IMP Reference Guide
develop.714915d50b,2024/12/07
The Integrative Modeling Platform
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Set the position and radius of a particle to enclose the refined. More...
#include <IMP/core/CoverRefined.h>
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:
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 () |
Create with the given refiner and radius key.
Slack is the amount added to the radius.
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overridevirtual |
Apply the function to a single value
Implements IMP::SingletonModifier.
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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.
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overridevirtual |
Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
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overridevirtual |
Overload this method to specify the outputs.
Implements IMP::ParticleOutputs.
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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.