Apply a harmonic to the distance between two particles. More...

#include <IMP/example/ExamplePairScore.h>

Inheritance diagram for IMP::example::ExamplePairScore:

Detailed Description

Apply a harmonic to the distance between two particles.

The source code is as follows:

/**
 *  \file IMP/example/ExamplePairScore.h
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 */
#ifndef IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H
#define IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H
#include <IMP/example/example_config.h>
#include <IMP/core/XYZ.h>
#include <IMP/PairScore.h>
#include <IMP/pair_macros.h>
#include <IMP/UnaryFunction.h>
#include <IMP/Pointer.h>
#include <cereal/access.hpp>
IMPEXAMPLE_BEGIN_NAMESPACE
//! Apply a harmonic to the distance between two particles.
/** The source code is as follows:
    \include ExamplePairScore.h
    \include ExamplePairScore.cpp
*/
class IMPEXAMPLEEXPORT ExamplePairScore : public PairScore {
  double x0_, k_;
 public:
  ExamplePairScore(double x0, double k);
  ExamplePairScore() {}
  virtual double evaluate_index(Model *m,
                                const ParticleIndexPair &p,
                                DerivativeAccumulator *da) const override;
  virtual ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_PAIR_SCORE_METHODS(ExamplePairScore);
  IMP_OBJECT_METHODS(ExamplePairScore);
  // Serialization support
 private:
  friend class cereal::access;
  template<class Archive> void serialize(Archive &ar) {
    ar(cereal::base_class<PairScore>(this), x0_, k_);
  }
  IMP_OBJECT_SERIALIZE_DECL(ExamplePairScore);
};
IMP_OBJECTS(ExamplePairScore, ExamplePairScores);
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H */

/**
 *  \file ExamplePairScore.cpp
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 */
#include <IMP/example/ExamplePairScore.h>
#include <IMP/core/XYZ.h>
#include <IMP/UnaryFunction.h>
#include <boost/lambda/lambda.hpp>
IMPEXAMPLE_BEGIN_NAMESPACE
ExamplePairScore::ExamplePairScore(double x0, double k) : x0_(x0), k_(k) {}
Float ExamplePairScore::evaluate_index(Model *m,
                                       const ParticleIndexPair &pip,
                                       DerivativeAccumulator *da) const {
  // turn on logging for this method
  IMP_OBJECT_LOG;
  // assume they have coordinates
  core::XYZ d0(m, pip[0]);
  core::XYZ d1(m, pip[1]);
  // log something
  double diff =
      (d0.get_coordinates() - d1.get_coordinates()).get_magnitude() - x0_;
  IMP_LOG_VERBOSE("The distance off from x0 is " << diff << std::endl);
  double score = .5 * k_ * square(diff);
  if (da) {
    // derivatives are requested
    algebra::Vector3D delta = d0.get_coordinates() - d1.get_coordinates();
    algebra::Vector3D udelta = delta.get_unit_vector();
    double dv = k_ * diff;
    // add to the particle derivatives
    d0.add_to_derivatives(udelta * dv, *da);
    d1.add_to_derivatives(-udelta * dv, *da);
  }
  return score;
}
ModelObjectsTemp ExamplePairScore::do_get_inputs(
    Model *m, const ParticleIndexes &pis) const {
  return IMP::get_particles(m, pis);
}
IMP_OBJECT_SERIALIZE_IMPL(IMP::example::ExamplePairScore);
IMPEXAMPLE_END_NAMESPACE

Definition at line 26 of file ExamplePairScore.h.

Public Member Functions
	ExamplePairScore (double x0, double k)

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const override
	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 override

virtual double	evaluate_index (Model m, const ParticleIndexPair &p, DerivativeAccumulator da) const override
	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 overridefinal
	Compute the score and the derivative if needed over a set. More...

double	evaluate_indexes_delta (Model m, const ParticleIndexPairs &p, DerivativeAccumulator da, const std::vector< unsigned > &indexes, std::vector< double > &score) const overridefinal
	Compute the change in score and the derivative if needed over a set. More...

double	evaluate_indexes_scores (Model m, const ParticleIndexPairs &p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const overridefinal
	Compute the score and the derivative if needed over a set. More...

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	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

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 ParticlePair &	PassArgument

typedef const ParticleIndexPair &	PassIndexArgument

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::example::ExamplePairScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::example::ExamplePairScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

overridevirtual

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: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 37 of file ExamplePairScore.h.

virtual double IMP::example::ExamplePairScore::evaluate_index	(	Model *	m,
		const ParticleIndexPair &	vt,
		DerivativeAccumulator *	da
	)		const

overridevirtual

Compute the score and the derivative if needed.

Parameters

m	the model of vt
vt	the index in m of an object of type ParticlePair
da	a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed.

Implements IMP::PairScore.

double IMP::example::ExamplePairScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

finaloverridevirtual

Compute the score and the derivative if needed over a set.

Parameters

m	the model of o
o	objects of type ParticlePair, specified by index
da	a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed.
lower_bound	index of first item in o to evaluate
upper_bound	index one past last item in o to evaluate

Note: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 37 of file ExamplePairScore.h.

double IMP::example::ExamplePairScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		const std::vector< unsigned > &	indexes,
		std::vector< double > &	score
	)		const

finaloverridevirtual

Compute the change in score and the derivative if needed over a set.

The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.

Note: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 37 of file ExamplePairScore.h.

double IMP::example::ExamplePairScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score
	)		const

finaloverridevirtual

Compute the score and the derivative if needed over a set.

Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].

Note: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 37 of file ExamplePairScore.h.

virtual ::IMP::VersionInfo IMP::example::ExamplePairScore::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 38 of file ExamplePairScore.h.

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

ExamplePairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation