IMP  2.0.1
The Integrative Modeling Platform
IMP::atom::Atom Class Reference

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
 
Particleget_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 >
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 DecoratorTraitsget_decorator_traits () const
 
unsigned int get_number_of_children () const
 
Hierarchy get_parent () const
 
const HierarchyTraitsget_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
 
Particleget_particle () const
 
Modelget_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 DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_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)
 

Detailed Description

Atoms always are Mass particles.

See Also
Hierarchy
Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 233 of file atom/Atom.h.

Member Function Documentation

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

Create a decorator with the passed type.

Examples:
atom/dope_and_excluded_volume.cpp.
static Atom IMP::atom::Atom::setup_particle ( Particle p,
AtomType  t 
)
static

Create a decorator with the passed type.

Definition at line 250 of file atom/Atom.h.

static Atom IMP::atom::Atom::setup_particle ( Particle p,
Atom  o 
)
static

Create a decorator by copying from o.


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