IMP  2.2.0
The Integrative Modeling Platform
Public Member Functions | Static Public Member Functions | List of all members
IMP::atom::Chain Class Reference

Store info for a chain of a protein. More...

#include <IMP/atom/Chain.h>

+ Inheritance diagram for IMP::atom::Chain:

Public Member Functions

 Chain (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Chain (const IMP::kernel::ParticleAdaptor &d)
 
std::string get_id () const
 Return the chain id.
 
char get_id_char () const
 Return the chain id. More...
 
void set_id (std::string c)
 Set the chain id.
 
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 Chain decorate_particle (::IMP::kernel::Particle *p)
 
static StringKey get_id_key ()
 The key used to store the chain.
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static Chain setup_particle (IMP::kernel::ParticleAdaptor decorator, std::string id)
 
static Chain setup_particle (kernel::Model *m, ParticleIndex pi, std::string id)
 
static Chain setup_particle (kernel::Model *m, ParticleIndex pi, char id)
 
static Chain setup_particle (IMP::kernel::ParticleAdaptor decorator, char id)
 
static Chain setup_particle (IMP::kernel::ParticleAdaptor decorator, Chain other)
 
static Chain setup_particle (kernel::Model *m, ParticleIndex pi, Chain 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

See Also
Hierarchy
Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 21 of file Chain.h.

Member Function Documentation

static Chain IMP::atom::Chain::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 40 of file Chain.h.

char IMP::atom::Chain::get_id_char ( ) const
Deprecated:
As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the string version.

Definition at line 58 of file Chain.h.

+ Here is the call graph for this function:

static Chain IMP::atom::Chain::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
std::string  id 
)
static

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

Examples:
atom/dope_and_excluded_volume.cpp.

Definition at line 41 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
std::string  id 
)
static
See Also
setup_particle(m, pi, id )

Definition at line 41 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
char  id 
)
static
See Also
setup_particle(m, pi, id )

Definition at line 42 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle ( kernel::Model *  m,
ParticleIndex  pi,
char  id 
)
static

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

Definition at line 42 of file Chain.h.

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

Definition at line 43 of file Chain.h.

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

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

Definition at line 43 of file Chain.h.

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