Detailed Description

Lennard-Jones score between a pair of particles.

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

\[ -\epsilon \left[ w_{rep} \left(\frac{r_{min}}{r}\right)^{12} - 2 w_{att} \left(\frac{r_{min}}{r}\right)^{6}\right] \]

where \(\epsilon\) is the depth of the well between the two particles, \(r_{min}\) the sum of the particles' radii, \(r\) the inter-particle distance, and \(w_{rep}\) and \(w_{att}\) the weights on the repulsive and attractive parts of the potential respectively; both weights are 1.0 by default.

The well depth is the geometric mean of the individual particles' well depths (as extracted by LennardJones::get_well_depth).

Note that because this score uses radii and well depths set in the particles themselves, the strength of the interaction cannot be changed for a particular pair of atoms (as is done in the CHARMM forcefield with the rarely-used NBFIX directive, for example). If the well depth or radius of a single particle is modified, that will affect its interaction with all particles.

Definition at line 41 of file LennardJonesPairScore.h.

Public Member Functions
	LennardJonesPairScore (SmoothingFunction *f)

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

double	evaluate_if_good_indexes (kernel::Model m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) const

virtual double	evaluate_index (kernel::Model m, const kernel::ParticleIndexPair &p, DerivativeAccumulator da) const
	Compute the score and the derivative if needed. More...

double	evaluate_indexes (kernel::Model m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound) const
	Compute the score and the derivative if needed over a set. More...

double	get_attractive_weight () const

double	get_repulsive_weight () const

virtual std::string	get_type_name () const

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

void	set_attractive_weight (double attractive_weight)

void	set_repulsive_weight (double repulsive_weight)

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

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

virtual double	evaluate (const kernel::ParticlePair &vt, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed. More...

virtual double	evaluate_if_good_index (kernel::Model m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator da, double max) const
	Compute the score and the derivative if needed. More...

Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const

virtual ParticlesTemp	get_input_particles (Particle *p) const

ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

Public Member Functions inherited from IMP::base::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::kernel::PairScore
typedef kernel::ParticlePair	Argument

typedef kernel::ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const kernel::ParticlePair &	PassArgument

typedef const kernel::ParticleIndexPair &	PassIndexArgument

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

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

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

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

double IMP::atom::LennardJonesPairScore::evaluate_if_good_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Compute the score and the derivative if needed as in evaluate_index(). 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.

Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented from IMP::kernel::PairScore.

Definition at line 84 of file LennardJonesPairScore.h.

virtual double IMP::atom::LennardJonesPairScore::evaluate_index	(	kernel::Model *	m,
		const kernel::ParticleIndexPair &	vt,
		DerivativeAccumulator *	da
	)		const

virtual

Compute the score and the derivative if needed.

evaluate the score and the derivative if needed over vt

Parameters

m	the model of vt
vt	the index in m of an object of type ParticlePair
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed

Reimplemented from IMP::kernel::PairScore.

double IMP::atom::LennardJonesPairScore::evaluate_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Compute the score and the derivative if needed over a set.

evaluate the score and the derivative if needed over a set of objects in o

Parameters

m	the model of o
o	objects of type ParticlePair, specified by index
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed
lower_bound	index of first item in o to evaluate
upper_bound	index of last item in o to evaluate

Note: Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented from IMP::kernel::PairScore.

Definition at line 84 of file LennardJonesPairScore.h.

virtual ::IMP::base::VersionInfo IMP::atom::LennardJonesPairScore::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 85 of file LennardJonesPairScore.h.

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

LennardJonesPairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation