IMP  2.3.0
The Integrative Modeling Platform
IMP::isd::RepulsiveDistancePairScore Class Reference

A repulsive potential on the distance between two atoms. More...

#include <IMP/isd/RepulsiveDistancePairScore.h>

+ Inheritance diagram for IMP::isd::RepulsiveDistancePairScore:

Detailed Description

A repulsive potential on the distance between two atoms.

See Also
XYZR
SphereDistancePairScore
DistancePairScore
LennardJonesPairScore

Definition at line 26 of file RepulsiveDistancePairScore.h.

Public Member Functions

 RepulsiveDistancePairScore (double d0, double k)
 
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_rest_length () const
 
double get_stiffness () 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...
 
- 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::isd::RepulsiveDistancePairScore::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::isd::RepulsiveDistancePairScore::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 40 of file RepulsiveDistancePairScore.h.

virtual double IMP::isd::RepulsiveDistancePairScore::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
mthe model of vt
vtthe index in m of an object of type ParticlePair
daa derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed

Reimplemented from IMP::kernel::PairScore.

double IMP::isd::RepulsiveDistancePairScore::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
mthe model of o
oobjects of type ParticlePair, specified by index
daa derivative accumulator that reweighting 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::kernel::PairScore.

Definition at line 40 of file RepulsiveDistancePairScore.h.

virtual ::IMP::base::VersionInfo IMP::isd::RepulsiveDistancePairScore::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 41 of file RepulsiveDistancePairScore.h.


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