IMP  2.1.0
The Integrative Modeling Platform
Public Member Functions | List of all members
IMP::example::ExampleRestraint Class Reference

Restrain a particle to be in the x,y plane. More...

#include <IMP/example/ExampleRestraint.h>

+ Inheritance diagram for IMP::example::ExampleRestraint:

Public Member Functions

 ExampleRestraint (kernel::Particle *p, double k)
 Create the restraint. More...
 
void do_add_score_and_derivatives (IMP::ScoreAccumulator sa) const
 
IMP::kernel::ModelObjectsTemp do_get_inputs () const
 
virtual std::string get_type_name () 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::Restraint
 Restraint (kernel::Model *m, std::string name)
 
 Restraint (std::string name="Restraint %1%")
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 
Restraint * create_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraint * create_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunction * create_scoring_function (double weight=1.0, double max=NO_MAX) const
 
ContainersTemp get_input_containers () const
 
ParticlesTemp get_input_particles () const
 
virtual double get_last_score () const
 
double get_score () const
 
bool get_was_good () const
 
void set_weight (Float weight)
 
Float get_weight () const
 
double get_maximum_score () const
 
void set_maximum_score (double s)
 
- Public Member Functions inherited from IMP::kernel::ModelObject
 ModelObject (kernel::Model *m, std::string name)
 
 ModelObject (std::string name)
 
virtual void do_set_model (kernel::Model *)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed.
 
bool get_has_required_score_states () const
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
bool get_is_part_of_model () const
 
Model * get_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTemp & get_required_score_states () const
 
void set_has_dependencies (bool tf)
 
void set_has_required_score_states (bool tf)
 
virtual void set_model (kernel::Model *m)
 
- 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

- Protected Member Functions inherited from IMP::kernel::Restraint
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
 Object ()
 

Detailed Description

Note
Be sure to check out the swig wrapper file and how it wraps this class.

The source code is as follows:

/**
* \file IMP/example/ExampleRestraint.h
* \brief A restraint on a list of particle pairs.
*
* Copyright 2007-2013 IMP Inventors. All rights reserved.
*
*/
#ifndef IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#define IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#include <IMP/example/example_config.h>
#include <IMP/SingletonScore.h>
#include <IMP/kernel/Restraint.h>
#include <IMP/PairContainer.h>
#include <IMP/PairScore.h>
#include <IMP/restraint_macros.h>
IMPEXAMPLE_BEGIN_NAMESPACE
//! Restrain a particle to be in the x,y plane
/** \note Be sure to check out the swig wrapper file and how it
wraps this class.
The source code is as follows:
\include ExampleRestraint.h
\include ExampleRestraint.cpp
*/
class IMPEXAMPLEEXPORT ExampleRestraint : public kernel::Restraint {
base::Pointer<kernel::Particle> p_;
double k_;
public:
//! Create the restraint.
/** kernel::Restraints should store the particles they are to act on,
preferably in a Singleton or PairContainer as appropriate.
*/
ExampleRestraint(kernel::Particle *p, double k);
void do_add_score_and_derivatives(IMP::ScoreAccumulator sa) const
IMP_OVERRIDE;
IMP::kernel::ModelObjectsTemp do_get_inputs() const;
IMP_OBJECT_METHODS(ExampleRestraint);
};
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_RESTRAINT_H */
/**
* \file example/ExampleRestraint.cpp
* \brief Restrain a list of particle pairs.
*
* Copyright 2007-2013 IMP Inventors. All rights reserved.
*
*/
#include <IMP/example/ExampleRestraint.h>
#include <IMP/core/XYZ.h>
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleRestraint::ExampleRestraint(kernel::Particle *p, double k)
: kernel::Restraint(p->get_model(), "ExampleRestraint%1%"), p_(p), k_(k) {}
/* Apply the pair score to each particle pair listed in the container.
*/
void ExampleRestraint::do_add_score_and_derivatives(ScoreAccumulator sa) const {
IMP_OBJECT_LOG;
core::XYZ d(p_);
IMP_LOG_VERBOSE("The z coordinate of " << d->get_name() << " is " << d.get_z()
<< std::endl);
double score = .5 * k_ * square(d.get_z());
if (sa.get_derivative_accumulator()) {
double deriv = k_ * d.get_z();
d.add_to_derivative(2, deriv, *sa.get_derivative_accumulator());
}
sa.add_score(score);
}
/* Return all particles whose attributes are read by the restraints. To
do this, ask the pair score what particles it uses.*/
ModelObjectsTemp ExampleRestraint::do_get_inputs() const {
return kernel::ModelObjectsTemp(1, p_);
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 29 of file ExampleRestraint.h.

Constructor & Destructor Documentation

IMP::example::ExampleRestraint::ExampleRestraint ( kernel::Particle *  p,
double  k 
)

kernel::Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.

Member Function Documentation

void IMP::example::ExampleRestraint::do_add_score_and_derivatives ( IMP::ScoreAccumulator  sa) const
virtual

A restraint should override this to compute the score and derivatives.

Reimplemented from IMP::kernel::Restraint.

IMP::kernel::ModelObjectsTemp IMP::example::ExampleRestraint::do_get_inputs ( ) const
virtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::kernel::ModelObject.

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