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::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...
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 (kernel::Model *m, kernel::ParticleIndex pi)
	Hierarchy (kernel::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
Hierarchies	get_children () const
	Return the children in the order they were added. More...
template<class C >
C	get_children () const
	Get the children in a container of your choosing, eg kernel::ParticlesTemp. More...
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
State	get_as_state () 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
	Return i such that get_parent().get_child(i) == this More...
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
bool	get_is_valid () const
Model *	get_model () const
	Returns the Model containing the particle. More...
Particle *	get_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
Particle *	operator-> () const

Static Public Member Functions
static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)
static Fragment	setup_particle (IMP::kernel::ParticleAdaptor decorator)
static Fragment	setup_particle (kernel::Model *m, ParticleIndex pi)
static Fragment	setup_particle (kernel::Model *m, ParticleIndex pi, Fragment other)
static Fragment	setup_particle (IMP::kernel::ParticleAdaptor decorator, Fragment other)
static Fragment	setup_particle (IMP::kernel::ParticleAdaptor decorator, Ints residue_indexes)
static Fragment	setup_particle (kernel::Model *m, ParticleIndex pi, 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 HierarchyTraits. More...
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 const DecoratorTraits &	get_default_decorator_traits ()
static const HierarchyTraits &	get_default_traits ()
	Get the default hierarchy traits. More...
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 (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 (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexes children, 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 (IMP::kernel::ParticleAdaptor d, kernel::ParticlesTemp 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())

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)

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.

Here is the call graph for this function:

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 63 of file Fragment.h.

static Fragment IMP::atom::Fragment::setup_particle ( kernel::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::kernel::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 ( kernel::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::kernel::ParticleAdaptor  decorator, Ints  residue_indexes  )

static

See Also

setup_particle(m, pi, residue_indexes )

Definition at line 66 of file Fragment.h.

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

• Fragment.h