Detailed Description

Score the improper dihedral based on a UnaryFunction,.

This scores the improper dihedral using information stored in its Dihedral decorator. The score is based on the difference between the stored ideal improper angle and the actual angle and scaled by the stiffness. That is stiffness * (improper_angle-ideal_value). The difference is in radians between -pi and +pi; it is the shortest distance from one angle to the other.

Just as for regular dihedral angles, the improper angle is defined as the angle between the plane in which the first three atoms lie and the plane in which the last three atoms lie.

Note: The multiplicity of the the Dihedral is not used.

See Also: CHARMMTopology::add_impropers(), Dihedral.

Definition at line 35 of file ImproperSingletonScore.h.

Public Member Functions
	ImproperSingletonScore (UnaryFunction *f)
	Use f to penalize deviations in angle. More...

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

double	evaluate_if_good_indexes (kernel::Model m, const kernel::ParticleIndexes &p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) const

virtual double	evaluate_index (kernel::Model m, kernel::ParticleIndex p, DerivativeAccumulator da) const
	Compute the score and the derivative if needed. More...

double	evaluate_indexes (kernel::Model m, const kernel::ParticleIndexes &p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound) const
	Compute the score and the derivative if needed over a set. More...

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

Public Member Functions inherited from IMP::kernel::SingletonScore
	SingletonScore (std::string name="SingletonScore %1%")

Restraints	create_current_decomposition (kernel::Model *m, kernel::ParticleIndex vt) const

virtual double	evaluate (kernel::Particle vt, DerivativeAccumulator da) const
	Compute the score and the derivative if needed. More...

virtual double	evaluate_if_good_index (kernel::Model m, kernel::ParticleIndex vt, DerivativeAccumulator da, double max) const
	Compute the score and the derivative if needed. More...

Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const

virtual ParticlesTemp	get_input_particles (Particle *p) const

ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Additional Inherited Members
Public Types inherited from IMP::kernel::SingletonScore
typedef kernel::Particle *	Argument

typedef kernel::ParticleIndex	IndexArgument

typedef SingletonModifier	Modifier

typedef kernel::Particle *	PassArgument

typedef kernel::ParticleIndex	PassIndexArgument

Protected Member Functions inherited from IMP::kernel::SingletonScore
virtual Restraints	do_create_current_decomposition (kernel::Model *m, kernel::ParticleIndex vt) const

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::atom::ImproperSingletonScore::ImproperSingletonScore ( UnaryFunction * f )

Use f to penalize deviations in angle.

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::atom::ImproperSingletonScore::do_get_inputs	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

double IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Compute the score and the derivative if needed as in evaluate_index(). but may terminate the computation early if the total score is higher than max.

Returns: the score if score<= max or some arbitrary value > max otherwise.

Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

virtual double IMP::atom::ImproperSingletonScore::evaluate_index	(	kernel::Model *	m,
		kernel::ParticleIndex	vt,
		DerivativeAccumulator *	da
	)		const

virtual

Compute the score and the derivative if needed.

evaluate the score and the derivative if needed over vt

Parameters

m	the model of vt
vt	the index in m of an object of type Particle
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed

Reimplemented from IMP::kernel::SingletonScore.

double IMP::atom::ImproperSingletonScore::evaluate_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Compute the score and the derivative if needed over a set.

evaluate the score and the derivative if needed over a set of objects in o

Parameters

m	the model of o
o	objects of type Particle, specified by index
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed
lower_bound	index of first item in o to evaluate
upper_bound	index of last item in o to evaluate

Note: Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

virtual ::IMP::base::VersionInfo IMP::atom::ImproperSingletonScore::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 46 of file ImproperSingletonScore.h.

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

ImproperSingletonScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation