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 23 of file ZBiasSingletonScore.h.

Public Member Functions
	ZBiasSingletonScore (double k, double max_r=HALF_SQRT_MAX_DOUBLE, double z=std::numeric_limits< double >::min())

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

std::pair< double, algebra::Vector3D >	evaluate_deriv (const core::XYZR &d) const

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...

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

def	get_derived_object
	Return this object cast to the most derived subclass. More...

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`,
		double	z = `std::numeric_limits<double>::min()`
	)

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

Parameters

k	force constant (positive for pulling towards z, negative for pushing away from z)
max_r	maximal distance from z axis (radius relative to pore axis) in which force is applied. if 0.0, no limitation
z	z of xy plane to bias towards / against (relevant only if k is non-zero)

Definition at line 41 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 100 of file ZBiasSingletonScore.h.

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std::pair<double, algebra::Vector3D> IMP::npctransport::ZBiasSingletonScore::evaluate_deriv ( const core::XYZR & d ) const

evaluates the derivative accoridng to the particle position

Parameters

d	core::XYZR position of the particle

Returns: a pair with the score and the derivative vector

Definition at line 58 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 105 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 85 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 105 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 105 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 105 of file ZBiasSingletonScore.h.

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

returns the force constant for pulling

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 106 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