A decorator for a particle representing an atom. More...

#include <IMP/atom/Atom.h>

Inheritance diagram for IMP::atom::Atom:

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

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

AtomType	get_atom_type () const

Element	get_element () const
	get element

double	get_occupancy () const

double	get_temperature_factor () const

void	set_atom_type (AtomType t)
	Set the name and corresponding element and mass.

void	set_occupancy (double occupancy)

void	set_temperature_factor (double tempFactor)

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

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

static Atom	setup_particle (IMP::kernel::ParticleAdaptor decorator, AtomType atom_type)

static Atom	setup_particle (kernel::Model *m, ParticleIndex pi, AtomType atom_type)

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...

The atom index in the input file
This index is not necessarily unique over any particular set of atoms and so should never be used as an atom identifier except during I/O.
Int	get_input_index () const

void	set_input_index (Int t)

Keys
These methods provide access to the various keys used to store things in the Atom. These can be used if you want to use an attribute to search a set of particles.
static IntKey	get_atom_type_key ()

static IntKey	get_element_key ()

static IntKey	get_input_index_key ()

static FloatKey	get_occupancy_key ()

static FloatKey	get_temperature_factor_key ()

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

Atoms always are Mass particles.

See Also: Hierarchy

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 234 of file atom/Atom.h.

Member Function Documentation

static Atom IMP::atom::Atom::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 241 of file atom/Atom.h.

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

static

return true if the particle has the needed attributes

Definition at line 247 of file atom/Atom.h.

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static bool IMP::atom::Atom::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 241 of file atom/Atom.h.

static bool IMP::atom::Atom::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 241 of file atom/Atom.h.

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

static

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

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 242 of file atom/Atom.h.

static Atom IMP::atom::Atom::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		AtomType	atom_type
	)

static

Add the required attributes using the passed AtomType. Setup the particle so it can be used with this decorator.

Definition at line 244 of file atom/Atom.h.

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

atom/Atom.h

Public Member Functions

Static Public Member Functions

The atom index in the input file

Keys

Additional Inherited Members

Detailed Description

Member Function Documentation