CDPL.Chem.Hydrogen3DCoordinatesCalculator Class Reference

Hydrogen3DCoordinatesCalculator. More...

Inheritance diagram for CDPL.Chem.Hydrogen3DCoordinatesCalculator:

Public Member Functions
None	__init__ ()
	Constructs the Hydrogen3DCoordinatesCalculator instance.
None	__init__ (MolecularGraph molgraph, Math.Vector3DArray coords, bool undef_only=True)
	Constructs the Hydrogen3DCoordinatesCalculator instance and calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	undefinedOnly (bool undef_only)
	Allows to specify whether already defined hydrogen atom coordinates have to be recalculated or are left unchanged. More...
bool	undefinedOnly ()
	Tells whether already defined hydrogen atom coordinates are recalculated or left unchanged. More...
None	setAtom3DCoordinatesFunction (Atom3DCoordinatesFunction func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...
Atom3DCoordinatesFunction	getAtom3DCoordinatesFunction ()
	Returns the function that was registered for the retrieval of atom 3D-coordinates. More...
None	setAtom3DCoordinatesCheckFunction (AtomPredicate func)
	Specifies a function that tells whether 3D coordinates are available for it's argument atom. More...
AtomPredicate	getAtom3DCoordinatesCheckFunction ()
	Returns the function that was registered to determine whether for a given atom 3D coordinates are available. More...
None	setup (MolecularGraph molgraph)
None	calculate (MolecularGraph molgraph, Math.Vector3DArray coords, bool init_coords=True)
	Calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph. More...
None	calculate (Math.Vector3DArray coords, bool init_coords=True)

Properties
	objectID = property(getObjectID)
	undefOnly = property(undefinedOnly, undefinedOnly)
	atomCoordsFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesCheckFunction)
	atomCoordsCheckFunction = property(getAtom3DCoordinatesCheckFunction, setAtom3DCoordinatesCheckFunction)

Detailed Description

Hydrogen3DCoordinatesCalculator.

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.__init__	(	MolecularGraph	molgraph,
		Math.Vector3DArray	coords,
		bool	undef_only = True
	)

Constructs the Hydrogen3DCoordinatesCalculator instance and calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph.

The calculated coordinates can be retrieved by a call to getResult().

Parameters

molgraph	The molecular graph for which to calculate 3D-coordinates.
coords	An array containing the heavy atom and calculated hydrogen 3D-coordinates. The coordinates are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the coordinates of an atom are accessible via its index).
undef_only	Specifies whether or not to recalculate already defined hydrogen atom coordinates.

Member Function Documentation

getObjectID()

int CDPL.Chem.Hydrogen3DCoordinatesCalculator.getObjectID

(

)

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

Different Python Hydrogen3DCoordinatesCalculator 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 Hydrogen3DCoordinatesCalculator 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.

undefinedOnly() [1/2]

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.undefinedOnly

(

bool

undef_only

)

Allows to specify whether already defined hydrogen atom coordinates have to be recalculated or are left unchanged.

Parameters

undef_only

True if already defined hydrogen atom coordinates have to be left unchanged, and False otherwise.

Note

The default setting is to calculate coordinates only for hydrogens with not yet defined positions.

undefinedOnly() [2/2]

bool CDPL.Chem.Hydrogen3DCoordinatesCalculator.undefinedOnly

(

)

Tells whether already defined hydrogen atom coordinates are recalculated or left unchanged.

Returns

True if already defined hydrogen atom coordinates are left unchanged, and False otherwise.

setAtom3DCoordinatesFunction()

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.setAtom3DCoordinatesFunction

(

Atom3DCoordinatesFunction

func

)

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

Parameters

func	The atom 3D-coordinates function.

getAtom3DCoordinatesFunction()

Atom3DCoordinatesFunction CDPL.Chem.Hydrogen3DCoordinatesCalculator.getAtom3DCoordinatesFunction

(

)

Returns the function that was registered for the retrieval of atom 3D-coordinates.

Returns

The registered atom 3D-coordinates function.

setAtom3DCoordinatesCheckFunction()

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.setAtom3DCoordinatesCheckFunction

(

AtomPredicate

func

)

Specifies a function that tells whether 3D coordinates are available for it's argument atom.

Parameters

func	The atom 3D coordinates check function.

getAtom3DCoordinatesCheckFunction()

AtomPredicate CDPL.Chem.Hydrogen3DCoordinatesCalculator.getAtom3DCoordinatesCheckFunction

(

)

Returns the function that was registered to determine whether for a given atom 3D coordinates are available.

Returns

The registered atom 3D coordinates check function.

setup()

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.setup

(

MolecularGraph

molgraph

)

Parameters

molgraph

calculate() [1/2]

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.calculate	(	MolecularGraph	molgraph,
		Math.Vector3DArray	coords,
		bool	init_coords = True
	)

Calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to calculate 3D-coordinates.
coords	An array containing the heavy atom and calculated hydrogen 3D-coordinates. The coordinates are stored in the same order as the atoms appear in the atom list of the molecular graph (i.e. the coordinates of an atom are accessible via its index).
init_coords	If False, defined atom coordinates are already present in coords and thus won't get assigned again.

calculate() [2/2]

None CDPL.Chem.Hydrogen3DCoordinatesCalculator.calculate	(	Math.Vector3DArray	coords,
		bool	init_coords = True
	)

Parameters

coords
init_coords