IMP::core::ChildrenRefiner Class Reference

Return the hierarchy children of a particle. More...

#include <IMP/core/ChildrenRefiner.h>

Inheritance diagram for IMP::core::ChildrenRefiner:

Detailed Description

Return the hierarchy children of a particle.

A simple example using is

## \example core/cover_particles.py
# Show how to maintain a sphere per residue which includes all atoms
# of the residue. The derivatives are propagated from the sphere
# cover to the atoms so that restraints can be used at multiple
# levels.

import IMP
import IMP.core
import IMP.atom
import IMP.atom
import sys

IMP.setup_from_argv(sys.argv, "cover particles")

m = IMP.Model()
prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
pr = IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits())
for r in res:
    # add coordinates and a radius to the residue particle
    IMP.core.XYZR.setup_particle(r)
    # make sure that the coordinates and the radius define a sphere
    # which contains all of the leaves (atoms) of the residue
    IMP.core.Cover.setup_particle(r.get_particle(), pr)
# update the coordinates of the residue particles so that they cover the atoms
m.update()

See Also

Hierarchy

Hierarchy

Definition at line 27 of file ChildrenRefiner.h.

Public Member Functions
	ChildrenRefiner (HierarchyTraits tr)
	Create a refiner for a particular type of hierarchy. More...
virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const
	Overload this method to specify the inputs. More...
virtual bool	get_can_refine (Particle *) const
	Return true if this refiner can refine that particle. More...
virtual const ParticlesTemp	get_refined (Particle *) const
	Refine the passed particle into a set of particles. 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::Refiner
	Refiner (std::string name="Refiner %1%", bool is_by_ref=false)
bool	get_is_by_ref_supported ()
virtual unsigned int	get_number_of_refined (Particle *a) const
virtual Particle *	get_refined (Particle *a, unsigned int i) const
	Get the ith refined particle. More...
virtual ParticleIndexes	get_refined_indexes (Model *m, ParticleIndex pi) const
	Return the indexes of the particles returned by get_refined() More...
virtual ParticleIndexes const &	get_refined_indexes_by_ref (Model *m, ParticleIndex pi) const
	Return the indexes of the particles returned by get_refined() More...
RefinedIterator	refined_begin (Particle *a) const
RefinedIterator	refined_end (Particle *a) 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::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::Refiner
typedef internal::IndexingIterator < Accessor >	RefinedIterator
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::core::ChildrenRefiner::ChildrenRefiner

(

HierarchyTraits

tr

)

Create a refiner for a particular type of hierarchy.

Member Function Documentation

virtual ModelObjectsTemp IMP::core::ChildrenRefiner::do_get_inputs ( Model *  m, const ParticleIndexes &  pis  ) const

virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual bool IMP::core::ChildrenRefiner::get_can_refine ( Particle *  ) const

virtual

Return true if this refiner can refine that particle.

This should not throw, so be careful what fields are touched.

Reimplemented from IMP::Refiner.

virtual const ParticlesTemp IMP::core::ChildrenRefiner::get_refined ( Particle *  a ) const

virtual

Refine the passed particle into a set of particles.

As a precondition can_refine_particle(a) should be true.

Parameters

a	coarse particle to be refined

Implements IMP::Refiner.

virtual ::IMP::VersionInfo IMP::core::ChildrenRefiner::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 43 of file ChildrenRefiner.h.

---

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

• ChildrenRefiner.h