IMP Reference Guide  develop.182d9373c4,2021/04/12 The Integrative Modeling Platform
IMP::atom::LennardJonesPairScore Class Reference

Lennard-Jones score between a pair of particles. More...

#include <IMP/atom/LennardJonesPairScore.h>

Inheritance diagram for IMP::atom::LennardJonesPairScore:

## 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 ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
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

virtual double evaluate_index (Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
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) 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::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::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)

Public Types inherited from IMP::PairScore
typedef ParticlePair Argument

typedef ParticleIndexPair IndexArgument

typedef PairModifier Modifier

typedef const ParticlePairPassArgument

typedef const ParticleIndexPairPassIndexArgument

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

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

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

Reimplemented from IMP::PairScore.

Definition at line 84 of file LennardJonesPairScore.h.

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

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::LennardJonesPairScore::evaluate_indexes ( Model * m, const 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.

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 of last item in o to evaluate
Note
Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented from IMP::PairScore.

Definition at line 84 of file LennardJonesPairScore.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 85 of file LennardJonesPairScore.h.

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