IMP::core::CoverRefined Class Reference

This class sets the position and radius of each particle to enclose the refined. More...

#include <IMP/core/CoverRefined.h>

Inheritance diagram for IMP::core::CoverRefined:

Detailed Description

This class sets the position and radius of each particle to enclose the refined.

See Also

DerivativesFromRefined

DerivativesToRefined

CentroidOfRefined

atom::CoverBond

Set the coordinates and radius of the passed particle to cover the particles listed by the particle refiner. An example showing a how to use such a score state to maintain a cover of the atoms of a protein by a sphere per residue.

## \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

m = IMP.kernel.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()

Note

The particle passed must be an XYZR. The class CoverRefined uses CGAL in order to improve its functionality. It will fall back on less good code without it.

Definition at line 42 of file CoverRefined.h.

Public Member Functions
	CoverRefined (Refiner *ref, Float slack=0)
	Create with the given refiner and radius key. More...
virtual void	apply_index (kernel::Model *m, kernel::ParticleIndex a) 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...
void	set_slack (Float slack)
	Set how much extra to add to the radius. 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::Particle *	Argument
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 ()

Constructor & Destructor Documentation

IMP::core::CoverRefined::CoverRefined	(	Refiner *	ref,
		Float	slack = 0
	)

Create with the given refiner and radius key.

Slack is the amount added to the radius.

Member Function Documentation

virtual void IMP::core::CoverRefined::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::core::CoverRefined::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 60 of file CoverRefined.h.

virtual kernel::ModelObjectsTemp IMP::core::CoverRefined::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::core::CoverRefined::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::core::CoverRefined::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 61 of file CoverRefined.h.

void IMP::core::CoverRefined::set_slack

(

Float

slack

)

Set how much extra to add to the radius.

Definition at line 52 of file CoverRefined.h.

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

• CoverRefined.h