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

A decorator for a molecule.

#include <IMP/atom/Molecule.h>

+ Inheritance diagram for IMP::atom::Molecule:

Public Member Functions

 Molecule (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Molecule (const IMP::kernel::ParticleAdaptor &d)
 
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 >
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
 
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::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 Molecule 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::Particle *p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static Molecule setup_particle (kernel::Model *m, ParticleIndex pi)
 
static Molecule setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Molecule setup_particle (IMP::kernel::ParticleAdaptor decorator, Molecule other)
 
static Molecule setup_particle (kernel::Model *m, ParticleIndex pi, Molecule 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 DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_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 bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi, const HierarchyTraits &tr=get_default_traits())
 
static bool particle_is_instance (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())
 
static Hierarchy setup_particle (IMP::kernel::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())
 
static Hierarchy setup_particle (kernel::Model *m, ParticleIndex pi, 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())
 
- 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...
 

Additional Inherited Members

- Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits DecoratorTraits
 
- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (kernel::Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Detailed Description

Definition at line 24 of file Molecule.h.

Member Function Documentation

static Molecule IMP::atom::Molecule::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 35 of file Molecule.h.

static bool IMP::atom::Molecule::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 35 of file Molecule.h.

static bool IMP::atom::Molecule::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 35 of file Molecule.h.

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

Mark the particle as denoting a molecule. Setup the particle so it can be used with this decorator.

Definition at line 37 of file Molecule.h.

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

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

Definition at line 38 of file Molecule.h.


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