CDPL.ForceField.MMFF94GradientCalculator Class Reference

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

Inheritance diagram for CDPL.ForceField.MMFF94GradientCalculator:

Public Member Functions
None	__init__ ()
	Constructs the calculator without an associated ForceField.MMFF94InteractionData instance. More...
None	__init__ (MMFF94GradientCalculator calc)
	Initializes a copy of the MMFF94GradientCalculator instance calc. More...
None	__init__ (MMFF94InteractionData ia_data, int num_atoms)
	Constructs the calculator and associates it with the supplied ForceField.MMFF94InteractionData instance. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
MMFF94GradientCalculator	assign (MMFF94GradientCalculator calc)
	Replaces the current state of self with a copy of the state of the MMFF94GradientCalculator instance calc. More...
None	setEnabledInteractionTypes (int types)
	Enables/disables specific MMFF94 interaction-type contributions. More...
int	getEnabledInteractionTypes ()
	Returns the currently enabled interaction-type contributions. More...
None	setup (MMFF94InteractionData ia_data, int num_atoms)
	Associates the calculator with the supplied ForceField.MMFF94InteractionData instance and atom count. More...
float	getTotalEnergy ()
	Returns the total MMFF94 energy computed by the most recent call() call. More...
float	getBondStretchingEnergy ()
	Returns the bond-stretching energy contribution computed by the most recent call() call. More...
float	getAngleBendingEnergy ()
	Returns the angle-bending energy contribution computed by the most recent call() call. More...
float	getStretchBendEnergy ()
	Returns the stretch-bend coupling energy contribution computed by the most recent call() call. More...
float	getOutOfPlaneBendingEnergy ()
	Returns the out-of-plane bending energy contribution computed by the most recent call() call. More...
float	getTorsionEnergy ()
	Returns the torsion energy contribution computed by the most recent call() call. More...
float	getElectrostaticEnergy ()
	Returns the electrostatic energy contribution computed by the most recent call() call. More...
float	getVanDerWaalsEnergy ()
	Returns the Van der Waals energy contribution computed by the most recent call() call. More...
None	setFixedAtomMask (Util.BitSet mask)
	Sets the bit mask flagging atoms whose gradient components shall be zeroed after calculation. More...
None	resetFixedAtomMask ()
	Clears the fixed-atom mask so that all atoms contribute to the gradient.
Util.BitSet	getFixedAtomMask ()
	Returns the bit mask flagging atoms whose gradient components are zeroed after evaluation. More...
float	__call__ (Math.Vector3DArray coords)
	Computes the total MMFF94 energy of the conformation specified by coords without calculating the gradient. More...
float	__call__ (Math.Vector3DArray coords, Math.Vector3DArray grad)
	Computes the total MMFF94 energy and the per-atom gradient of the conformation specified by coords. More...

Properties
	objectID = property(getObjectID)
	enabledInteractionTypes = property(getEnabledInteractionTypes, setEnabledInteractionTypes)
	totalEnergy = property(getTotalEnergy)
	bondStretchingEnergy = property(getBondStretchingEnergy)
	angleBendingEnergy = property(getAngleBendingEnergy)
	stretchBendEnergy = property(getStretchBendEnergy)
	outOfPlaneBendingEnergy = property(getOutOfPlaneBendingEnergy)
	torsionEnergy = property(getTorsionEnergy)
	electrostaticEnergy = property(getElectrostaticEnergy)
	vanDerWaalsEnergy = property(getVanDerWaalsEnergy)
	fixedAtomMask = property(getFixedAtomMask)

Detailed Description

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.

Constructor & Destructor Documentation

__init__() [1/3]

None CDPL.ForceField.MMFF94GradientCalculator.__init__

(

)

Constructs the calculator without an associated ForceField.MMFF94InteractionData instance.

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

__init__() [2/3]

None CDPL.ForceField.MMFF94GradientCalculator.__init__

(

MMFF94GradientCalculator

calc

)

Initializes a copy of the MMFF94GradientCalculator instance calc.

Parameters

calc	The MMFF94GradientCalculator instance to copy.

__init__() [3/3]

None CDPL.ForceField.MMFF94GradientCalculator.__init__	(	MMFF94InteractionData	ia_data,
		int	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

getObjectID()

int CDPL.ForceField.MMFF94GradientCalculator.getObjectID

(

)

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

Different Python MMFF94GradientCalculator 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 MMFF94GradientCalculator 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()

MMFF94GradientCalculator CDPL.ForceField.MMFF94GradientCalculator.assign

(

MMFF94GradientCalculator

calc

)

Replaces the current state of self with a copy of the state of the MMFF94GradientCalculator instance calc.

Parameters

calc	The MMFF94GradientCalculator instance to copy.

Returns

self

setEnabledInteractionTypes()

None CDPL.ForceField.MMFF94GradientCalculator.setEnabledInteractionTypes

(

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()

int CDPL.ForceField.MMFF94GradientCalculator.getEnabledInteractionTypes

(

)

Returns the currently enabled interaction-type contributions.

Returns

The bitwise-OR combination of ForceField.InteractionType flags.

setup()

None CDPL.ForceField.MMFF94GradientCalculator.setup	(	MMFF94InteractionData	ia_data,
		int	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.

getTotalEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getTotalEnergy

(

)

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

Returns

A reference to the total energy.

getBondStretchingEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getBondStretchingEnergy

(

)

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

Returns

A reference to the bond-stretching energy.

getAngleBendingEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getAngleBendingEnergy

(

)

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

Returns

A reference to the angle-bending energy.

getStretchBendEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getStretchBendEnergy

(

)

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

Returns

A reference to the stretch-bend energy.

getOutOfPlaneBendingEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getOutOfPlaneBendingEnergy

(

)

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

Returns

A reference to the out-of-plane bending energy.

getTorsionEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getTorsionEnergy

(

)

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

Returns

A reference to the torsion energy.

getElectrostaticEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getElectrostaticEnergy

(

)

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

Returns

A reference to the electrostatic energy.

getVanDerWaalsEnergy()

float CDPL.ForceField.MMFF94GradientCalculator.getVanDerWaalsEnergy

(

)

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

Returns

A reference to the Van der Waals energy.

setFixedAtomMask()

None CDPL.ForceField.MMFF94GradientCalculator.setFixedAtomMask

(

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).

getFixedAtomMask()

Util.BitSet CDPL.ForceField.MMFF94GradientCalculator.getFixedAtomMask

(

)

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

Returns

A reference to the fixed-atom bit mask.

__call__() [1/2]

float CDPL.ForceField.MMFF94GradientCalculator.__call__

(

Math.Vector3DArray

coords

)

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

Parameters

coords

The 3D coordinates of the molecule.

Returns

A reference to the computed total energy.

__call__() [2/2]

float CDPL.ForceField.MMFF94GradientCalculator.__call__	(	Math.Vector3DArray	coords,
		Math.Vector3DArray	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.

Parameters

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

Returns

A reference to the computed total energy.