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 >
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 DecoratorTraits &	get_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
Model *	get_model () const
	Returns the Model containing the particle.

Particle *	get_particle () const

ParticleIndex	get_particle_index () const

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () 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 DecoratorTraits &	get_default_decorator_traits ()

static const HierarchyTraits &	get_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:

Representation.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation