Detailed Description

A decorator for a residue.

As with the Atom, the names of residues may be expanded dynamically. This can be easily done in an analogous manner when we need it.

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 135 of file Residue.h.

Public Member Functions
	Residue (::IMP::Model *m,::IMP::ParticleIndex id)

	Residue (const IMP::ParticleAdaptor &d)

Int	get_index () const
	The residues index in the chain. More...

char	get_insertion_code () const

bool	get_is_dna () const

bool	get_is_protein () const

bool	get_is_rna () const

ResidueType	get_residue_type () const

void	set_index (Int t)

void	set_insertion_code (char insertion_code)

void	set_residue_type (ResidueType t)
	Update the stored ResidueType and the atom::Hierarchy::Name. 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 IntKey	get_index_key ()

static IntKey	get_insertion_code_key ()

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

static bool	get_is_setup (Model *m, ParticleIndex pi)

static IntKey	get_residue_type_key ()

static Residue	setup_particle (Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)

static Residue	setup_particle (IMP::ParticleAdaptor decorator, ResidueType t, int index, int insertion_code)

static Residue	setup_particle (Model *m, ParticleIndex pi, ResidueType t, int index)

static Residue	setup_particle (IMP::ParticleAdaptor decorator, ResidueType t, int index)

static Residue	setup_particle (IMP::ParticleAdaptor decorator, ResidueType t)

static Residue	setup_particle (Model *m, ParticleIndex pi, ResidueType t)

static Residue	setup_particle (IMP::ParticleAdaptor decorator, Residue other)

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

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 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

Int IMP::atom::Residue::get_index ( ) const

The residues index in the chain.

returns the value of the index attribute

Definition at line 194 of file Residue.h.

void IMP::atom::Residue::set_index ( Int t )

sets the value of the index attribute to t

Definition at line 194 of file Residue.h.

void IMP::atom::Residue::set_residue_type ( ResidueType t )

Update the stored ResidueType and the atom::Hierarchy::Name.

static Residue IMP::atom::Residue::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		ResidueType	t,
		int	index,
		int	insertion_code
	)

static

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

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 158 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		ResidueType	t,
		int	index
	)

static

Setup the particle as a Residue with the passed type and index. Setup the particle so it can be used with this decorator.

Definition at line 160 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	Model *	m,
		ParticleIndex	pi,
		ResidueType	t
	)

static

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

Definition at line 161 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	IMP::ParticleAdaptor	decorator,
		ResidueType	t
	)

static

See Also: setup_particle(m, pi, t )

Definition at line 161 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	IMP::ParticleAdaptor	decorator,
		Residue	other
	)

static

See Also: setup_particle(m, pi, other )

Definition at line 162 of file Residue.h.

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

static

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

Definition at line 162 of file Residue.h.

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

Residue.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation