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IMP Reference Guide  develop.716bca0a46,2020/04/04
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:

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 234 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 >
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 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::Decorator
bool get_is_valid () const
 Returns true if constructed with a non-default constructor. More...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_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
 
Particleoperator-> () const
 

Static Public Member Functions

static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static Atom setup_particle (Model *m, ParticleIndex pi, Atom other)
 
static Atom setup_particle (IMP::ParticleAdaptor decorator, Atom other)
 
static Atom setup_particle (Model *m, ParticleIndex pi, AtomType atom_type)
 
static Atom setup_particle (IMP::ParticleAdaptor decorator, 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 const DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_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)
 

Member Function Documentation

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

get element

Definition at line 261 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 317 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 247 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 317 of file atom/Atom.h.

static Atom IMP::atom::Atom::setup_particle ( IMP::ParticleAdaptor  decorator,
Atom  other 
)
static
See Also
setup_particle(m, pi, other )

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

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

Setup the particle so that 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 ( IMP::ParticleAdaptor  decorator,
AtomType  atom_type 
)
static
See Also
setup_particle(m, pi, atom_type )

Definition at line 244 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. Setup the particle so that 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: