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IMP Reference Guide  develop.d247202c1c,2019/10/23
The Integrative Modeling Platform
IMP::core::KClosePairsPairScore Class Reference

Apply a score to a fixed number of close pairs from the two sets. More...

#include <IMP/core/ClosePairsPairScore.h>

+ Inheritance diagram for IMP::core::KClosePairsPairScore:

Detailed Description

Apply a score to a fixed number of close pairs from the two sets.

Apply the score to the k closest pairs (sphere distance). The envisioned use case is that the two particles each represent a protein and the refiners return the geometry for that protein.

Rigid bodies are special cased for efficiency.

See Also
ClosePairsScoreState

Definition at line 30 of file ClosePairsPairScore.h.

Public Member Functions

 KClosePairsPairScore (PairScore *f, Refiner *r, int k=1)
 only score the k closest pairs. More...
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
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...
 
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...
 
ParticlePairsTemp get_close_pairs (const ParticlePair &pp) 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...
 
- Public Member Functions inherited from IMP::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
- 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 ()
 

Constructor & Destructor Documentation

IMP::core::KClosePairsPairScore::KClosePairsPairScore ( PairScore f,
Refiner r,
int  k = 1 
)

only score the k closest pairs.

Member Function Documentation

virtual ModelObjectsTemp IMP::core::KClosePairsPairScore::do_get_inputs ( Model m,
const ParticleIndexes pis 
) const
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual double IMP::core::KClosePairsPairScore::evaluate_if_good_index ( Model m,
const ParticleIndexPair vt,
DerivativeAccumulator da,
double  max 
) const
virtual

Compute the score and the derivative if needed, only if "good".

This functions similarly to evaluate_index(), but may terminate the computation early if the score is higher than max.

Returns
the score if score<= max or some arbitrary value > max otherwise.

Reimplemented from IMP::PairScore.

double IMP::core::KClosePairsPairScore::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 62 of file ClosePairsPairScore.h.

virtual double IMP::core::KClosePairsPairScore::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::core::KClosePairsPairScore::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 62 of file ClosePairsPairScore.h.

virtual ::IMP::VersionInfo IMP::core::KClosePairsPairScore::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 63 of file ClosePairsPairScore.h.


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