Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates. More...

#include <MMFF94GradientCalculator.hpp>

Public Member Functions
	MMFF94GradientCalculator ()
	Constructs the calculator without an associated ForceField::MMFF94InteractionData instance. More...

	MMFF94GradientCalculator (const MMFF94InteractionData &ia_data, std::size_t num_atoms)
	Constructs the calculator and associates it with the supplied ForceField::MMFF94InteractionData instance. More...

void	setEnabledInteractionTypes (unsigned int types)
	Enables/disables specific MMFF94 interaction-type contributions. More...

unsigned int	getEnabledInteractionTypes () const
	Returns the currently enabled interaction-type contributions. More...

void	setup (const MMFF94InteractionData &ia_data, std::size_t num_atoms)
	Associates the calculator with the supplied ForceField::MMFF94InteractionData instance and atom count. More...

template<typename CoordsArray >
const ValueType &	operator() (const CoordsArray &coords)
	Computes the total MMFF94 energy of the conformation specified by coords without calculating the gradient. More...

template<typename CoordsArray , typename GradVector >
const ValueType &	operator() (const CoordsArray &coords, GradVector &grad)
	Computes the total MMFF94 energy and the per-atom gradient of the conformation specified by coords. More...

const ValueType &	getTotalEnergy () const
	Returns the total MMFF94 energy computed by the most recent operator()() call. More...

const ValueType &	getBondStretchingEnergy () const
	Returns the bond-stretching energy contribution computed by the most recent operator()() call. More...

const ValueType &	getAngleBendingEnergy () const
	Returns the angle-bending energy contribution computed by the most recent operator()() call. More...

const ValueType &	getStretchBendEnergy () const
	Returns the stretch-bend coupling energy contribution computed by the most recent operator()() call. More...

const ValueType &	getOutOfPlaneBendingEnergy () const
	Returns the out-of-plane bending energy contribution computed by the most recent operator()() call. More...

const ValueType &	getTorsionEnergy () const
	Returns the torsion energy contribution computed by the most recent operator()() call. More...

const ValueType &	getElectrostaticEnergy () const
	Returns the electrostatic energy contribution computed by the most recent operator()() call. More...

const ValueType &	getVanDerWaalsEnergy () const
	Returns the Van der Waals energy contribution computed by the most recent operator()() call. More...

const Util::BitSet &	getFixedAtomMask () const
	Returns the bit mask flagging atoms whose gradient components are zeroed after evaluation. More...

void	setFixedAtomMask (const Util::BitSet &mask)
	Sets the bit mask flagging atoms whose gradient components shall be zeroed after calculation. More...

void	resetFixedAtomMask ()
	Clears the fixed-atom mask so that all atoms contribute to the gradient. More...

Detailed Description

template<typename ValueType>
class CDPL::ForceField::MMFF94GradientCalculator< ValueType >

Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates.

The calculator takes a ForceField::MMFF94InteractionData instance and the atom count of the molecule and computes both the total MMFF94 energy and the analytical Cartesian gradient \( \partial E / \partial \mathbf{r}_i \) for each atom. The per-component energies are retained and made available via the dedicated accessors. A bit mask can be set to mark atoms whose gradient contributions are zeroed, freezing them during an energy minimization run.

Template Parameters

ValueType The floating-point value type used to represent the computed energies and gradient vector elements.

Constructor & Destructor Documentation

◆ MMFF94GradientCalculator() [1/2]

template<typename ValueType >

CDPL::ForceField::MMFF94GradientCalculator< ValueType >::MMFF94GradientCalculator ( )

Constructs the calculator without an associated ForceField::MMFF94InteractionData instance.

operator()() will return zero until setup() has been called.

◆ MMFF94GradientCalculator() [2/2]

template<typename ValueType >

CDPL::ForceField::MMFF94GradientCalculator< ValueType >::MMFF94GradientCalculator	(	const MMFF94InteractionData &	ia_data,
		std::size_t	num_atoms
	)

Constructs the calculator and associates it with the supplied ForceField::MMFF94InteractionData instance.

Parameters

ia_data	The MMFF94 interaction data to use during energy/gradient calculation.
num_atoms	The number of atoms in the parameterized molecular graph.

Member Function Documentation

◆ setEnabledInteractionTypes()

template<typename ValueType >

void CDPL::ForceField::MMFF94GradientCalculator< ValueType >::setEnabledInteractionTypes ( unsigned int types )

Enables/disables specific MMFF94 interaction-type contributions.

Parameters

types Bitwise-OR combination of ForceField::InteractionType flags.

Note: Only enabled contributions are evaluated.

◆ getEnabledInteractionTypes()

template<typename ValueType >

unsigned int CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getEnabledInteractionTypes ( ) const

Returns the currently enabled interaction-type contributions.

Returns: The bitwise-OR combination of ForceField::InteractionType flags.

