IMP logo
IMP Reference Guide  develop.07f7673d5c,2020/04/01
The Integrative Modeling Platform
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

1 ## \example core/cover_particles.py
2 # Show how to maintain a sphere per residue which includes all atoms
3 # of the residue. The derivatives are propagated from the sphere
4 # cover to the atoms so that restraints can be used at multiple
5 # levels.
6 
7 import IMP
8 import IMP.core
9 import IMP.atom
10 import IMP.atom
11 import sys
12 
13 IMP.setup_from_argv(sys.argv, "cover particles")
14 
15 m = IMP.Model()
16 prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
17 res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
19 for r in res:
20  # add coordinates and a radius to the residue particle
22  # make sure that the coordinates and the radius define a sphere
23  # which contains all of the leaves (atoms) of the residue
24  IMP.core.Cover.setup_particle(r.get_particle(), pr)
25 # update the coordinates of the residue particles so that they cover the atoms
26 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 Particleget_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
acoarse 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: