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

A decorator to associate a particle with a part of a protein/DNA/RNA. More...

#include <IMP/atom/Fragment.h>

+ Inheritance diagram for IMP::atom::Fragment:

Public Member Functions

 Fragment (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Fragment (const IMP::kernel::ParticleAdaptor &d)
 
bool get_contains_residue (int rindex) const
 Return true if this fragment contains a given residue. More...
 
IntPairs get_residue_index_ranges () const
 
Ints get_residue_indexes () const
 
void set_residue_indexes (Ints o)
 Add the residues whose indexes are listed in the passed vector.
 
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 Fragment decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static Fragment setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Fragment setup_particle (kernel::Model *m, ParticleIndex pi)
 
static Fragment setup_particle (IMP::kernel::ParticleAdaptor decorator, Fragment other)
 
static Fragment setup_particle (kernel::Model *m, ParticleIndex pi, Fragment other)
 
static Fragment setup_particle (kernel::Model *m, ParticleIndex pi, Ints residue_indexes)
 
static Fragment setup_particle (IMP::kernel::ParticleAdaptor decorator, Ints residue_indexes)
 
- 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

The decorator stores an optional list of resdiue indexes.

Definition at line 20 of file Fragment.h.

Member Function Documentation

static Fragment IMP::atom::Fragment::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 65 of file Fragment.h.

bool IMP::atom::Fragment::get_contains_residue ( int  rindex) const

This could be made more efficient.

IntPairs IMP::atom::Fragment::get_residue_index_ranges ( ) const
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the get_residue_indexes() method instead.
static bool IMP::atom::Fragment::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 65 of file Fragment.h.

static bool IMP::atom::Fragment::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 65 of file Fragment.h.

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

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

Definition at line 66 of file Fragment.h.

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

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

Definition at line 67 of file Fragment.h.

static Fragment IMP::atom::Fragment::setup_particle ( kernel::Model m,
ParticleIndex  pi,
Ints  residue_indexes 
)
static

Setup a fragment with the passed residue indexes. Setup the particle so it can be used with this decorator.

Definition at line 69 of file Fragment.h.


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