IMP  2.3.0
The Integrative Modeling Platform
IMP::core::DerivativesFromRefined Class Reference

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

#include <IMP/core/DerivativesFromRefined.h>

Inherits SingletonDerivativeModifier.

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)
16 for r in res:
17  # add coordinates and a radius to the residue particle
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: