IMP  2.0.0
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:

Public Member Functions

 LennardJonesPairScore (SmoothingFunction *f)
 
virtual void do_show (std::ostream &out) const
 
double get_attractive_weight () const
 
double get_repulsive_weight () const
 
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 (Model *m, const ParticleIndexPair &vt) const
 
virtual double evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_if_good_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
virtual double evaluate_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
ContainersTemp get_input_containers (Particle *p) const
 
ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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)
 

Related Functions

(Note that these are not member functions.)

typedef IMP::base::Vector
< IMP::base::WeakPointer
< LennardJonesPairScore > > 
LennardJonesPairScoresTemp
 

Additional Inherited Members

- Public Types inherited from IMP::kernel::PairScore
typedef ParticlePair Argument
 
typedef ParticleIndexPair IndexArgument
 
typedef PairModifier Modifier
 
typedef const ParticlePairPassArgument
 
typedef const ParticleIndexPairPassIndexArgument
 
- Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 

Detailed Description

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 interparticle 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 modifed, that will affect its interaction with all particles.

Definition at line 41 of file LennardJonesPairScore.h.

Friends And Related Function Documentation

Pass a set of objects.

Definition at line 81 of file LennardJonesPairScore.h.


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