Store info for a chain of a protein. More...

#include <IMP/atom/Chain.h>

Inheritance diagram for IMP::atom::Chain:

Detailed Description

Store info for a chain of a protein.

See Also: Hierarchy

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 21 of file Chain.h.

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

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

std::string	get_id () const
	Return the chain id. More...

char	get_id_char () const
	Return the chain id. More...

void	set_id (std::string c)
	Set the chain id. More...

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 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

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 kernel::ParticlesTemp. More...

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

State	get_as_state () 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
	Return i such that `get_parent().get_child(i) == this` More...

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
bool	get_is_valid () const

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 StringKey	get_id_key ()
	The key used to store the chain. More...

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

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

static Chain	setup_particle (kernel::Model *m, ParticleIndex pi, std::string id)

static Chain	setup_particle (IMP::kernel::ParticleAdaptor decorator, std::string id)

static Chain	setup_particle (IMP::kernel::ParticleAdaptor decorator, char id)

static Chain	setup_particle (kernel::Model *m, ParticleIndex pi, char id)

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

static Chain	setup_particle (IMP::kernel::ParticleAdaptor decorator, Chain 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 HierarchyTraits. More...

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 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::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 (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 (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexes children, 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 (IMP::kernel::ParticleAdaptor d, kernel::ParticlesTemp 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())

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)

Member Function Documentation

std::string IMP::atom::Chain::get_id ( ) const

Return the chain id.

Definition at line 51 of file Chain.h.

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char IMP::atom::Chain::get_id_char ( ) const

Return the chain id.

Deprecated:: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the string version.

Definition at line 58 of file Chain.h.

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static StringKey IMP::atom::Chain::get_id_key ( )

static

The key used to store the chain.

void IMP::atom::Chain::set_id ( std::string c )

Set the chain id.

Definition at line 63 of file Chain.h.

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static Chain IMP::atom::Chain::setup_particle	(	IMP::kernel::ParticleAdaptor	decorator,
		std::string	id
	)

static

See Also: setup_particle(m, pi, id )

Definition at line 41 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		std::string	id
	)

static

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

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 41 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		char	id
	)

static

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

Definition at line 42 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle	(	IMP::kernel::ParticleAdaptor	decorator,
		char	id
	)

static

See Also: setup_particle(m, pi, id )

Definition at line 42 of file Chain.h.

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

static

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

Definition at line 43 of file Chain.h.

static Chain IMP::atom::Chain::setup_particle	(	IMP::kernel::ParticleAdaptor	decorator,
		Chain	other
	)

static

See Also: setup_particle(m, pi, other )

Definition at line 43 of file Chain.h.

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

Chain.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation