A decorator for a residue. More...

#include <IMP/atom/Residue.h>

Inheritance diagram for IMP::atom::Residue:

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

	Residue (const IMP::kernel::ParticleAdaptor &d)

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

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.

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 Residue	decorate_particle (::IMP::kernel::Particle *p)

static IntKey	get_index_key ()

static IntKey	get_insertion_code_key ()

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

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)

static IntKey	get_residue_type_key ()

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

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

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

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

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

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

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

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

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

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

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 133 of file Residue.h.

Member Function Documentation

static Residue IMP::atom::Residue::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 154 of file Residue.h.

static bool IMP::atom::Residue::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 154 of file Residue.h.

static bool IMP::atom::Residue::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 154 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	kernel::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 156 of file Residue.h.

static Residue IMP::atom::Residue::setup_particle	(	kernel::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 158 of file Residue.h.

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

static

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

Definition at line 159 of file Residue.h.

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

static

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

Definition at line 160 of file Residue.h.

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

Residue.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation