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 >
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 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
ParticleIndex	get_particle_index () const

Particle *	get_particle () const

Model *	get_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 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 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:

Fragment.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation