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...

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 >
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

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
Model *	get_model () const
	Returns the Model containing the particle.

Particle *	get_particle () const

ParticleIndex	get_particle_index () const

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () const

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 Fragment	setup_particle (kernel::Model *m, ParticleIndex pi)

static Fragment	setup_particle (IMP::kernel::ParticleAdaptor decorator)

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 (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 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 DecoratorTraits &	get_default_decorator_traits ()

static const HierarchyTraits &	get_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 Hierarchy	setup_particle (kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (IMP::kernel::ParticleAdaptor d, 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())

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)

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 62 of file Fragment.h.

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

This could be made more efficient.

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.

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

Fragment.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation