Detailed Description

An example 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.

 ## \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.kernel.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 2007-2015 IMP Inventors. All rights reserved.
 *
 */
#ifndef IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#define IMPEXAMPLE_EXAMPLE_RESTRAINT_H
#include <IMP/example/example_config.h>
#include <IMP/kernel/Restraint.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 kernel::Restraint {
  kernel::ParticleIndex p_;
  double k_;
 public:
  //! Create the restraint.
  /** kernel::Restraints should store the particles they are to act on,
      preferably in a Singleton or PairContainer as appropriate.
   */
  ExampleRestraint(kernel::Model *m, kernel::ParticleIndex p, double k);
  void do_add_score_and_derivatives(kernel::ScoreAccumulator sa) const
      IMP_OVERRIDE;
  kernel::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 2007-2015 IMP Inventors. All rights reserved.
 *
 */
#include <IMP/example/ExampleRestraint.h>
#include <IMP/core/XYZ.h>
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleRestraint::ExampleRestraint(kernel::Model *m, kernel::ParticleIndex p,
                                   double k)
    : kernel::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(kernel::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.*/
kernel::ModelObjectsTemp ExampleRestraint::do_get_inputs() const {
  return kernel::ModelObjectsTemp(1, get_model()->get_particle(p_));
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 33 of file ExampleSingletonModifier.h.

Public Member Functions
	ExampleSingletonModifier (const algebra::BoundingBoxD< 3 > &bb)

virtual void	apply_index (kernel::Model *m, kernel::ParticleIndex p) const

virtual void	apply_indexes (kernel::Model *m, const kernel::ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

virtual kernel::ModelObjectsTemp	do_get_outputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

virtual std::string	get_type_name () const

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

Public Member Functions inherited from IMP::kernel::SingletonModifier
	SingletonModifier (std::string name="SingletonModifier %1%")

virtual void	apply (kernel::Particle *vt) const

Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const

virtual ParticlesTemp	get_input_particles (Particle *p) const

ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

Public Member Functions inherited from IMP::kernel::ParticleOutputs
virtual ContainersTemp	get_output_containers (Particle *p) const

virtual ParticlesTemp	get_output_particles (Particle *p) const

ModelObjectsTemp	get_outputs (kernel::Model *m, const ParticleIndexes &pis) const

Public Member Functions inherited from IMP::base::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
Public Types inherited from IMP::kernel::SingletonModifier
typedef kernel::Particle *	Argument

typedef kernel::ParticleIndex	IndexArgument

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

virtual void IMP::example::ExampleSingletonModifier::apply_index	(	kernel::Model *	m,
		kernel::ParticleIndex	v
	)		const

virtual

Apply the function to a single value

Reimplemented from IMP::kernel::SingletonModifier.

virtual void IMP::example::ExampleSingletonModifier::apply_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	o,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Apply the function to a collection of kernel::ParticlesTemp If bounds are passed, only apply to ones between the upper and lower bounds.

Reimplemented from IMP::kernel::SingletonModifier.

Definition at line 46 of file ExampleSingletonModifier.h.

virtual kernel::ModelObjectsTemp IMP::example::ExampleSingletonModifier::do_get_inputs	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

virtual kernel::ModelObjectsTemp IMP::example::ExampleSingletonModifier::do_get_outputs	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the outputs.

Reimplemented from IMP::kernel::ParticleOutputs.

virtual ::IMP::base::VersionInfo IMP::example::ExampleSingletonModifier::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 47 of file ExampleSingletonModifier.h.

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

ExampleSingletonModifier.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation