IMP  2.2.1
The Integrative Modeling Platform
Public Member Functions | Static Public Member Functions | List of all members
IMP::atom::Residue Class Reference
Hierarchies of particles

A decorator for a residue. More...

#include <IMP/atom/Residue.h>

+ Inheritance diagram for IMP::atom::Residue:

Public Member Functions

 Residue (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Residue (const IMP::kernel::ParticleAdaptor &d)
 
Int get_index () const
 The residues index in the chain.
 
char get_insertion_code () const
 
bool get_is_dna () const
 
bool get_is_protein () const
 
bool get_is_rna () const
 
ResidueType get_residue_type () const
 
void set_index (Int t)
 
void set_insertion_code (char insertion_code)
 
void set_residue_type (ResidueType t)
 Update the stored ResidueType and the atom::Hierarchy::Name.
 
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 >
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
 
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
Model * get_model () const
 Returns the Model containing the particle.
 
Particle * get_particle () const
 
ParticleIndex get_particle_index () const
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particle * operator-> () const
 

Static Public Member Functions

static Residue decorate_particle (::IMP::kernel::Particle *p)
 
static IntKey get_index_key ()
 
static IntKey get_insertion_code_key ()
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static IntKey get_residue_type_key ()
 
static Residue setup_particle (IMP::kernel::ParticleAdaptor decorator, ResidueType t, int index, int insertion_code)
 
static Residue setup_particle (kernel::Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
 
static Residue setup_particle (kernel::Model *m, ParticleIndex pi, ResidueType t, int index)
 
static Residue setup_particle (IMP::kernel::ParticleAdaptor decorator, ResidueType t, int index)
 
static Residue setup_particle (IMP::kernel::ParticleAdaptor decorator, ResidueType t)
 
static Residue setup_particle (kernel::Model *m, ParticleIndex pi, ResidueType t)
 
static Residue setup_particle (IMP::kernel::ParticleAdaptor decorator, Residue other)
 
static Residue setup_particle (kernel::Model *m, ParticleIndex pi, Residue other)
 
- 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 DecoratorTraits & get_default_decorator_traits ()
 
static const HierarchyTraits & get_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 Hierarchy setup_particle (kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (IMP::kernel::ParticleAdaptor d, 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())
 

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)
 

Detailed Description

As with the Atom, the names of residues may be expanded dynamically. This can be easily done in an analogous manner when we need it.

Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 133 of file Residue.h.

Member Function Documentation

static Residue IMP::atom::Residue::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 154 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
ResidueType  t,
int  index,
int  insertion_code 
)
static

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

Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 156 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
ResidueType  t,
int  index 
)
static

Setup the particle as a Residue with the passed type and index. Setup the particle so it can be used with this decorator.

Definition at line 158 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
ResidueType  t 
)
static

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

Definition at line 159 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
ResidueType  t 
)
static
See Also
setup_particle(m, pi, t )

Definition at line 159 of file Residue.h.

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

Definition at line 160 of file Residue.h.

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

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

Definition at line 160 of file Residue.h.

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