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_any_sorted_residue (const Ints &rinds) const
	Return true if this fragment contains any of the sorted residues. More...

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 >
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 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::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...

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 (Model *m, ParticleIndex pi)

static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static Fragment	setup_particle (IMP::ParticleAdaptor pa)

static Fragment	setup_particle (Model *m, ParticleIndex pi)

static Fragment	setup_particle (Model *m, ParticleIndex pi, Fragment other)

static Fragment	setup_particle (IMP::ParticleAdaptor pa, Fragment other)

static Fragment	setup_particle (IMP::ParticleAdaptor pa, 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 TriggerKey	get_changed_key ()
	The key used to signal to the Model that the Hierarchy has changed. More...

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::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)

Related Functions inherited from IMP::atom::Hierarchy
Hierarchy	create_clone (Hierarchy d)
	Clone the Hierarchy. More...

Hierarchy	create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy. More...

Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes. More...

void	destroy (Hierarchy d)
	Delete the Hierarchy. More...

algebra::BoundingBoxD< 3 >	get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)
	Gather all the molecular particles of a certain level in the hierarchy. More...

Bonds	get_internal_bonds (Hierarchy mhd)
	Get the bonds internal to this tree. More...

bool	get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen. More...

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index. More...

Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy. More...

void	show (Hierarchy h, std::ostream &out=std::cout)
	Print out a molecular hierarchy. More...

Member Function Documentation

bool IMP::atom::Fragment::get_contains_any_sorted_residue ( const Ints & rinds ) const

Return true if this fragment contains any of the sorted residues.

The input list of residue indexes must be sorted.

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 ( IMP::ParticleAdaptor pa )

static

Returns: a Fragment object that decorates the particle specified by pa

See Also: setup_particle(m, p)

Definition at line 67 of file Fragment.h.

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

static

Returns: a Fragment object that decorates particle pi

Definition at line 67 of file Fragment.h.

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

static

Returns: a Fragment object that decorates particle pi

Definition at line 68 of file Fragment.h.

static Fragment IMP::atom::Fragment::setup_particle	(	IMP::ParticleAdaptor	pa,
		Fragment	other
	)

static

Returns: a Fragment object that decorates the particle specified by pa

See Also: setup_particle(m, pi, other )

Definition at line 68 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.

Returns: a Fragment object that decorates particle pi

Definition at line 70 of file Fragment.h.

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

static

Returns: a Fragment object that decorates the particle specified by pa

See Also: setup_particle(m, pi, residue_indexes )

Definition at line 70 of file Fragment.h.

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

Fragment.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation