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

Restrain the diameter of a set of points. More...

#include <IMP/example/ExampleComplexRestraint.h>

+ Inheritance diagram for IMP::example::ExampleComplexRestraint:

Public Member Functions

 ExampleComplexRestraint (UnaryFunction *f, SingletonContainer *sc, Float diameter, std::string name="ExampleComplexRestraint%1%")
 Use f to restrain particles in sc to be within diameter of one another. More...
 
virtual
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)
 

Public Attributes

virtual double const
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) 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::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

This restraint shows how to write a restraint that includes a ScoreState which is needed to compute some invariant.

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/ExampleComplexRestraint.h
* \brief A restraint to maintain the diameter of a set of points
*
* Copyright 2007-2013 IMP Inventors. All rights reserved.
*/
#ifndef IMPEXAMPLE_EXAMPLE_COMPLEX_RESTRAINT_H
#define IMPEXAMPLE_EXAMPLE_COMPLEX_RESTRAINT_H
#include <IMP/example/example_config.h>
#include <IMP/PairContainer.h>
#include <IMP/SingletonContainer.h>
#include <IMP/kernel/Restraint.h>
#include <IMP/restraint_macros.h>
#include <IMP/ScoreState.h>
#include <IMP/UnaryFunction.h>
IMPEXAMPLE_BEGIN_NAMESPACE
//! Restrain the diameter of a set of points
/** This restraint shows how to write a restraint that includes
a ScoreState which is needed to compute some invariant.
\note Be sure to check out the swig wrapper file and how it
wraps this class.
The source code is as follows:
\include ExampleComplexRestraint.h
\include ExampleComplexRestraint.cpp
*/
class IMPEXAMPLEEXPORT ExampleComplexRestraint : public kernel::Restraint {
base::Pointer<ScoreState> ss_;
kernel::ParticleIndex p_;
Float diameter_;
base::Pointer<SingletonContainer> sc_;
base::Pointer<UnaryFunction> f_;
FloatKey dr_;
public:
//! Use f to restrain particles in sc to be within diameter of one another
/** f should have a minimum at 0 and be an upper bound-style function.
*/
ExampleComplexRestraint(UnaryFunction *f, SingletonContainer *sc,
Float diameter,
std::string name = "ExampleComplexRestraint%1%");
virtual double
unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
const IMP_OVERRIDE;
virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
IMP_OBJECT_METHODS(ExampleComplexRestraint);
};
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_COMPLEX_RESTRAINT_H */
/**
* \file example/ExampleComplexRestraint.cpp
* \brief Restrain the diameter of a set of points.
*
* Copyright 2007-2013 IMP Inventors. All rights reserved.
*
*/
#include "IMP/example/ExampleComplexRestraint.h"
#include <IMP/PairContainer.h>
#include <IMP/particle_index.h>
#include <IMP/core/XYZR.h>
#include <IMP/core/FixedRefiner.h>
#include <IMP/core/CoverRefined.h>
#include <IMP/core/SingletonConstraint.h>
#include <IMP/core/DistancePairScore.h>
#include <IMP/core/internal/evaluate_distance_pair_score.h>
#include <boost/lambda/lambda.hpp>
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleComplexRestraint::ExampleComplexRestraint(UnaryFunction *f,
SingletonContainer *sc,
Float diameter,
std::string name)
: kernel::Restraint(sc->get_model(), name),
diameter_(diameter),
sc_(sc),
f_(f) {
IMP_USAGE_CHECK(sc->get_indexes().size() > 2,
"Need at least two particles to restrain diameter");
IMP_USAGE_CHECK(diameter > 0, "The diameter must be positive");
f_->set_was_used(true);
sc_->set_was_used(true);
p_ = get_model()->add_particle(get_name() + " particle");
core::XYZR d = core::XYZR::setup_particle(get_model(), p_);
d.set_coordinates_are_optimized(false);
base::Pointer<core::CoverRefined> cr =
new core::CoverRefined(new core::FixedRefiner(IMP::get_particles(
get_model(), sc_->get_indexes())),
0);
ss_ = new core::SingletonConstraint(cr, nullptr, get_model(), p_);
}
double ExampleComplexRestraint::unprotected_evaluate(
DerivativeAccumulator *da) const {
IMP_CHECK_OBJECT(sc_.get());
double v = 0;
core::XYZ dp(get_model(), p_);
double radius = diameter_ / 2.0;
IMP_CONTAINER_FOREACH(SingletonContainer, sc_,
v += core::internal::evaluate_distance_pair_score(
dp, core::XYZ(get_model(), _1),
da, f_.get(), boost::lambda::_1 - radius););
return v;
}
ModelObjectsTemp ExampleComplexRestraint::do_get_inputs() const {
kernel::ModelObjectsTemp
ret(IMP::get_particles(get_model(), sc_->get_all_possible_indexes()));
ret.push_back(get_model()->get_particle(p_));
ret.push_back(sc_);
return ret;
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 34 of file ExampleComplexRestraint.h.

Constructor & Destructor Documentation

IMP::example::ExampleComplexRestraint::ExampleComplexRestraint ( UnaryFunction *  f,
SingletonContainer *  sc,
Float  diameter,
std::string  name = "ExampleComplexRestraint%1%" 
)

f should have a minimum at 0 and be an upper bound-style function.

Member Function Documentation

virtual IMP::kernel::ModelObjectsTemp IMP::example::ExampleComplexRestraint::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: