IMP  2.2.1
The Integrative Modeling Platform
IMP::atom::BondSingletonScore Class Reference

Score the bond based on a UnaryFunction,. More...

#include <IMP/atom/BondSingletonScore.h>

+ Inheritance diagram for IMP::atom::BondSingletonScore:

Public Member Functions

 BondSingletonScore (UnaryFunction *f)
 Use f to penalize deviations in length.
 
virtual kernel::ModelObjectsTemp do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
 
double evaluate_if_good_indexes (kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (kernel::Model *m, kernel::ParticleIndex p, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
double evaluate_indexes (kernel::Model *m, const kernel::ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual std::string get_type_name () const
 
UnaryFunctionget_unary_function () const
 
virtual ::IMP::base::VersionInfo get_version_info () const
 Get information about the module and version of the object.
 
- Public Member Functions inherited from IMP::kernel::SingletonScore
 SingletonScore (std::string name="SingletonScore %1%")
 
Restraints create_current_decomposition (kernel::Model *m, kernel::ParticleIndex vt) const
 
virtual double evaluate (kernel::Particle *vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed. More...
 
virtual double evaluate_if_good_index (kernel::Model *m, kernel::ParticleIndex vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed.
 
- 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 ()
 
virtual void do_destroy ()
 
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::SingletonScore
typedef kernel::ParticleArgument
 
typedef kernel::ParticleIndex IndexArgument
 
typedef SingletonModifier Modifier
 
typedef kernel::ParticlePassArgument
 
typedef kernel::ParticleIndex PassIndexArgument
 
- Protected Member Functions inherited from IMP::kernel::SingletonScore
virtual Restraints do_create_current_decomposition (kernel::Model *m, kernel::ParticleIndex vt) const
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 

Detailed Description

The score is based on the difference between the stored length and the actual length and scaled by the stiffness. That is stiffness * (distance-bond_length)

See Also
Bond
Bonded

Definition at line 27 of file BondSingletonScore.h.

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::atom::BondSingletonScore::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::BondSingletonScore::evaluate_if_good_indexes ( kernel::Model m,
const kernel::ParticleIndexes o,
DerivativeAccumulator da,
double  max,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

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

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 38 of file BondSingletonScore.h.

double IMP::atom::BondSingletonScore::evaluate_indexes ( kernel::Model m,
const kernel::ParticleIndexes o,
DerivativeAccumulator da,
unsigned int  lower_bound,
unsigned int  upper_bound 
) const
virtual

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

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 38 of file BondSingletonScore.h.


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