A decorator for a residue. More...

#include <IMP/atom/Residue.h>

Inheritance diagram for IMP::atom::Residue:

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

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

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

static IntKey	get_index_key ()

static IntKey	get_insertion_code_key ()

static IntKey	get_residue_type_key ()

static bool	particle_is_instance (Particle *p)

static Residue	setup_particle (Model *m, ParticleIndex pi, ResidueType t=UNK, int index=-1, int insertion_code=32)
	Add the required attributes to the particle and create a Residue.

static Residue	setup_particle (Particle *p, ResidueType t=UNK, int index=-1, int insertion_code=32)

static Residue	setup_particle (Particle *p, Residue o)
	Copy data from the other Residue to the particle p.

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...

Related Functions
(Note that these are not member functions.)
Hierarchy	get_next_residue (Residue rd)

Atoms	get_phi_dihedral_atoms (Residue rd)

Hierarchy	get_previous_residue (Residue rd)

Atoms	get_psi_dihedral_atoms (Residue rd)

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)

Related Functions inherited from IMP::core::Hierarchy
template<class HD , class F >
HD	find_breadth_first (HD h, F f)
	Find the first node which matches some criteria.

template<class H , class Out , class F >
Out	gather (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria.

template<class H , class Out , class K , class V >
Out	gather_by_attribute (H h, K k, V v, Out out)
	Gather all the particles in the hierarchy which match on an attribute.

template<class H , class Out , class K0 , class V0 , class K1 , class V1 >
Out	gather_by_attributes (H h, K0 k0, V0 v0, K1 k1, V1 v1, Out out)
	Gather all the particles in the hierarchy which match on two attributes.

template<class H , class Out , class F >
Out	gather_slice (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria. More...

GenericHierarchies	get_all_descendants (Hierarchy mhd)
	Get all the particles in the subtree.

GenericHierarchies	get_internal (Hierarchy mhd)
	Get all the non-leaves of the bit of hierarchy.

GenericHierarchies	get_leaves (Hierarchy mhd)
	Get all the leaves of the bit of hierarchy. More...

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

template<class ND >
std::ostream &	show (Hierarchy h, std::ostream &out=std::cout)
	Print the hierarchy using a given decorator as to display each node. More...

template<class HD , class F >
F	visit_breadth_first (HD d, F f)
	Apply the visitor to each particle, breadth first. More...

template<class HD , class F >
F	visit_breadth_first_with_data (HD d, F f, typename F::result_type i)
	Apply functor F to each particle, traversing the hierarchy breadth first. More...

template<class HD , class F >
F	visit_depth_first (HD d, F f)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

template<class HD , class F >
F	visit_depth_first_with_data (HD d, F f, typename F::result_type i)
	Apply functor F to each particle, traversing the hierarchy depth first. 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)

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.

Friends And Related Function Documentation

Hierarchy get_next_residue ( Residue rd )

Note: Currently, this function only works if the parent of rd is the chain. This should be fixed later. Ask if you need it.

The return type is Hierarchy since the particle representing the next residue might not be a Residue particle.

Atoms get_phi_dihedral_atoms ( Residue rd )

Hierarchy get_previous_residue ( Residue rd )

See Also: get_next_residue

Atoms get_psi_dihedral_atoms ( Residue rd )

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

Public Member Functions

Static Public Member Functions

Related Functions

Additional Inherited Members

Detailed Description

Friends And Related Function Documentation