◆ setup()

template<typename ValueType >

void CDPL::ForceField::MMFF94GradientCalculator< ValueType >::setup	(	const MMFF94InteractionData &	ia_data,
		std::size_t	num_atoms
	)

Associates the calculator with the supplied ForceField::MMFF94InteractionData instance and atom count.

Parameters

ia_data	The new MMFF94 interaction data to use for energy/gradient calculation.
num_atoms	The number of atoms in the parameterized molecular graph.

◆ operator()() [1/2]

template<typename ValueType >

template<typename CoordsArray >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::operator() ( const CoordsArray & coords )

Computes the total MMFF94 energy of the conformation specified by coords without calculating the gradient.

Template Parameters

CoordsArray The atom coordinate array type.

Parameters

coords The 3D coordinates of the molecule.

Returns: A const reference to the computed total energy.

◆ operator()() [2/2]

template<typename ValueType >

template<typename CoordsArray , typename GradVector >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::operator()	(	const CoordsArray &	coords,
		GradVector &	grad
	)

Computes the total MMFF94 energy and the per-atom gradient of the conformation specified by coords.

Gradients of atoms marked in the fixed-atom mask (see setFixedAtomMask()) are zeroed after calculation.

Template Parameters

CoordsArray	The atom coordinate array type.
GradVector	The gradient vector type (must satisfy ForceField::GradientVectorTraits requirements).

Parameters

coords	The atom 3D coordinates.
grad	The output gradient vector.

Returns: A const reference to the computed total energy.

◆ getTotalEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getTotalEnergy ( ) const

Returns the total MMFF94 energy computed by the most recent operator()() call.

Returns: A const reference to the total energy.

◆ getBondStretchingEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getBondStretchingEnergy ( ) const

Returns the bond-stretching energy contribution computed by the most recent operator()() call.

Returns: A const reference to the bond-stretching energy.

◆ getAngleBendingEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getAngleBendingEnergy ( ) const

Returns the angle-bending energy contribution computed by the most recent operator()() call.

Returns: A const reference to the angle-bending energy.

◆ getStretchBendEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getStretchBendEnergy ( ) const

Returns the stretch-bend coupling energy contribution computed by the most recent operator()() call.

Returns: A const reference to the stretch-bend energy.

◆ getOutOfPlaneBendingEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getOutOfPlaneBendingEnergy ( ) const

Returns the out-of-plane bending energy contribution computed by the most recent operator()() call.

Returns: A const reference to the out-of-plane bending energy.

◆ getTorsionEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getTorsionEnergy ( ) const

Returns the torsion energy contribution computed by the most recent operator()() call.

Returns: A const reference to the torsion energy.

◆ getElectrostaticEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getElectrostaticEnergy ( ) const

Returns the electrostatic energy contribution computed by the most recent operator()() call.

Returns: A const reference to the electrostatic energy.

◆ getVanDerWaalsEnergy()

template<typename ValueType >

const ValueType& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getVanDerWaalsEnergy ( ) const

Returns the Van der Waals energy contribution computed by the most recent operator()() call.

Returns: A const reference to the Van der Waals energy.

◆ getFixedAtomMask()

template<typename ValueType >

const Util::BitSet& CDPL::ForceField::MMFF94GradientCalculator< ValueType >::getFixedAtomMask ( ) const

Returns the bit mask flagging atoms whose gradient components are zeroed after evaluation.

Returns: A const reference to the fixed-atom bit mask.

◆ setFixedAtomMask()

template<typename ValueType >

void CDPL::ForceField::MMFF94GradientCalculator< ValueType >::setFixedAtomMask ( const Util::BitSet & mask )

Sets the bit mask flagging atoms whose gradient components shall be zeroed after calculation.

Parameters

mask	The new fixed-atom bit mask (bit i set freezes atom i during minimization).

◆ resetFixedAtomMask()

template<typename ValueType >

void CDPL::ForceField::MMFF94GradientCalculator< ValueType >::resetFixedAtomMask ( )

Clears the fixed-atom mask so that all atoms contribute to the gradient.

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

MMFF94GradientCalculator.hpp

Public Member Functions

Detailed Description

template<typename ValueType> class CDPL::ForceField::MMFF94GradientCalculator< ValueType >

Constructor & Destructor Documentation

◆ MMFF94GradientCalculator() [1/2]

◆ MMFF94GradientCalculator() [2/2]

Member Function Documentation

◆ setEnabledInteractionTypes()

◆ getEnabledInteractionTypes()

◆ setup()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ getTotalEnergy()

◆ getBondStretchingEnergy()

◆ getAngleBendingEnergy()

◆ getStretchBendEnergy()

◆ getOutOfPlaneBendingEnergy()

◆ getTorsionEnergy()

◆ getElectrostaticEnergy()

◆ getVanDerWaalsEnergy()

◆ getFixedAtomMask()

◆ setFixedAtomMask()

◆ resetFixedAtomMask()

template<typename ValueType>
class CDPL::ForceField::MMFF94GradientCalculator< ValueType >