Detailed Description

An example singleton modifier.

A simple singleton modifier which ensures the x,y,z coordinates stay in a box by wrapping them.

Such a class could be coupled with an IMP::core::SingletonConstraint or IMP::container::SingletonsConstraint 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.add_bool_flag("test", "Run a minimal test on the script")
 
 # parse standard IMP flags
 IMP.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(m, 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/ExampleSingletonModifier.h
 *  \brief A singleton modifier which wraps an attribute into a
 *  given range.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 */
#ifndef IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H
#define IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H
#include <IMP/example/example_config.h>
#include <IMP/SingletonModifier.h>
#include <IMP/algebra/BoundingBoxD.h>
#include <IMP/singleton_macros.h>
#include <cereal/access.hpp>
#include <cereal/types/base_class.hpp>
IMPEXAMPLE_BEGIN_NAMESPACE
//! An example singleton modifier
/** A simple singleton modifier which ensures the x,y,z coordinates
    stay in a box by wrapping them.
    Such a class could be coupled with an IMP::core::SingletonConstraint
    or IMP::container::SingletonsConstraint to keep a set of particles
    in a box.
    \include range_restriction.py
    The source code is as follows:
    \include ExampleSingletonModifier.h
    \include ExampleSingletonModifier.cpp
 */
class IMPEXAMPLEEXPORT ExampleSingletonModifier : public SingletonModifier {
  algebra::BoundingBoxD<3> bb_;
  friend class cereal::access;
  template<class Archive> void serialize(Archive &ar) {
    ar(cereal::base_class<SingletonModifier>(this), bb_);
  }
  IMP_OBJECT_SERIALIZE_DECL(ExampleSingletonModifier);
 public:
  ExampleSingletonModifier(const algebra::BoundingBoxD<3> &bb);
  ExampleSingletonModifier() {}
  // note, Doxygen wants a semicolon at the end of macro lines
  virtual void apply_index(Model *m, ParticleIndex p) const
      override;
  virtual ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  virtual ModelObjectsTemp do_get_outputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_SINGLETON_MODIFIER_METHODS(ExampleSingletonModifier);
  IMP_OBJECT_METHODS(ExampleSingletonModifier);
};
IMPEXAMPLE_END_NAMESPACE
#endif /* IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H */

/**
 *  \file example/ExampleSingletonModifier.cpp
 *  \brief A singleton modifier which wraps an attribute into a
 *  given range.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */
#include "IMP/example/ExampleSingletonModifier.h"
#include "IMP/core/XYZ.h"
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleSingletonModifier::ExampleSingletonModifier(
    const algebra::BoundingBox3D &bb)
    : bb_(bb) {}
void ExampleSingletonModifier::apply_index(Model *m,
                                           ParticleIndex pi) const {
  core::XYZ d(m, pi);
  for (unsigned int i = 0; i < 3; ++i) {
    // shift the coordinate until it is in the box
    while (d.get_coordinate(i) < bb_.get_corner(0)[i]) {
      d.set_coordinate(i, d.get_coordinate(i) +
                              (bb_.get_corner(1)[i] - bb_.get_corner(0)[i]));
    }
    while (d.get_coordinate(i) > bb_.get_corner(1)[i]) {
      d.set_coordinate(i, d.get_coordinate(i) -
                              (bb_.get_corner(1)[i] - bb_.get_corner(0)[i]));
    }
  }
}
/* Only the passed particle is used */
ModelObjectsTemp ExampleSingletonModifier::do_get_inputs(
    Model *m, const ParticleIndexes &pis) const {
  return IMP::get_particles(m, pis);
}
ModelObjectsTemp ExampleSingletonModifier::do_get_outputs(
    Model *m, const ParticleIndexes &pis) const {
  return do_get_inputs(m, pis);
}
IMP_OBJECT_SERIALIZE_IMPL(IMP::example::ExampleSingletonModifier);
IMPEXAMPLE_END_NAMESPACE

Definition at line 35 of file ExampleSingletonModifier.h.

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

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

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

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const override
	Overload this method to specify the inputs. More...

virtual ModelObjectsTemp	do_get_outputs (Model *m, const ParticleIndexes &pis) const override
	Overload this method to specify the outputs. More...

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::SingletonModifier
	SingletonModifier (std::string name="SingletonModifier %1%")

virtual void	apply_indexes_moved (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
	Get the ModelObjects read when the given list of particles is used. More...

Public Member Functions inherited from IMP::ParticleOutputs
ModelObjectsTemp	get_outputs (Model *m, const ParticleIndexes &pis) const
	Get the ModelObjects changed when the given list of particles is used. 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
Public Types inherited from IMP::SingletonModifier
typedef Particle *	Argument

typedef ParticleIndex	IndexArgument

Protected Member Functions inherited from IMP::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	(	Model *	m,
		ParticleIndex	v
	)		const

overridevirtual

Apply the function to a single value

Implements IMP::SingletonModifier.

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

finaloverridevirtual

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

Reimplemented from IMP::SingletonModifier.

Definition at line 55 of file ExampleSingletonModifier.h.

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

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

overridevirtual

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 56 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