IMP  2.0.0
The Integrative Modeling Platform
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)
 Use f to restrain particles in sc to be within diameter of one another. More...
 
virtual void do_show (std::ostream &out) const
 
void set_model (Model *m)
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) 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
 
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 (Model *m, std::string name)
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () 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)
 

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
 
virtual void do_update_dependencies ()
 

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/Restraint.h>
#include <IMP/ScoreState.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 Restraint
{
Pointer<ScoreState> ss_;
Pointer<Particle> p_;
Float diameter_;
Pointer<SingletonContainer> sc_;
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.
*/
SingletonContainer *sc, Float diameter);
void set_model(Model *m);
};
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/core/XYZR.h>
#include <IMP/core/internal/evaluate_distance_pair_score.h>
#include <boost/lambda/lambda.hpp>
IMPEXAMPLE_BEGIN_NAMESPACE
Float diameter):
Restraint(sc->get_model(), "ExampleComplexRestraint%1%"),
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);
}
void ExampleComplexRestraint::set_model(Model *m) {
if (m) {
IMP_LOG_TERSE( "Creating components of ExampleComplexRestraint"
<< std::endl);
Model *m= sc_->get_model();
p_= new Particle(m);
core::XYZR d= core::XYZR::setup_particle(p_);
d.set_coordinates_are_optimized(false);
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, p_);
m->add_score_state(ss_);
} else {
IMP_LOG_TERSE( "Removing components of ExampleComplexRestraint"
<< std::endl);
if (ss_) {
IMP_CHECK_OBJECT(ss_.get());
IMP_CHECK_OBJECT(p_.get());
get_model()->remove_score_state(ss_);
get_model()->remove_particle(p_);
ss_=nullptr;
p_=nullptr;
}
}
Restraint::set_model(m);
}
double
ExampleComplexRestraint::unprotected_evaluate(DerivativeAccumulator *da) const {
IMP_CHECK_OBJECT(sc_.get());
double v=0;
core::XYZ dp(p_);
double radius= diameter_/2.0;
v+= core::internal::evaluate_distance_pair_score(dp,
core::XYZ(_1),
da, f_.get(),
boost::lambda::_1-radius);
);
return v;
}
void ExampleComplexRestraint::do_show(std::ostream &out) const {
out << "diameter " << diameter_ << std::endl;
}
ParticlesTemp ret(IMP::get_particles(get_model(), sc_->get_indexes()));
ret.push_back(p_);
return ret;
}
return ContainersTemp(1, sc_);
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 34 of file ExampleComplexRestraint.h.

Constructor & Destructor Documentation

IMP::example::ExampleComplexRestraint::ExampleComplexRestraint ( UnaryFunction f,
SingletonContainer sc,
Float  diameter 
)

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


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