IMP logo
IMP Reference Guide  develop.c9d213c767,2020/05/28
The Integrative Modeling Platform
IMP::example::ExampleSingletonModifier Class Reference

An example singleton modifier. More...

#include <IMP/example/ExampleSingletonModifier.h>

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

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.

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.add_bool_flag("test", "Run a minimal test on the script")
12 
13 # parse standard IMP flags
14 IMP.setup_from_argv(sys.argv, "A trivial example of an example.")
15 
16 
18  IMP.algebra.Vector3D(10, 10, 10))
19 
20 m = IMP.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/ExampleSingletonModifier.h
* \brief A singleton modifier which wraps an attribute into a
* given range.
*
* Copyright 2007-2020 IMP Inventors. All rights reserved.
*/
#ifndef IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H
#define IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H
#include <IMP/example/example_config.h>
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_;
public:
ExampleSingletonModifier(const algebra::BoundingBoxD<3> &bb);
// note, Doxygen wants a semicolon at the end of macro lines
virtual void apply_index(Model *m, ParticleIndex p) const
Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE;
Model *m, const ParticleIndexes &pis) const IMP_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 2007-2020 IMP Inventors. All rights reserved.
*
*/
#include "IMP/core/XYZ.h"
IMPEXAMPLE_BEGIN_NAMESPACE
ExampleSingletonModifier::ExampleSingletonModifier(
: 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);
}
IMPEXAMPLE_END_NAMESPACE

Definition at line 33 of file ExampleSingletonModifier.h.

Public Member Functions

 ExampleSingletonModifier (const algebra::BoundingBoxD< 3 > &bb)
 
virtual void apply_index (Model *m, ParticleIndex p) const
 
virtual void apply_indexes (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
virtual ModelObjectsTemp do_get_outputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the outputs. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
- Public Member Functions inherited from IMP::SingletonModifier
 SingletonModifier (std::string name="SingletonModifier %1%")
 
- 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 ParticleArgument
 
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
virtual

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
virtual

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 46 of file ExampleSingletonModifier.h.

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

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 47 of file ExampleSingletonModifier.h.


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