IMP::example::ExampleSingletonModifier Class Reference

An example singleton modifer. More...

#include <IMP/example/ExampleSingletonModifier.h>

Inheritance diagram for IMP::example::ExampleSingletonModifier:

Public Member Functions
	ExampleSingletonModifier (const algebra::BoundingBoxD< 3 > &bb)
virtual void	do_show (std::ostream &out) const
Public Member Functions inherited from IMP::kernel::SingletonModifier
	SingletonModifier (std::string name="SingletonModifier %1%")
virtual void	apply (Particle *) const =0
virtual void	apply_index (Model *m, ParticleIndex v) const
virtual void	apply_indexes (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
ContainersTemp	get_input_containers (Particle *p) const
ParticlesTemp	get_input_particles (Particle *p) const
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
ContainersTemp	get_output_containers (Particle *p) const
ParticlesTemp	get_output_particles (Particle *p) const
ModelObjectsTemp	get_outputs (Model *m, const ParticleIndexes &pis) 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
Public Types inherited from IMP::kernel::SingletonModifier
typedef Particle *	Argument
typedef ParticleIndex	IndexArgument
Protected Member Functions inherited from IMP::kernel::SingletonModifier
virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
virtual ModelObjectsTemp	do_get_outputs (Model *m, const ParticleIndexes &pis) const =0
Related Functions inherited from IMP::kernel::SingletonModifier
typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonModifier > >	SingletonModifiersTemp

Detailed Description

A simple singleton modifier which restrains the x,y,z coordinates to a box by wrapping them.

Such a class could be coupled with an IMP::core::SingletonRestraint or IMP::core::SingletonsRestraint to keep a set of particles in a box.

## \example example/range_restriction.py
## This example shows how to use the example singleton modifier to constrain the
## coordinates of a set of particles to remain within a box.

import IMP.example
import IMP.core
import IMP.container
import sys

# you can use this argument to shorten the test, if necessary
IMP.base.add_bool_flag("test", "Run a minimal test on the script")

# parse standard IMP flags
IMP.base.setup_from_argv(sys.argv, "A trivial example of an example.")


bb= IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),
                              IMP.algebra.Vector3D(10,10,10))

m= IMP.Model()
ps= IMP.core.create_xyzr_particles(m, 20, 1)
sc= IMP.container.ListSingletonContainer(ps)

# apply the range restriction modifier to each each particle in sc
ss= IMP.container.SingletonsConstraint(IMP.example.ExampleSingletonModifier(bb), None, sc)
m.add_score_state(ss)

# now optimize and things
# ...

The source code is as follows:

/**
 *  \file IMP/example/ExampleRestraint.h
 *  \brief A restraint on a list of particle pairs.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#define IMPEXAMPLE_EXAMPLE_RESTRAINT_H

#include <IMP/example/example_config.h>
#include <IMP/SingletonScore.h>
#include <IMP/Restraint.h>
#include <IMP/PairContainer.h>
#include <IMP/PairScore.h>
#include <IMP/restraint_macros.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
{
  base::Pointer<Particle> 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(Particle *p, double k);
  void do_add_score_and_derivatives(IMP::ScoreAccumulator sa)
    const IMP_OVERRIDE;
  IMP::ModelObjectsTemp do_get_inputs() const;
  IMP_OBJECT_METHODS(ExampleRestraint);
};

IMPEXAMPLE_END_NAMESPACE

#endif  /* IMPEXAMPLE_EXAMPLE_RESTRAINT_H */

/**
 *  \file example/ExampleRestraint.cpp
 *  \brief Restrain a list of particle pairs.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/example/ExampleRestraint.h>
#include <IMP/core/XYZ.h>

IMPEXAMPLE_BEGIN_NAMESPACE

ExampleRestraint::ExampleRestraint(Particle *p,
                                   double k) :
  Restraint(p->get_model(), "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(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,p_);
}

IMPEXAMPLE_END_NAMESPACE

Definition at line 33 of file ExampleSingletonModifier.h.

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

• ExampleSingletonModifier.h