IMP  2.4.0
The Integrative Modeling Platform
Public Member Functions | Static Public Member Functions | List of all members
IMP::atom::Domain Class Reference

A decorator to associate a particle with a part of a protein. More...

#include <IMP/atom/Domain.h>

+ Inheritance diagram for IMP::atom::Domain:

Detailed Description

A decorator to associate a particle with a part of a protein.

The decorator stores the indexes of the first and last residues in this domain.

Definition at line 21 of file Domain.h.

Public Member Functions

 Domain (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Domain (const IMP::kernel::ParticleAdaptor &d)
 
IntRange get_index_range () const
 
void set_index_range (IntRange ir)
 
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 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
 
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 kernel::ParticlesTemp. More...
 
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
 
State get_as_state () 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
 Return i such that get_parent().get_child(i) == this More...
 
GenericHierarchies get_children () const
 
kernel::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::kernel::Decorator
bool get_is_valid () const
 
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 (kernel::Model *m, kernel::ParticleIndex pi)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static Domain setup_particle (IMP::kernel::ParticleAdaptor decorator, Domain other)
 
static Domain setup_particle (kernel::Model *m, ParticleIndex pi, Domain other)
 
static Domain setup_particle (IMP::kernel::ParticleAdaptor decorator, IntRange residues)
 
static Domain setup_particle (kernel::Model *m, ParticleIndex pi, IntRange residues)
 
- 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 HierarchyTraits. More...
 
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 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::kernel::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())
 
static bool get_is_setup (kernel::Model *, kernel::ParticleIndex, HierarchyTraits=Hierarchy::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 (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexes children, 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 (IMP::kernel::ParticleAdaptor d, kernel::ParticlesTemp 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())
 

Additional Inherited Members

- Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits DecoratorTraits
 
- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Member Function Documentation

IntRange IMP::atom::Domain::get_index_range ( ) const

Get the range of indexes in the domain [begin...end)

Definition at line 54 of file Domain.h.

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

Definition at line 61 of file Domain.h.

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

Setup the particle so that it can be used with this decorator

Definition at line 61 of file Domain.h.

static Domain IMP::atom::Domain::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
IntRange  residues 
)
static

Setup the particle so that it can be used with this decorator

Definition at line 62 of file Domain.h.

static Domain IMP::atom::Domain::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
IntRange  residues 
)
static
See Also
setup_particle(m, pi, residues )

Definition at line 62 of file Domain.h.

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