Score that biases particles to go down the Z axis. More...

#include <IMP/npctransport/ZBiasSingletonScore.h>

Inheritance diagram for IMP::npctransport::ZBiasSingletonScore:

Detailed Description

Score that biases particles to go down the Z axis.

Definition at line 22 of file ZBiasSingletonScore.h.

Public Member Functions
	ZBiasSingletonScore (double k, double max_r=HALF_SQRT_MAX_DOUBLE)

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const override
	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, bool all_indexes_checked=false) const override

virtual double	evaluate_index (Model m, ParticleIndex pi, DerivativeAccumulator da) const override
	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, bool all_indexes_checked=false) const overridefinal
	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, bool all_indexes_checked=false) const overridefinal
	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, bool all_indexes_checked=false) const overridefinal
	Compute the score and the derivative if needed over a set. More...

double	get_k () const

virtual std::string	get_type_name () const override

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

void	set_k (double k)

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

virtual bool	check_indexes (Model *m, const ParticleIndexes &pis) const
	Check the given particle indexes for necessary attributes. More...

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::npctransport::ZBiasSingletonScore::ZBiasSingletonScore	(	double	k,
		double	max_r = `HALF_SQRT_MAX_DOUBLE`
	)

Exclude particles from the range of z coordinates [bottom_..top_] with repulsive force constant k

Parameters

k	repulsive force constant
max_r	maximal distance from origin on x,y plane (radius relative to pore axis) in which force is applied. if 0.0, no limitation

Definition at line 38 of file ZBiasSingletonScore.h.

Member Function Documentation

virtual ModelObjectsTemp IMP::npctransport::ZBiasSingletonScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 81 of file ZBiasSingletonScore.h.

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double IMP::npctransport::ZBiasSingletonScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		bool	all_indexes_checked = `false`
	)		const

overridevirtual

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: An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 86 of file ZBiasSingletonScore.h.

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

overridevirtual

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.

Definition at line 62 of file ZBiasSingletonScore.h.

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double IMP::npctransport::ZBiasSingletonScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		bool	all_indexes_checked = `false`
	)		const

finaloverridevirtual

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
all_indexes_checked	if true, all of the passed indexes have already been checked by check_indexes() for needed particle attributes, so a faster implementation (that doesn't check them again) can be used if available.

Note: An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 86 of file ZBiasSingletonScore.h.

double IMP::npctransport::ZBiasSingletonScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		const std::vector< unsigned > &	indexes,
		std::vector< double > &	score,
		bool	all_indexes_checked = `false`
	)		const

finaloverridevirtual

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.

Note: An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 86 of file ZBiasSingletonScore.h.

double IMP::npctransport::ZBiasSingletonScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score,
		bool	all_indexes_checked = `false`
	)		const

finaloverridevirtual

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].

Note: An implementation for this is provided by the IMP_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 86 of file ZBiasSingletonScore.h.

double IMP::npctransport::ZBiasSingletonScore::get_k ( ) const

returns the force constant for pulling to high z (negative = pull to low z)

Definition at line 50 of file ZBiasSingletonScore.h.

virtual ::IMP::VersionInfo IMP::npctransport::ZBiasSingletonScore::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 87 of file ZBiasSingletonScore.h.

void IMP::npctransport::ZBiasSingletonScore::set_k ( double k )

sets the force constant for pulling to high z (negative = pull to low z)

Parameters

k	force constant

Definition at line 58 of file ZBiasSingletonScore.h.

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

ZBiasSingletonScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation