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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)
 

Additional Inherited Members

- 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
mthe model of vt
vtthe index in m of an object of type ParticlePair
daa 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
mthe model of o
oobjects of type ParticlePair, specified by index
daa derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed.
lower_boundindex of first item in o to evaluate
upper_boundindex 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: