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 Particle * | Argument |
| 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 |
| Related Functions inherited from IMP::kernel::SingletonModifier | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < SingletonModifier > > | SingletonModifiersTemp |
Detailed Description
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
Slack is the amount added to the radius.
The documentation for this class was generated from the following file: