IMP  2.4.0
The Integrative Modeling Platform
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IMP::example::ExampleSingletonModifier Class Reference

An example singleton modifer. More...

#include <IMP/example/ExampleSingletonModifier.h>

+ Inheritance diagram for IMP::example::ExampleSingletonModifier:

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.

1 ## \example example/range_restriction.py
2 # This example shows how to use the example singleton modifier to constrain the
3 # coordinates of a set of particles to remain within a box.
4 
5 import IMP.example
6 import IMP.core
7 import IMP.container
8 import sys
9 
10 # you can use this argument to shorten the test, if necessary
11 IMP.base.add_bool_flag("test", "Run a minimal test on the script")
12 
13 # parse standard IMP flags
14 IMP.base.setup_from_argv(sys.argv, "A trivial example of an example.")
15 
16 
18  IMP.algebra.Vector3D(10, 10, 10))
19 
20 m = IMP.kernel.Model()
21 ps = IMP.core.create_xyzr_particles(m, 20, 1)
23 
24 # apply the range restriction modifier to each each particle in sc
27 m.add_score_state(ss)
28 
29 # now optimize and things
30 # ...

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>
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 {
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_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/core/XYZ.h>
IMPEXAMPLE_BEGIN_NAMESPACE
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 {
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::ParticleArgument
 
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: