IMP::example::ExamplePairScore Class Reference
Apply a harmonic to the distance between two particles. More...
#include <IMP/example/ExamplePairScore.h>
Inheritance diagram for IMP::example::ExamplePairScore:Public Member Functions | |
| ExamplePairScore (double x0, double k) | |
| virtual void | do_show (std::ostream &out) const |
| Public Member Functions inherited from IMP::kernel::PairScore | |
| PairScore (std::string name="PairScore %1%") | |
| Restraints | create_current_decomposition (Model *m, const ParticleIndexPair &vt) const |
| virtual double | evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const |
| Compute the score and the derivative if needed. | |
| 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, unsigned int lower_bound, unsigned int upper_bound) 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, unsigned int lower_bound, unsigned int upper_bound) const |
| ContainersTemp | get_input_containers (Particle *p) const |
| ParticlesTemp | get_input_particles (Particle *p) const |
| ModelObjectsTemp | get_inputs (Model *m, const ParticleIndexes &pis) const |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| 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. 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) |
Related Functions | |
(Note that these are not member functions.) | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < ExamplePairScore > > | ExamplePairScoresTemp |
| Related Functions inherited from IMP::kernel::PairScore | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < PairScore > > | PairScoresTemp |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Additional Inherited Members | |
| Public Types inherited from IMP::kernel::PairScore | |
| typedef ParticlePair | Argument |
| typedef ParticleIndexPair | IndexArgument |
| typedef PairModifier | Modifier |
| typedef const ParticlePair & | PassArgument |
| typedef const ParticleIndexPair & | PassIndexArgument |
| Protected Member Functions inherited from IMP::kernel::PairScore | |
| virtual Restraints | do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const |
| virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const =0 |
Detailed Description
The source code is as follows:
/**
* \file IMP/example/ExamplePairScore.h
* \brief A Score on the distance between a pair of particles.
*
* Copyright 2007-2013 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>
IMPEXAMPLE_BEGIN_NAMESPACE
//! Apply a harmonic to the distance between two particles.
/** The source code is as follows:
\include ExamplePairScore.h
\include ExamplePairScore.cpp
*/
{
double x0_, k_;
public:
ExamplePairScore(double x0, double k);
IMP_PAIR_SCORE(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 2007-2013 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) {}
DerivativeAccumulator *da) const
{
// turn on logging for this method
// 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;
}
// 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);
}
// 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
Definition at line 25 of file ExamplePairScore.h.
Friends And Related Function Documentation
|
related |
Pass a set of objects.
Definition at line 33 of file ExamplePairScore.h.
The documentation for this class was generated from the following file: