cutoff beyond which atoms are not considered. More...
float	getDistanceCutoff ()
	Returns the currently configured distance cutoff. More...
Chem.DoubleVector3D2AtomFunctor	getDensityFunction ()
	Returns the currently configured density function. More...
None	setDensityFunction (Chem.DoubleVector3D2AtomFunctor func)
	Sets the density function used to evaluate per-atom contributions. More...
None	setDensityCombinationFunction (Math.DoubleDVectorFunctor func)
	Sets the function used to combine per-atom density contributions. More...
Math.DoubleDVectorFunctor	getDensityCombinationFunction ()
	Returns the currently configured density-combination function. More...
None	setAtom3DCoordinatesFunction (Chem.Atom3DCoordinatesFunction func)
	Specifies a function for the retrieval of atom 3D-coordinates for grid calculation. More...
Chem.Atom3DCoordinatesFunction	getAtom3DCoordinatesFunction ()
	Returns the function used for the retrieval of atom 3D-coordinates. More...
None	calculate (Chem.AtomContainer atoms, Grid.DSpatialGrid grid)
	Calculates the combined per-atom density at each cell of grid for the given atoms. More...

Properties
	objectID = property(getObjectID)
	distanceCutoff = property(getDistanceCutoff, setDistanceCutoff)
	densityFunction = property(getDensityFunction, setDensityFunction)
	densityCombFunction = property(getDensityCombinationFunction, setDensityCombinationFunction)
	atomCoordsFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesFunction)

Detailed Description

Calculator that fills a spatial grid with combined per-atom density contributions.

For each grid cell, the density contributions of all atoms within the configured cutoff distance are evaluated using a user-supplied density function and combined into a single cell value via a user-supplied combination function (defaulting to a sum).

Constructor & Destructor Documentation

__init__() [1/3]

None CDPL.GRAIL.AtomDensityGridCalculator.__init__

(

Chem.DoubleVector3D2AtomFunctor

func

)

Constructs the AtomDensityGridCalculator instance with the given density function.

Parameters

func	The density function.

__init__() [2/3]

None CDPL.GRAIL.AtomDensityGridCalculator.__init__	(	Chem.DoubleVector3D2AtomFunctor	density_func,
		Math.DoubleDVectorFunctor	comb_func
	)

Constructs the AtomDensityGridCalculator instance with the given density and density-combination functions.

Parameters

density_func	The density function.
comb_func	The function used to combine per-atom density contributions.

__init__() [3/3]

None CDPL.GRAIL.AtomDensityGridCalculator.__init__

(

AtomDensityGridCalculator

calc

)

Constructs a copy of the AtomDensityGridCalculator instance calc.

Parameters

calc	The AtomDensityGridCalculator to copy.

Member Function Documentation

getObjectID()

int CDPL.GRAIL.AtomDensityGridCalculator.getObjectID

(

)

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

Different Python AtomDensityGridCalculator 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 AtomDensityGridCalculator 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()

AtomDensityGridCalculator CDPL.GRAIL.AtomDensityGridCalculator.assign

(

AtomDensityGridCalculator

calc

)

Copy assignment operator.

Parameters

calc	The other AtomDensityGridCalculator instance.

Returns

self

setDistanceCutoff()

None CDPL.GRAIL.AtomDensityGridCalculator.setDistanceCutoff

(

float

dist

)

Sets the distance cutoff beyond which atoms are not considered.

Parameters

dist	The cutoff distance.

getDistanceCutoff()

float CDPL.GRAIL.AtomDensityGridCalculator.getDistanceCutoff

(

)

Returns the currently configured distance cutoff.

Returns

The configured cutoff distance.

getDensityFunction()

Chem.DoubleVector3D2AtomFunctor CDPL.GRAIL.AtomDensityGridCalculator.getDensityFunction

(

)

Returns the currently configured density function.

Returns

The configured density function.

setDensityFunction()

None CDPL.GRAIL.AtomDensityGridCalculator.setDensityFunction

(

Chem.DoubleVector3D2AtomFunctor

func

)

Sets the density function used to evaluate per-atom contributions.

Parameters

func	The density function.

setDensityCombinationFunction()

None CDPL.GRAIL.AtomDensityGridCalculator.setDensityCombinationFunction

(

Math.DoubleDVectorFunctor

func

)

Sets the function used to combine per-atom density contributions.

Parameters

func	The density-combination function.

getDensityCombinationFunction()

Math.DoubleDVectorFunctor CDPL.GRAIL.AtomDensityGridCalculator.getDensityCombinationFunction

(

)

Returns the currently configured density-combination function.

Returns

The configured density-combination function.

setAtom3DCoordinatesFunction()

None CDPL.GRAIL.AtomDensityGridCalculator.setAtom3DCoordinatesFunction

(

Chem.Atom3DCoordinatesFunction

func

)

Specifies a function for the retrieval of atom 3D-coordinates for grid calculation.

Parameters

func	The atom 3D-coordinates function.

getAtom3DCoordinatesFunction()

Chem.Atom3DCoordinatesFunction CDPL.GRAIL.AtomDensityGridCalculator.getAtom3DCoordinatesFunction

(

)

Returns the function used for the retrieval of atom 3D-coordinates.

Returns

The configured atom 3D-coordinates function.

calculate()

None CDPL.GRAIL.AtomDensityGridCalculator.calculate	(	Chem.AtomContainer	atoms,
		Grid.DSpatialGrid	grid
	)

Calculates the combined per-atom density at each cell of grid for the given atoms.

Parameters

atoms	The atoms contributing to the density.
grid	The output grid populated with per-cell density values.