IMP::atom::Molecule Class Reference

A decorator for a molecule. More...

#include <IMP/atom/Molecule.h>

Inheritance diagram for IMP::atom::Molecule:

Public Member Functions
	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
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 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 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 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

Definition at line 24 of file Molecule.h.

Member Function Documentation

static Molecule IMP::atom::Molecule::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 35 of file Molecule.h.

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

static

Mark the particle as denoting a molecule. Setup the particle so it can be used with this decorator.

Definition at line 37 of file Molecule.h.

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

static

See Also

setup_particle(m, pi, other )

Definition at line 38 of file Molecule.h.

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

static

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

Definition at line 38 of file Molecule.h.

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

• Molecule.h