Detailed Description

Score the bond based on a UnaryFunction,.

The score is based on the difference between the stored length and the actual length and scaled by the stiffness. That is stiffness * (distance-bond_length)

See Also: Bond; Bonded

Definition at line 27 of file BondSingletonScore.h.

Public Member Functions
	BondSingletonScore (UnaryFunction *f)
	Use f to penalize deviations in length. 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

UnaryFunction *	get_unary_function () 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::BondSingletonScore::BondSingletonScore ( UnaryFunction * f )

Use f to penalize deviations in length.

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::atom::BondSingletonScore::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::BondSingletonScore::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 38 of file BondSingletonScore.h.

virtual double IMP::atom::BondSingletonScore::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::BondSingletonScore::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 38 of file BondSingletonScore.h.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 39 of file BondSingletonScore.h.

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

BondSingletonScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation