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IMP Reference Guide  develop.716bca0a46,2020/04/04
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:

Detailed Description

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

The decorator stores an optional list of residue indexes.

Definition at line 20 of file Fragment.h.

Public Member Functions

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

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

Return true if this fragment contains a given residue.

This could be made more efficient.

void IMP::atom::Fragment::set_residue_indexes ( Ints  o)

Add the residues whose indexes are listed in the passed vector.

Definition at line 52 of file Fragment.h.

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

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

Definition at line 63 of file Fragment.h.

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

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

Definition at line 64 of file Fragment.h.

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

Definition at line 64 of file Fragment.h.

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

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

Definition at line 66 of file Fragment.h.

static Fragment IMP::atom::Fragment::setup_particle ( IMP::ParticleAdaptor  decorator,
Ints  residue_indexes 
)
static
See Also
setup_particle(m, pi, residue_indexes )

Definition at line 66 of file Fragment.h.


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