IMP  2.0.0
The Integrative Modeling Platform
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:

Public Member Functions

 CoverRefined (Refiner *ref, Float slack=0)
 Create with the given refiner and radius key. More...
 
virtual void do_show (std::ostream &out) const
 
void set_slack (Float slack)
 Set how nmuch extra to add to the radius.
 
- Public Member Functions inherited from IMP::kernel::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, unsigned int lower_bound, unsigned int upper_bound) const
 
ContainersTemp get_input_containers (Particle *p) const
 
ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 
ContainersTemp get_output_containers (Particle *p) const
 
ParticlesTemp get_output_particles (Particle *p) const
 
ModelObjectsTemp get_outputs (Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
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. 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 ParticleArgument
 
typedef ParticleIndex IndexArgument
 
- Protected Member Functions inherited from IMP::kernel::SingletonModifier
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 
virtual ModelObjectsTemp do_get_outputs (Model *m, const ParticleIndexes &pis) const =0
 

Detailed Description

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.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 43 of file CoverRefined.h.

Constructor & Destructor Documentation

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

Slack is the amount added to the radius.


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