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

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 (Model *m, std::string name)

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

Model *	get_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 ()

Related Functions inherited from IMP::kernel::Restraint
typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > >	RestraintsTemp

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/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 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.
   */
  ExampleComplexRestraint(UnaryFunction *f,
                    SingletonContainer *sc, Float diameter);
  IMP_RESTRAINT(ExampleComplexRestraint);
  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/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):
  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;
  IMP_FOREACH_SINGLETON(sc_,
    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 ExampleComplexRestraint::get_input_particles() const {
  ParticlesTemp ret(IMP::get_particles(get_model(), sc_->get_indexes()));
  ret.push_back(p_);
  return ret;
}
ContainersTemp ExampleComplexRestraint::get_input_containers() const {
  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:

ExampleComplexRestraint.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation