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

#include <IMP/atom/Chain.h>

Inheritance diagram for IMP::atom::Chain:

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

	Chain (::IMP::kernel::Particle *p)

char	get_id () const
	Return the chain id.

void	set_id (char c)
	Set the chain id.

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::atom::Hierarchy
	Hierarchy (Particle *p)

	Hierarchy (Model *m, ParticleIndex 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 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 (Model *m, ParticleIndex id, const HierarchyTraits &tr)

	Hierarchy (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())

	Hierarchy (const HierarchyTraits &tr)

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

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

const HierarchyTraits &	get_traits () const

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

static IntKey	get_id_key ()
	The key used to store the chain.

static bool	particle_is_instance (Particle *p)

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

static Chain	setup_particle (Particle *p, char id)

static Chain	setup_particle (Particle *p, Chain o)

Static Public Member Functions inherited from IMP::atom::Hierarchy
static Hierarchy	decorate_particle (Particle *p)
	cast a particle which has the needed attributes

static const IMP::core::HierarchyTraits &	get_traits ()
	Get the molecular hierarchy HierararchyTraits.

static bool	particle_is_instance (Particle *p)

static bool	particle_is_instance (Model *m, ParticleIndex p)

static Hierarchy	setup_particle (Particle *p, const ParticlesTemp &children)

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp())

static Hierarchy	setup_particle (Particle *p)

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	particle_is_instance (Particle *, HierarchyTraits=Hierarchy::get_default_traits())

static Hierarchy	setup_particle (Particle *p, HierarchyTraits traits=Hierarchy::get_default_traits())
	Add the needed attributes to a particle.

static Hierarchy	setup_particle (Particle *p, const Particles &children, HierarchyTraits traits=Hierarchy::get_default_traits())
	Add the needed attributes to a particle and add the particles as children. More...

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	particle_is_instance (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

typedef Decorator	DecoratorTraitsBase

Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (Particle *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...

Restraint *	create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)

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

Hierarchy	create_protein (Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
	Create a coarse grained molecule. More...

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

Atom	get_atom (Residue rd, AtomType at)
	Return a particle atom from the residue. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)

HierarchyTree	get_hierarchy_tree (Hierarchy h)

Hierarchies	get_leaves (const Selection &h)

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

Residue	get_residue (Atom d, bool nothrow=false)
	Return the Residue containing this atom. More...

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	setup_as_approximation (Hierarchy h)

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

Hierarchy	read_pdb (base::TextInput input, Model model, PDBSelector selector, bool select_first_model=true)

Detailed Description

See Also: Hierarchy

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 21 of file Chain.h.

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

Chain.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description