Detailed Description

A soft linear repulsive score between two spheres. If the spheres penetrate each other, the score is ( k_ * [penetration-magnitude] kcal/mol), otherwise the score is 0.

Definition at line 69 of file linear_distance_pair_scores.h.

Public Member Functions
	LinearSoftSpherePairScore (double k, std::string name="LinearSSPairScore%1%")

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...

virtual double	evaluate_indexes (Model m, const ParticleIndexPairs &pips, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=false) const override
	Compute the score and the derivative if needed over a set. More...

double	get_k () const
	returns the k for sphere-sphere repulsion More...

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::PairScore
	PairScore (std::string name="PairScore %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, 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...

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

virtual double	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
	Compute the score and the derivative if needed over a set. 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)

Protected Member Functions
double	evaluate_index (algebra::Sphere3D const &s0, algebra::Sphere3D const &s1, algebra::Sphere3D &ds0, algebra::Sphere3D &ds1, DerivativeAccumulator *da) const

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 ()

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

Member Function Documentation

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

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::LinearSoftSpherePairScore::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 100 of file linear_distance_pair_scores.h.

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double IMP::npctransport::LinearSoftSpherePairScore::evaluate_index	(	algebra::Sphere3D const &	s0,
		algebra::Sphere3D const &	s1,
		algebra::Sphere3D &	ds0,
		algebra::Sphere3D &	ds1,
		DerivativeAccumulator *	da
	)		const

protected

evaluates the soft linear repulsive score, for spheres s0 and s1, outputting derivatives to ds0 and ds1 scaled by da, if da is not null

virtual double IMP::npctransport::LinearSoftSpherePairScore::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.

virtual double IMP::npctransport::LinearSoftSpherePairScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		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.

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.

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

returns the k for sphere-sphere repulsion

Definition at line 120 of file linear_distance_pair_scores.h.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 122 of file linear_distance_pair_scores.h.

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

linear_distance_pair_scores.h

Detailed Description

Public Member Functions

Protected Member Functions

Additional Inherited Members

Member Function Documentation