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

#include <IMP/atom/Atom.h>

Inheritance diagram for IMP::atom::Atom:

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

	Atom (::IMP::kernel::Particle *p)

AtomType	get_atom_type () const

Element	get_element () const
	get element

double	get_occupancy () const

Particle *	get_particle () 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 (Particle *p)

	Hierarchy (Model *m, ParticleIndex 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 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 (Model *m, ParticleIndex id, const HierarchyTraits &tr)

	Hierarchy (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())

	Hierarchy (const HierarchyTraits &tr)

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

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

const HierarchyTraits &	get_traits () const

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	particle_is_instance (Particle *p)
	return true if the particle has the needed attributes

static Atom	setup_particle (Model *m, ParticleIndex pi, AtomType t)

static Atom	setup_particle (Particle *p, AtomType t)

static Atom	setup_particle (Particle *p, Atom o)

Static Public Member Functions inherited from IMP::atom::Hierarchy
static Hierarchy	decorate_particle (Particle *p)
	cast a particle which has the needed attributes

static const IMP::core::HierarchyTraits &	get_traits ()
	Get the molecular hierarchy HierararchyTraits.

static bool	particle_is_instance (Particle *p)

static bool	particle_is_instance (Model *m, ParticleIndex p)

static Hierarchy	setup_particle (Particle *p, const ParticlesTemp &children)

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp())

static Hierarchy	setup_particle (Particle *p)

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	particle_is_instance (Particle *, HierarchyTraits=Hierarchy::get_default_traits())

static Hierarchy	setup_particle (Particle *p, HierarchyTraits traits=Hierarchy::get_default_traits())
	Add the needed attributes to a particle.

static Hierarchy	setup_particle (Particle *p, const Particles &children, HierarchyTraits traits=Hierarchy::get_default_traits())
	Add the needed attributes to a particle and add the particles as children. More...

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	particle_is_instance (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

typedef Decorator	DecoratorTraitsBase

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

	Decorator (Particle *p)

Related Functions inherited from IMP::atom::Hierarchy
Hierarchy	create_clone (Hierarchy d)
	Clone the Hierarchy. More...

Hierarchy	create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy. More...

Restraint *	create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)

Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes. More...

Hierarchy	create_protein (Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
	Create a coarse grained molecule. More...

void	destroy (Hierarchy d)
	Delete the Hierarchy. More...

Atom	get_atom (Residue rd, AtomType at)
	Return a particle atom from the residue. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)

HierarchyTree	get_hierarchy_tree (Hierarchy h)

Hierarchies	get_leaves (const Selection &h)

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

Residue	get_residue (Atom d, bool nothrow=false)
	Return the Residue containing this atom. More...

Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index. More...

Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy. More...

void	setup_as_approximation (Hierarchy h)

void	show (Hierarchy h, std::ostream &out=std::cout)
	Print out a molecular hierarchy.

Hierarchy	read_pdb (base::TextInput input, Model model, PDBSelector selector, bool select_first_model=true)