IMP  2.1.0
The Integrative Modeling Platform
IMP::atom::Bonded Class Reference

A decorator for a particle which has bonds. More...

#include <IMP/atom/bond_decorators.h>

+ Inheritance diagram for IMP::atom::Bonded:

Public Member Functions

 Bonded (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Bonded (const IMP::kernel::ParticleAdaptor &d)
 
Bond get_bond (unsigned int i) const
 Get a Bond of the ith bond. More...
 
kernel::ParticleIndexes get_bond_indexes () const
 
Bonded get_bonded (unsigned int i) const
 Get a Bonded of the ith bonded particle. More...
 
kernel::ParticleIndexes get_bonds () const
 
unsigned int get_number_of_bonds () const
 
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 Bonded decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static Bonded setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Bonded setup_particle (kernel::Model *m, ParticleIndex pi)
 
- Static Public Member Functions inherited from IMP::kernel::Decorator
static bool get_is_setup (Particle *p)
 Return true if the particle can be cast to the decorator. More...
 

Iterate through the bonds

BondIterator bonds_begin () const
 
BondIterator bonds_end () const
 

Iterate through the bondeds

BondedIterator bondeds_begin () const
 
BondedIterator bondeds_end () const
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (kernel::Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Detailed Description

See Also
Bond

Definition at line 89 of file bond_decorators.h.

Member Function Documentation

static Bonded IMP::atom::Bonded::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 112 of file bond_decorators.h.

Bond IMP::atom::Bonded::get_bond ( unsigned int  i) const
Returns
decorator of the ith child, or throw an exception if there is no such bond

Definition at line 140 of file bond_decorators.h.

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Bonded IMP::atom::Bonded::get_bonded ( unsigned int  i) const
Returns
decorator of the ith child, or throw an exception if there is no such bond
Note
I don't entirely like having this here as it duplicates functionality available otherwise, however it is such a fundamental operation and kind of a pain to write. It also means that we could later pull the edge endpoints into the vertex if desired.

Definition at line 156 of file bond_decorators.h.

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kernel::ParticleIndexes IMP::atom::Bonded::get_bonds ( ) const
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_bond_indexes() instead.

Definition at line 127 of file bond_decorators.h.

static bool IMP::atom::Bonded::particle_is_instance ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 112 of file bond_decorators.h.

static bool IMP::atom::Bonded::particle_is_instance ( IMP::kernel::Model m,
IMP::kernel::ParticleIndex  pi 
)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 112 of file bond_decorators.h.

static Bonded IMP::atom::Bonded::setup_particle ( kernel::Model m,
ParticleIndex  pi 
)
static

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

Definition at line 113 of file bond_decorators.h.


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