Detailed Description

Accumulate the derivatives of the refined particles.

See Also: DerivativesToRefined; CoverRefined; CentroidOfRefinedSingletonModifer 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

12 m = IMP.kernel.Model()

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

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

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

16 for r in res:

17 # add coordinates and a radius to the residue particle

18 IMP.core.XYZR.setup_particle(r)

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

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

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

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

23 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 (kernel::Model *m, kernel::ParticleIndex a) const

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

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

virtual kernel::ModelObjectsTemp	do_get_outputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const

Constructor & Destructor Documentation

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

Copy ks from the particles returned by r.

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