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

#include <IMP/atom/Atom.h>

Inheritance diagram for IMP::atom::Atom:

Detailed Description

A decorator for a particle representing an atom.

Atoms always are Mass particles.

See Also: Hierarchy

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 238 of file atom/Atom.h.

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

	Atom (const IMP::ParticleAdaptor &d)

AtomType	get_atom_type () const

Element	get_element () const
	get element More...

double	get_occupancy () const

double	get_temperature_factor () const

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

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 (Model *m, ParticleIndex pi)

	Hierarchy (ParticleAdaptor pi)

	Hierarchy ()
	Null constructor. More...

	Hierarchy (IMP::core::Hierarchy h)
	The traits must match. More...

void	add_child (Hierarchy o)
	Add a child and check that the types are appropriate. More...

Hierarchy	get_child (unsigned int i) const
	Get the ith child based on the order they were added. More...

Hierarchies	get_children () const
	Return the children in the order they were added. More...

template<class C >
C	get_children () const
	Get the children in a container of your choosing, eg ParticlesTemp. More...

bool	get_is_valid (bool print_info=false) const
	Return true if the hierarchy is valid. More...

Hierarchy	get_parent () const
	Get the parent particle. More...

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

Public Member Functions inherited from IMP::core::Hierarchy
	Hierarchy (const IMP::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits())

	Hierarchy (::IMP::Model *m,::IMP::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

ParticleIndex	get_child_index (unsigned int i) const

int	get_child_index () const
	Return i such that `get_parent().get_child(i) == this` More...

GenericHierarchies	get_children () const

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::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...

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

Particle *	get_particle () const
	Returns the particle decorated by this decorator. More...

ParticleIndex	get_particle_index () const
	Returns the particle index decorated by this decorator. More...

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () const

Static Public Member Functions
static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)
	return true if the particle has the needed attributes More...

static Atom	setup_particle (Model *m, ParticleIndex pi, Atom other)

static Atom	setup_particle (IMP::ParticleAdaptor pa, Atom other)

static Atom	setup_particle (Model *m, ParticleIndex pi, AtomType atom_type)
	Add the required attributes using the passed AtomType. More...

static Atom	setup_particle (IMP::ParticleAdaptor pa, AtomType atom_type)

Static Public Member Functions inherited from IMP::atom::Hierarchy
static bool	get_is_setup (Model *m, ParticleIndex p)
	Check if the particle has the needed attributes for a cast to succeed. More...

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

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
	Create a Hierarchy of level t by adding the needed attributes. More...

Static Public Member Functions inherited from IMP::core::Hierarchy
static TriggerKey	get_changed_key ()
	The key used to signal to the Model that the Hierarchy has changed. More...

static const DecoratorTraits &	get_default_decorator_traits ()

static const HierarchyTraits &	get_default_traits ()
	Get the default hierarchy traits. More...

static bool	get_is_setup (const IMP::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())

static bool	get_is_setup (Model *, ParticleIndex, HierarchyTraits=Hierarchy::get_default_traits())

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

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())

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

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

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())

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::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor 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...

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

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

algebra::BoundingBoxD< 3 >	get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)
	Gather all the molecular particles of a certain level in the hierarchy. More...

Bonds	get_internal_bonds (Hierarchy mhd)
	Get the bonds internal to this tree. More...

bool	get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen. More...

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

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

Member Function Documentation

Element IMP::atom::Atom::get_element ( ) const

get element

Definition at line 265 of file atom/Atom.h.

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Int IMP::atom::Atom::get_input_index ( ) const

returns the value of the input_index attribute, or -1 if \ the input_index attribute is missing

Definition at line 321 of file atom/Atom.h.

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

static

return true if the particle has the needed attributes

Definition at line 251 of file atom/Atom.h.

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void IMP::atom::Atom::set_atom_type ( AtomType t )

Set the name and corresponding element and mass.

void IMP::atom::Atom::set_input_index ( Int t )

sets the input_index attribute to t

Definition at line 321 of file atom/Atom.h.

static Atom IMP::atom::Atom::setup_particle	(	IMP::ParticleAdaptor	pa,
		Atom	other
	)

static

Returns: a Atom object that decorates the particle specified by pa

See Also: setup_particle(m, pi, other )

Definition at line 246 of file atom/Atom.h.

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

static

Returns: a Atom object that decorates particle pi

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 246 of file atom/Atom.h.

static Atom IMP::atom::Atom::setup_particle	(	IMP::ParticleAdaptor	pa,
		AtomType	atom_type
	)

static

Returns: a Atom object that decorates the particle specified by pa

See Also: setup_particle(m, pi, atom_type )

Definition at line 248 of file atom/Atom.h.

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

static

Add the required attributes using the passed AtomType.

Returns: a Atom object that decorates particle pi

Definition at line 248 of file atom/Atom.h.

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

atom/Atom.h

Detailed Description

Public Member Functions

Static Public Member Functions

The atom index in the input file

Keys

Additional Inherited Members

Member Function Documentation