IMP  2.2.0
The Integrative Modeling Platform
IMP::atom::Representation Class Reference

A decorator for a representation. More...

#include <IMP/atom/Representation.h>

+ Inheritance diagram for IMP::atom::Representation:

Public Member Functions

 Representation (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Representation (const IMP::kernel::ParticleAdaptor &d)
 
void add_representation (kernel::ParticleIndexAdaptor rep, RepresentationType type=BALLS, double resolution=-1)
 
Hierarchy get_representation (double resolution, RepresentationType type=BALLS)
 
Hierarchies get_representations (RepresentationType type=BALLS)
 
Floats get_resolutions (RepresentationType type=BALLS) const
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::atom::Hierarchy
 Hierarchy (kernel::Model *m, kernel::ParticleIndex pi)
 
 Hierarchy (kernel::ParticleAdaptor pi)
 
 Hierarchy ()
 null constructor
 
 Hierarchy (IMP::core::Hierarchy h)
 The traits must match.
 
void add_child (Hierarchy o)
 Add a child and check that the types are appropriate. More...
 
Hierarchy get_child (unsigned int i) const
 
Hierarchies get_children () const
 Return the children in the order they were added.
 
template<class C >
get_children () const
 Get the children in a container of your choosing, eg kernel::ParticlesTemp.
 
bool get_is_valid (bool print_info) const
 Return true if the hierarchy is valid. More...
 
Hierarchy get_parent () const
 
void show (std::ostream &out=std::cout) const
 
Atom get_as_atom () const
 
Residue get_as_residue () const
 
Chain get_as_chain () const
 
Molecule get_as_molecule () const
 
Domain get_as_domain () const
 
Fragment get_as_fragment () const
 
core::XYZ get_as_xyz () const
 
core::XYZR get_as_xyzr () const
 
Mass get_as_mass () const
 
- Public Member Functions inherited from IMP::core::Hierarchy
 Hierarchy (const IMP::kernel::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits())
 
 Hierarchy (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id, const HierarchyTraits &tr=get_default_traits())
 
void add_child (Hierarchy h) const
 
void add_child_at (Hierarchy h, unsigned int pos)
 
void clear_children ()
 
Hierarchy get_child (unsigned int i) const
 
kernel::ParticleIndex get_child_index (unsigned int i) const
 
int get_child_index () const
 
GenericHierarchies get_children () const
 
kernel::ParticleIndexes get_children_indexes () const
 
const DecoratorTraitsget_decorator_traits () const
 
unsigned int get_number_of_children () const
 
Hierarchy get_parent () const
 
HierarchyTraits get_traits ()
 
void remove_child (unsigned int i)
 
void remove_child (Hierarchy h)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::kernel::Decorator
Modelget_model () const
 Returns the Model containing the particle.
 
Particleget_particle () const
 
ParticleIndex get_particle_index () const
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particleoperator-> () const
 

Static Public Member Functions

static Representation decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static Representation setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Representation setup_particle (kernel::Model *m, ParticleIndex pi)
 
static Representation setup_particle (kernel::Model *m, ParticleIndex pi, double resolution)
 
static Representation setup_particle (IMP::kernel::ParticleAdaptor decorator, double resolution)
 
- Static Public Member Functions inherited from IMP::atom::Hierarchy
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex p)
 
static const
IMP::core::HierarchyTraits
get_traits ()
 Get the molecular hierarchy HierararchyTraits.
 
static Hierarchy setup_particle (kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
 
- Static Public Member Functions inherited from IMP::core::Hierarchy
static Hierarchy decorate_particle (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())
 
static const DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_default_traits ()
 Get the default hierarchy traits.
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())
 
static bool get_is_setup (kernel::Model *, kernel::ParticleIndex, HierarchyTraits=Hierarchy::get_default_traits())
 
static Hierarchy setup_particle (kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::kernel::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::kernel::ParticleAdaptor d, kernel::ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::kernel::ParticleAdaptor d, kernel::ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())
 

Additional Inherited Members

- Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits DecoratorTraits
 
- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Detailed Description

It stores a number of copies of its sub hierarchy each with an associated resolution. You can used it to get the representation at a given resolution.

Note
The particle returned for a given representation should be thought of as replacing this particle (not as a child of it).
Only one Representation node is allowed in any path up the tree as nesting them does not have a clear meaning.

Definition at line 40 of file Representation.h.

Member Function Documentation

void IMP::atom::Representation::add_representation ( kernel::ParticleIndexAdaptor  rep,
RepresentationType  type = BALLS,
double  resolution = -1 
)

Representation for given resolution. The resolution is computed using get_resolution().

Note
The resolution parameter will go away, as, most likely will the type.
static Representation IMP::atom::Representation::decorate_particle ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 54 of file Representation.h.

Hierarchy IMP::atom::Representation::get_representation ( double  resolution,
RepresentationType  type = BALLS 
)

Return the children at the resolution closest to resolution of the passed type.

Hierarchies IMP::atom::Representation::get_representations ( RepresentationType  type = BALLS)

Return all children at all resolutions.

Floats IMP::atom::Representation::get_resolutions ( RepresentationType  type = BALLS) const

Return a list of all resolutions that are available for a specific RepresentationType.

static Representation IMP::atom::Representation::setup_particle ( kernel::Model m,
ParticleIndex  pi 
)
static

Setup the particle so it can be used with this decorator.

Definition at line 50 of file Representation.h.

static Representation IMP::atom::Representation::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
double  resolution 
)
static
See Also
setup_particle(m, pi, resolution )

Definition at line 52 of file Representation.h.

static Representation IMP::atom::Representation::setup_particle ( kernel::Model m,
ParticleIndex  pi,
double  resolution 
)
static

For testing only. Will go away. Setup the particle so that it can be used with this decorator

Definition at line 52 of file Representation.h.


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