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 2007-2022 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>
#include <cereal/access.hpp>
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 {
  ParticleIndex p_;
  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);
  // Default constructor, needed for serialization or Python pickle support
  ExampleRestraint() {}
  void do_add_score_and_derivatives(ScoreAccumulator sa) const
      override;
  ModelObjectsTemp do_get_inputs() const override;
  IMP_OBJECT_METHODS(ExampleRestraint);
 private:
  // Serialization support
  friend class cereal::access;
  template<class Archive> void serialize(Archive &ar) {
    // We must save/load everything in the Restraint base class
    // (e.g. restraint name, Model pointer) plus our own variables p_ and k_
    ar(cereal::base_class<Restraint>(this), p_, k_);
  }
  // ExampleRestraint is polymorphic (e.g. it is stored in
  // IMP.core.RestraintsScoringFunction as a Restraint, not an
  // ExampleRestraint) so tell the serialization subsystem how to handle this
  IMP_OBJECT_SERIALIZE_DECL(ExampleRestraint);
};
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_RESTRAINT_H */

/**
 *  \file example/ExampleRestraint.cpp
 *  \brief Restrain a list of particle pairs.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */
#include <IMP/example/ExampleRestraint.h>
#include <IMP/core/XYZ.h>
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleRestraint::ExampleRestraint(Model *m, ParticleIndex p,
                                   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 {
  IMP_OBJECT_LOG;
  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_));
}
// Complete the serialization support (see IMP_OBJECT_SERIALIZE_DECL in the
// header file)
IMP_OBJECT_SERIALIZE_IMPL(IMP::example::ExampleRestraint);
IMPEXAMPLE_END_NAMESPACE

Definition at line 26 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 override

ModelObjectsTemp	do_get_inputs () const override

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...

Public Member Functions inherited from IMP::Restraint
	Restraint (Model *m, std::string name)
	Create a restraint and register it with the model. More...

	Restraint ()
	Default constructor. More...

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
	Create a scoring function with only this restraint. More...

virtual RestraintInfo *	get_dynamic_info () const

bool	get_is_aggregate () const
	Return whether this restraint wraps a number of other restraints. More...

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 RestraintInfo *	get_static_info () const

bool	get_was_good () const

double	evaluate (bool calc_derivs) const

double	evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double	evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_if_good (bool calc_derivatives) const

double	evaluate_if_below (bool calc_derivatives, double max) const

virtual double	unprotected_evaluate (DerivativeAccumulator *da) const
	Return the unweighted score for the restraint. More...

virtual double	unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
	Return the unweighted score, taking moving particles into account. More...

virtual double	unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double	unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
	The function calling this will treat any score >= max as bad. More...

virtual double	unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double	unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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...

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_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 override

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 ()

Protected Attributes inherited from IMP::Restraint
bool	is_aggregate_

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

overridevirtual

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 43 of file ExampleRestraint.h.

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

ExampleRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation