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IMP Reference Guide  develop.d247202c1c,2019/10/23
The Integrative Modeling Platform
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.
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 import sys
12 
13 IMP.setup_from_argv(sys.argv, "cover particles")
14 
15 m = IMP.Model()
16 prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
17 res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
19 for r in res:
20  # add coordinates and a radius to the residue particle
22  # make sure that the coordinates and the radius define a sphere
23  # which contains all of the leaves (atoms) of the residue
24  IMP.core.Cover.setup_particle(r.get_particle(), pr)
25 # update the coordinates of the residue particles so that they cover the atoms
26 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
 
virtual void apply_indexes (Model *m, const ParticleIndexes &o, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the inputs. More...
 
virtual ModelObjectsTemp do_get_outputs (Model *m, const ParticleIndexes &pis) const
 Overload this method to specify the outputs. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
- Public Member Functions inherited from IMP::SingletonModifier
 SingletonModifier (std::string name="SingletonModifier %1%")
 
- 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 ParticleArgument
 
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
virtual

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
virtual

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
virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

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

Overload this method to specify the outputs.

Implements IMP::ParticleOutputs.

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

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: