CDPL::Chem::Hydrogen3DCoordinatesCalculator Class Reference

Hydrogen3DCoordinatesCalculator. More...

#include <Hydrogen3DCoordinatesCalculator.hpp>

Public Member Functions
	Hydrogen3DCoordinatesCalculator ()
	Constructs the Hydrogen3DCoordinatesCalculator instance. More...
	Hydrogen3DCoordinatesCalculator (const 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...
void	undefinedOnly (bool undef_only)
	Allows to specify whether already defined hydrogen atom coordinates have to be recalculated or are left unchanged. More...
bool	undefinedOnly () const
	Tells whether already defined hydrogen atom coordinates are recalculated or left unchanged. More...
void	setAtom3DCoordinatesCheckFunction (const AtomPredicate &func)
	Specifies a function that tells whether 3D coordinates are available for it's argument atom. More...
const AtomPredicate &	getAtom3DCoordinatesCheckFunction () const
	Returns the function that was registered to determine whether for a given atom 3D coordinates are available. More...
void	setAtom3DCoordinatesFunction (const Atom3DCoordinatesFunction &func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...
const Atom3DCoordinatesFunction &	getAtom3DCoordinatesFunction () const
	Returns the function that was registered for the retrieval of atom 3D-coordinates. More...
void	setup (const MolecularGraph &molgraph)
void	calculate (const MolecularGraph &molgraph, Math::Vector3DArray &coords, bool init_coords=true)
	Calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph. More...
void	calculate (Math::Vector3DArray &coords, bool init_coords=true)

Detailed Description

Hydrogen3DCoordinatesCalculator.

Constructor & Destructor Documentation

Hydrogen3DCoordinatesCalculator() [1/2]

CDPL::Chem::Hydrogen3DCoordinatesCalculator::Hydrogen3DCoordinatesCalculator

(

)

Constructs the Hydrogen3DCoordinatesCalculator instance.

Hydrogen3DCoordinatesCalculator() [2/2]

CDPL::Chem::Hydrogen3DCoordinatesCalculator::Hydrogen3DCoordinatesCalculator	(	const 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

undefinedOnly() [1/2]

void 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

(

)

const

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.

setAtom3DCoordinatesCheckFunction()

void CDPL::Chem::Hydrogen3DCoordinatesCalculator::setAtom3DCoordinatesCheckFunction

(

const 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()

const AtomPredicate& CDPL::Chem::Hydrogen3DCoordinatesCalculator::getAtom3DCoordinatesCheckFunction

(

)

const

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.

setAtom3DCoordinatesFunction()

void CDPL::Chem::Hydrogen3DCoordinatesCalculator::setAtom3DCoordinatesFunction

(

const Atom3DCoordinatesFunction &

func

)

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

Parameters

func	The atom 3D-coordinates function.

getAtom3DCoordinatesFunction()

const Atom3DCoordinatesFunction& CDPL::Chem::Hydrogen3DCoordinatesCalculator::getAtom3DCoordinatesFunction

(

)

const

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

Returns

The registered atom 3D-coordinates function.

setup()

void CDPL::Chem::Hydrogen3DCoordinatesCalculator::setup

(

const MolecularGraph &

molgraph

)

calculate() [1/2]

void CDPL::Chem::Hydrogen3DCoordinatesCalculator::calculate	(	const 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]

void CDPL::Chem::Hydrogen3DCoordinatesCalculator::calculate	(	Math::Vector3DArray &	coords,
		bool	init_coords = true
	)

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The documentation for this class was generated from the following file:

• Hydrogen3DCoordinatesCalculator.hpp