Score the improper dihedral based on a UnaryFunction,. More...

#include <IMP/atom/ImproperSingletonScore.h>

Inheritance diagram for IMP::atom::ImproperSingletonScore:

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 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 ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const
	Overload this method to specify the inputs. More...

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

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

double	evaluate_indexes (Model m, const 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...

double	evaluate_indexes_delta (Model m, const ParticleIndexes &p, DerivativeAccumulator da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
	Compute the change in score and the derivative if needed over a set. More...

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

virtual std::string	get_type_name () const

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

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

Restraints	create_current_decomposition (Model *m, ParticleIndex vt) const

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

Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
	Get the ModelObjects read when the given list of particles is used. More...

Public Member Functions inherited from IMP::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::SingletonScore
typedef Particle *	Argument

typedef ParticleIndex	IndexArgument

typedef SingletonModifier	Modifier

typedef Particle *	PassArgument

typedef ParticleIndex	PassIndexArgument

Protected Member Functions inherited from IMP::SingletonScore
virtual Restraints	do_create_current_decomposition (Model *m, ParticleIndex vt) const
	Override this to return your own decomposition. More...

Protected Member Functions inherited from IMP::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 ModelObjectsTemp IMP::atom::ImproperSingletonScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

virtual

Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), 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.

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

Reimplemented from IMP::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

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

virtual

Compute the score and the derivative if needed.

Parameters

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

Implements IMP::SingletonScore.

double IMP::atom::ImproperSingletonScore::evaluate_indexes	(	Model *	m,
		const 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.

Parameters

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

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

Reimplemented from IMP::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

double IMP::atom::ImproperSingletonScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		const std::vector< unsigned > &	indexes,
		std::vector< double > &	score
	)		const

virtual

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

The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.

Reimplemented from IMP::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

double IMP::atom::ImproperSingletonScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score
	)		const

virtual

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

Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].

Reimplemented from IMP::SingletonScore.

Definition at line 45 of file ImproperSingletonScore.h.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::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