IMP  2.0.0
The Integrative Modeling Platform
IMP::atom::Residue Class Reference

A decorator for a residue. More...

#include <IMP/atom/Residue.h>

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

Public Member Functions

 Residue (Model *m, ParticleIndex id)
 
 Residue (::IMP::kernel::Particle *p)
 
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 (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 Residue decorate_particle (::IMP::kernel::Particle *p)
 
static IntKey get_index_key ()
 
static IntKey get_insertion_code_key ()
 
static IntKey get_residue_type_key ()
 
static bool particle_is_instance (Particle *p)
 
static Residue setup_particle (Model *m, ParticleIndex pi, ResidueType t=UNK, int index=-1, int insertion_code=32)
 Add the required attributes to the particle and create a Residue.
 
static Residue setup_particle (Particle *p, ResidueType t=UNK, int index=-1, int insertion_code=32)
 
static Residue setup_particle (Particle *p, Residue o)
 Copy data from the other Residue to the particle p.
 
- 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...
 

Related Functions

(Note that these are not member functions.)

Hierarchy get_next_residue (Residue rd)
 
Atoms get_phi_dihedral_atoms (Residue rd)
 
Hierarchy get_previous_residue (Residue rd)
 
Atoms get_psi_dihedral_atoms (Residue rd)
 

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

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.

Friends And Related Function Documentation

Hierarchy get_next_residue ( Residue  rd)
related

Return the residue from the same chain with one higher index, or Hierarchy().

Note
Currently, this function only works if the parent of rd is the chain. This should be fixed later. Ask if you need it.

The return type is Hierarchy since the particle representing the next residue might not be a Residue particle.

Atoms get_phi_dihedral_atoms ( Residue  rd)
related

Return the atoms comprising the phi dihedral. If all atoms cannot be found, an empty list is returned.

Hierarchy get_previous_residue ( Residue  rd)
related

Return the residue from the same chain with one lower index, or Hierarchy().

See Also
get_next_residue
Atoms get_psi_dihedral_atoms ( Residue  rd)
related

Return the atoms comprising the psi dihedral. If all atoms cannot be found, an empty list is returned.


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