A decorator for keeping track of copies of a molecule. More...

#include <IMP/atom/Copy.h>

Inheritance diagram for IMP::atom::Copy:

Public Member Functions
	Copy (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	Copy (const IMP::kernel::ParticleAdaptor &d)

int	get_copy_index () const

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::atom::Molecule
	Molecule (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	Molecule (const IMP::kernel::ParticleAdaptor &d)

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

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
ParticleIndex	get_particle_index () const

Particle *	get_particle () const

Model *	get_model () const
	Returns the Model containing the particle.

	Decorator (Particle *p)

	Decorator ()

Static Public Member Functions
static Copy	decorate_particle (::IMP::kernel::Particle *p)

static IntKey	get_copy_index_key ()

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static Copy	setup_particle (IMP::kernel::ParticleAdaptor decorator, Int number)

static Copy	setup_particle (kernel::Model *m, ParticleIndex pi, Int number)

Static Public Member Functions inherited from IMP::atom::Molecule
static Molecule	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 bool	particle_is_instance (::IMP::kernel::Particle *p)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static Molecule	setup_particle (kernel::Model *m, ParticleIndex pi)

static Molecule	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static Molecule	setup_particle (IMP::kernel::ParticleAdaptor decorator, Molecule other)

static Molecule	setup_particle (kernel::Model *m, ParticleIndex pi, Molecule other)

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 bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi, const HierarchyTraits &tr=get_default_traits())

static bool	particle_is_instance (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())

static Hierarchy	setup_particle (IMP::kernel::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (kernel::Model *m, ParticleIndex pi, 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())

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	get_is_setup (Particle *p)
	Return true if the particle can be cast to the decorator. More...

Additional Inherited Members
Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits	DecoratorTraits

Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (kernel::Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

Detailed Description

This decorator is for differentiating and keeping track of identity when there are multiple copies of the a molecule in the system. It should only be applied to Molecule particles.

Definition at line 27 of file Copy.h.

Member Function Documentation

static Copy IMP::atom::Copy::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 37 of file Copy.h.

static bool IMP::atom::Copy::particle_is_instance	(	IMP::kernel::Model *	m,
		IMP::kernel::ParticleIndex	pi
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 37 of file Copy.h.

static bool IMP::atom::Copy::particle_is_instance ( ::IMP::kernel::Particle * p )

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 37 of file Copy.h.

static Copy IMP::atom::Copy::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		Int	number
	)

static

Create a decorator for the numberth copy. Setup the particle so it can be used with this decorator.

Definition at line 39 of file Copy.h.

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

Copy.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation