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IMP Reference Guide  develop.182d9373c4,2021/04/12
The Integrative Modeling Platform
IMP::core::CoverRefined Class Reference

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

#include <IMP/core/CoverRefined.h>

+ Inheritance diagram for IMP::core::CoverRefined:

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:

1 ## \example core/cover_particles.py
2 # Show how to maintain a sphere per residue which includes all atoms
3 # of the residue. The derivatives are propagated from the sphere
4 # cover to the atoms so that restraints can be used at multiple
5 # levels.
6 
7 import IMP
8 import IMP.core
9 import IMP.atom
10 import IMP.atom
11 import sys
12 
13 IMP.setup_from_argv(sys.argv, "cover particles")
14 
15 m = IMP.Model()
16 prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
17 res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
19 for r in res:
20  # add coordinates and a radius to the residue particle
22  # make sure that the coordinates and the radius define a sphere
23  # which contains all of the leaves (atoms) of the residue
24  IMP.core.Cover.setup_particle(r.get_particle(), pr)
25 # update the coordinates of the residue particles so that they cover the atoms
26 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
 
virtual void apply_indexes (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
virtual ModelObjectsTemp do_get_outputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the outputs. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::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::SingletonModifier
 SingletonModifier (std::string name="SingletonModifier %1%")
 
- 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 ParticleArgument
 
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
virtual

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
virtual

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
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

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: