Detailed Description

Set the position and radius of a particle to enclose the refined.

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 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()

Note: The particle passed must be an XYZR.

See Also: DerivativesFromRefined; DerivativesToRefined; CentroidOfRefined; atom::CoverBond

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 (Model *m, ParticleIndex a) const override

virtual void	apply_indexes (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const overridefinal

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const override
	Overload this method to specify the inputs. More...

virtual ModelObjectsTemp	do_get_outputs (Model *m, const ParticleIndexes &pis) const override
	Overload this method to specify the outputs. More...

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	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::SingletonModifier
	SingletonModifier (std::string name="SingletonModifier %1%")

virtual void	apply_indexes_moved (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) 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::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 Particle *	Argument

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 ()

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	(	Model *	m,
		ParticleIndex	v
	)		const

overridevirtual

Apply the function to a single value

Implements IMP::SingletonModifier.

virtual void IMP::core::CoverRefined::apply_indexes	(	Model *	m,
		const ParticleIndexes &	o,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

finaloverridevirtual

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 60 of file CoverRefined.h.

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

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual ModelObjectsTemp IMP::core::CoverRefined::do_get_outputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::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.

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

CoverRefined.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation