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IMP Reference Guide  develop.29b24c6ad6,2021/05/15
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:

Detailed Description

A decorator for a residue.

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 135 of file Residue.h.

Public Member Functions

 Residue (::IMP::Model *m,::IMP::ParticleIndex id)
 
 Residue (const IMP::ParticleAdaptor &d)
 
Int get_index () const
 The residues index in the chain. More...
 
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. More...
 
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 IntKey get_index_key ()
 
static IntKey get_insertion_code_key ()
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static IntKey get_residue_type_key ()
 
static Residue setup_particle (Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
 
static Residue setup_particle (IMP::ParticleAdaptor decorator, ResidueType t, int index, int insertion_code)
 
static Residue setup_particle (Model *m, ParticleIndex pi, ResidueType t, int index)
 
static Residue setup_particle (IMP::ParticleAdaptor decorator, ResidueType t, int index)
 
static Residue setup_particle (IMP::ParticleAdaptor decorator, ResidueType t)
 
static Residue setup_particle (Model *m, ParticleIndex pi, ResidueType t)
 
static Residue setup_particle (IMP::ParticleAdaptor decorator, Residue other)
 
static Residue setup_particle (Model *m, ParticleIndex pi, Residue other)
 
- 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())
 

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

Int IMP::atom::Residue::get_index ( ) const

The residues index in the chain.

returns the value of the index attribute

Definition at line 194 of file Residue.h.

void IMP::atom::Residue::set_index ( Int  t)

sets the value of the index attribute to t

Definition at line 194 of file Residue.h.

void IMP::atom::Residue::set_residue_type ( ResidueType  t)

Update the stored ResidueType and the atom::Hierarchy::Name.

static Residue IMP::atom::Residue::setup_particle ( 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 158 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle ( 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 160 of file Residue.h.

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

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

Definition at line 161 of file Residue.h.

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

Definition at line 161 of file Residue.h.

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

Definition at line 162 of file Residue.h.

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

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

Definition at line 162 of file Residue.h.


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