IMP::core::DerivativesFromRefined Class Reference

Accumulate the derivatives of the refined particles. More...

#include <IMP/core/DerivativesFromRefined.h>

Inheritance diagram for IMP::core::DerivativesFromRefined:

Detailed Description

Accumulate the derivatives of the refined particles.

See Also

DerivativesToRefined

CoverRefined

CentroidOfRefinedSingletonModifier 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 sys

IMP.setup_from_argv(sys.argv, "cover particles")

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()

Definition at line 29 of file DerivativesFromRefined.h.

Public Member Functions
	DerivativesFromRefined (Refiner *r, FloatKeys ks=XYZ::get_xyz_keys())
	Copy ks from the particles returned by r. 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...
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 ()

Constructor & Destructor Documentation

IMP::core::DerivativesFromRefined::DerivativesFromRefined	(	Refiner *	r,
		FloatKeys	ks = XYZ::get_xyz_keys()
	)

Copy ks from the particles returned by r.

Member Function Documentation

virtual void IMP::core::DerivativesFromRefined::apply_index ( Model *  m, ParticleIndex  v  ) const

overridevirtual

Apply the function to a single value

Implements IMP::SingletonModifier.

virtual void IMP::core::DerivativesFromRefined::apply_indexes ( Model *  m, const ParticleIndexes &  o, unsigned int  lower_bound, unsigned int  upper_bound  ) const

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 44 of file DerivativesFromRefined.h.

virtual ModelObjectsTemp IMP::core::DerivativesFromRefined::do_get_inputs ( Model *  m, const ParticleIndexes &  pis  ) const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual ModelObjectsTemp IMP::core::DerivativesFromRefined::do_get_outputs ( Model *  m, const ParticleIndexes &  pis  ) const

overridevirtual

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 45 of file DerivativesFromRefined.h.

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

• DerivativesFromRefined.h