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.
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 sys

11

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

13

14 m = IMP.Model()

15 prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)

16 res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)

17 pr = IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits())

18 for r in res:

19 # add coordinates and a radius to the residue particle

20 IMP.core.XYZR.setup_particle(r)

21 # make sure that the coordinates and the radius define a sphere

22 # which contains all of the leaves (atoms) of the residue

23 IMP.core.Cover.setup_particle(r.get_particle(), pr)

24 # update the coordinates of the residue particles so that they cover the atoms

25 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.

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

DerivativesFromRefined.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation