IMP  2.1.0
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 (::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 >
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 DecoratorTraitsget_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
 
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 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 DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_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.

+ Here is the call graph for this function:

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: