IMP::example::ExamplePairScore Class Reference

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Detailed Description

Apply a harmonic to the distance between two particles.

The source code is as follows:

/**
 *  \file example_system_local/ExamplePairScore.h
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2012 IMP Inventors. All rights reserved.
 */

#ifndef IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_PAIR_SCORE_H
#define IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_PAIR_SCORE_H

#include "example_system_local_config.h"
#include <IMP/core/XYZ.h>
#include <IMP/PairScore.h>
#include <IMP/UnaryFunction.h>
#include <IMP/Pointer.h>

IMPEXAMPLESYSTEMLOCAL_BEGIN_NAMESPACE

//! Apply a harmonic to the distance between two particles.
/** The source code is as follows:
    \include ExampleRestraint.h
    \include ExampleRestraint.cpp
*/
class IMPEXAMPLESYSTEMLOCALEXPORT ExamplePairScore : public PairScore
{
  double x0_, k_;
public:
  ExamplePairScore(double x0, double k);
  IMP_PAIR_SCORE(ExamplePairScore);
};

IMP_OBJECTS(ExamplePairScore, ExamplePairScores);


IMPEXAMPLESYSTEMLOCAL_END_NAMESPACE

#endif  /* IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_PAIR_SCORE_H */

/**
 *  \file ExamplePairScore.cpp
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2012 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(const ParticlePair &p,
                                 DerivativeAccumulator *da) const
{
  // turn on logging for this method
  IMP_OBJECT_LOG;
  // assume they have coordinates
  core::XYZ d0(p[0]);
  core::XYZ d1(p[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;
}


ParticlesTemp ExamplePairScore::get_input_particles(Particle *p) const {
  // return any particles that would be read if p is one of the particles
  // being scored. Don't worry about returning duplicates.
  return ParticlesTemp(1,p);
}
ContainersTemp ExamplePairScore::get_input_containers(Particle *) const {
  // return any containers that would be read if p is one of the particles
  // being scored. Don't worry about returning duplicates.
  return ContainersTemp();
}


void ExamplePairScore::do_show(std::ostream &out) const {
  out << "x0=" << x0_ << " and k=" << k_ << std::endl;
}

IMPEXAMPLE_END_NAMESPACE

Inheritance diagram for IMP::example::ExamplePairScore:

List of all members.

Public Member Functions
	ExamplePairScore (double x0, double k)
Public Member Functions inherited from IMP::PairScore
	PairScore (std::string name="PairScore %1%")
Restraints	create_current_decomposition (const ParticlePair &vt) const
virtual double	evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const =0
	Compute the score and the derivative if needed.
virtual double	evaluate (const ParticlePairsTemp &o, DerivativeAccumulator *da) 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.
virtual double	evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max) 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) const
virtual ContainersTemp	get_input_containers (Particle *p) const =0
virtual ParticlesTemp	get_input_particles (Particle *p) const =0
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
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.
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)

Static Public Member Functions
static ExamplePairScore *	get_from (IMP::base::Object *o)

Additional Inherited Members
Public Types inherited from IMP::PairScore
typedef ParticlePair	Argument
typedef ParticleIndexPair	IndexArgument

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

• ExamplePairScore.h