IMP::core::CoverRefined Class Reference

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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. import IMP import IMP.core import IMP.atom import IMP.atom 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. The class CoverRefined uses CGAL in order to improve its functionality. It will fall back on less good code without it.

Inheritance diagram for IMP::core::CoverRefined:

List of all members.

Public Member Functions
	CoverRefined (Refiner *ref, Float slack=0)
	Create with the given refiner and radius key.
void	set_slack (Float slack)
	Set how nmuch extra to add to the radius.
Public Member Functions inherited from IMP::SingletonModifier
	SingletonModifier (std::string name="SingletonModifier %1%")
virtual void	apply (Particle *) const =0
virtual void	apply_index (Model *m, ParticleIndex v) const
virtual void	apply_indexes (Model *m, const ParticleIndexes &o) const
virtual ContainersTemp	get_input_containers (Particle *p) const =0
virtual ParticlesTemp	get_input_particles (Particle *p) const =0
virtual ContainersTemp	get_output_containers (Particle *p) const =0
virtual ParticlesTemp	get_output_particles (Particle *p) const =0
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object.
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)

Static Public Member Functions
static CoverRefined *	get_from (IMP::base::Object *o)

Additional Inherited Members
Public Types inherited from IMP::SingletonModifier
typedef Particle *	Argument
typedef ParticleIndex	IndexArgument

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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.

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Member Function Documentation

void IMP::core::CoverRefined::set_slack

(

Float

slack

)

Set how nmuch extra to add to the radius.

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

• CoverRefined.h