IMP::examplesystemlocal::ExampleSingletonModifier Class Reference

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Detailed Description

An local singleton modifer.

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.

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

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 local/ExampleRestraint.h
 *  \brief A restraint on a list of particle pairs.
 *
 *  Copyright 2007-2012 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_RESTRAINT_H
#define IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_RESTRAINT_H

#include "example_system_local_config.h"
#include <IMP/SingletonScore.h>
#include <IMP/Restraint.h>
#include <IMP/PairContainer.h>
#include <IMP/PairScore.h>
#include <IMP/restraint_macros.h>

IMPEXAMPLESYSTEMLOCAL_BEGIN_NAMESPACE

//! Constraint 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 IMPEXAMPLESYSTEMLOCALEXPORT ExampleRestraint : public Restraint
{
  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);

  /** This macro declares the basic needed methods: evaluate and show
   */
  IMP_RESTRAINT(ExampleRestraint);
};

IMPEXAMPLESYSTEMLOCAL_END_NAMESPACE

#endif  /* IMP_EXAMPLE_SYSTEM_LOCAL_EXAMPLE_RESTRAINT_H */

/**
 *  \file example/ExampleRestraint.cpp
 *  \brief Restrain a list of particle pairs.
 *
 *  Copyright 2007-2012 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.
 */
double
ExampleRestraint::unprotected_evaluate(DerivativeAccumulator *accum) 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 (accum) {
    double deriv= k_*d.get_z();
    d.add_to_derivative(2, deriv, *accum);
  }
  return score;
}

/* Return all particles whose attributes are read by the restraints. To
   do this, ask the pair score what particles it uses.*/
ParticlesTemp ExampleRestraint::get_input_particles() const
{
  return ParticlesTemp(1,p_);
}

/* The only container used is pc_. */
ContainersTemp ExampleRestraint::get_input_containers() const
{
  return ContainersTemp();
}

void ExampleRestraint::do_show(std::ostream& out) const
{
  out << "particle= " << p_->get_name() << std::endl;
  out << "k= " << k_ << std::endl;
}

IMPEXAMPLE_END_NAMESPACE

Inheritance diagram for IMP::examplesystemlocal::ExampleSingletonModifier:

List of all members.

Public Member Functions
	ExampleSingletonModifier (const algebra::BoundingBoxD< 3 > &bb)
Public Member Functions inherited from IMP::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) const
virtual ContainersTemp	get_input_containers (Particle *p) const =0
virtual ParticlesTemp	get_input_particles (Particle *p) const =0
virtual ContainersTemp	get_output_containers (Particle *p) const =0
virtual ParticlesTemp	get_output_particles (Particle *p) const =0
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
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.
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)

Static Public Member Functions
static ExampleSingletonModifier *	get_from (IMP::base::Object *o)

Additional Inherited Members
Public Types inherited from IMP::SingletonModifier
typedef Particle *	Argument
typedef ParticleIndex	IndexArgument

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

• system_local/ExampleSingletonModifier.h