Coulomb (electrostatic) score between a pair of particles. More...

#include <IMP/atom/CoulombPairScore.h>

Inheritance diagram for IMP::atom::CoulombPairScore:

Detailed Description

Coulomb (electrostatic) score between a pair of particles.

The two particles in the pair must be Charged particles. The form of the potential is

$\frac{1}{4\pi\epsilon_0\epsilon_r} \frac{q_i q_j}{|r_{ij}|}$

where $\epsilon_0$ is the permittivity of vacuum, $\epsilon_r$ the relative dielectric (adjustable; 1.0 by default), $q_i$ and $q_j$ the charges on the two particles, and $|r_{ij}|$ the distance between them.

Definition at line 30 of file CoulombPairScore.h.

Public Member Functions
	CoulombPairScore (SmoothingFunction *f)

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

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 ParticleIndexPairs &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, const ParticleIndexPair &p, DerivativeAccumulator da) const override
	Compute the score and the derivative if needed. More...

double	evaluate_indexes (Model m, const ParticleIndexPairs &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 ParticleIndexPairs &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 ParticleIndexPairs &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_relative_dielectric () 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_relative_dielectric (double relative_dielectric)

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

Restraints	create_current_decomposition (Model *m, const ParticleIndexPair &vt) const

virtual double	evaluate_if_good_index (Model m, const ParticleIndexPair &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::PairScore
typedef ParticlePair	Argument

typedef ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const ParticlePair &	PassArgument

typedef const ParticleIndexPair &	PassIndexArgument

Protected Member Functions inherited from IMP::PairScore
virtual Restraints	do_create_current_decomposition (Model *m, const ParticleIndexPair &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 ()

Member Function Documentation

virtual bool IMP::atom::CoulombPairScore::check_indexes	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Check the given particle indexes for necessary attributes.

If implemented, this method should return true and should assert that all particles have all attributes needed to evaluate the score (or raise an exception). After successfully calling this method, evaluate_indexes() and similar methods can be called with all_indexes_checked=true, and can opt to skip these checks. It is the caller's responsibility to call check_indexes() again if the set of possible indexes changes, or particles or attributes are removed.

Reimplemented from IMP::PairScore.

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

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::atom::CoulombPairScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexPairs &	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_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 63 of file CoulombPairScore.h.

virtual double IMP::atom::CoulombPairScore::evaluate_index	(	Model *	m,
		const ParticleIndexPair &	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 ParticlePair
da	a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed.

Implements IMP::PairScore.

double IMP::atom::CoulombPairScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexPairs &	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 ParticlePair, 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_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 63 of file CoulombPairScore.h.

double IMP::atom::CoulombPairScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexPairs &	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_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 63 of file CoulombPairScore.h.

double IMP::atom::CoulombPairScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexPairs &	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_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 63 of file CoulombPairScore.h.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 64 of file CoulombPairScore.h.

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

CoulombPairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation