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IMP Reference Guide  develop.1a04b19ae7,2021/11/27
The Integrative Modeling Platform
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:

Detailed Description

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:

/**
* \file IMP/example/ExampleRestraint.h
* \brief A restraint on a list of particle pairs.
*
* Copyright 2007-2021 IMP Inventors. All rights reserved.
*
*/
#ifndef IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#define IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#include <IMP/example/example_config.h>
#include <IMP/Restraint.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 Restraint {
double k_;
public:
//! Create the restraint.
/** Restraints should store the particles they are to act on,
preferably in a Singleton or PairContainer as appropriate.
*/
ExampleRestraint(Model *m, ParticleIndex p, double k);
void do_add_score_and_derivatives(ScoreAccumulator sa) const
};
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_RESTRAINT_H */
/**
* \file example/ExampleRestraint.cpp
* \brief Restrain a list of particle pairs.
*
* Copyright 2007-2021 IMP Inventors. All rights reserved.
*
*/
#include <IMP/core/XYZ.h>
IMPEXAMPLE_BEGIN_NAMESPACE
double k)
: Restraint(m, "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 {
core::XYZ d(get_model(), 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 ModelObjectsTemp(1, get_model()->get_particle(p_));
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 25 of file ExampleRestraint.h.

Public Member Functions

 ExampleRestraint (Model *m, ParticleIndex p, double k)
 Create the restraint. More...
 
void do_add_score_and_derivatives (ScoreAccumulator sa) const
 
ModelObjectsTemp do_get_inputs () 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::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
void add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
virtual double get_last_last_score () const
 Get the unweighted score from the last-but-one time it was evaluated. More...
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () 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::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. 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

- Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- 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::example::ExampleRestraint::ExampleRestraint ( Model m,
ParticleIndex  p,
double  k 
)

Create the restraint.

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

Member Function Documentation

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::ModelObject.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 38 of file ExampleRestraint.h.


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