Detailed Description

Score for a slab with a toroidal pore.

Definition at line 25 of file SlabWithToroidalPorePairScore.h.

Public Member Functions
	SlabWithToroidalPorePairScore (double k)

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) const override

virtual double	evaluate_index (Model m, ParticleIndexPair const &pip, DerivativeAccumulator da) const override

virtual double	evaluate_indexes (Model m, const ParticleIndexPairs &pips, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound) const overridefinal

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%")

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) 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) 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

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 ()

Constructor & Destructor Documentation

IMP::npctransport::SlabWithToroidalPorePairScore::SlabWithToroidalPorePairScore ( double k )

Constructs a horizontal slab with a toroidal pore, centered at the z=0 plane Constructs a score over a horizontal slab with a ring toroidal pore

Parameters

k	the slab repulsive force constant in kcal/mol/A

Member Function Documentation

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

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexPairs &	p,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

overridevirtual

Evaluate score for particles pis[lower_bound..upper_bound] in model m. If da is not null, use it to accumulate derivatives in model.

Abort early and return maximal double value if score is larger than max (note this assumes all score components are non-negative, which is true for slab score)

Reimplemented from IMP::PairScore.

Definition at line 82 of file SlabWithToroidalPorePairScore.h.

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double IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_index	(	Model *	m,
		ParticleIndexPair const &	pip,
		DerivativeAccumulator *	da
	)		const

overridevirtual

evaluate score for particle pi in model m. If da is not null, use it to accumulate derivatives in model.

Implements IMP::PairScore.

Definition at line 163 of file SlabWithToroidalPorePairScore.h.

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double IMP::npctransport::SlabWithToroidalPorePairScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexPairs &	pips,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

finaloverridevirtual

evaluate score for particles pis[lower_bound..upper_bound] in model m. If da is not null, use it to accumulate derivatives in model.

Reimplemented from IMP::PairScore.

Definition at line 194 of file SlabWithToroidalPorePairScore.h.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 97 of file SlabWithToroidalPorePairScore.h.

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

SlabWithToroidalPorePairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation