IMP
2.0.0
The Integrative Modeling Platform
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A decorator for a residue. More...
#include <IMP/atom/Residue.h>
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) | |
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.
Return the residue from the same chain with one higher index, or Hierarchy().
The return type is Hierarchy since the particle representing the next residue might not be a Residue particle.
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Return the atoms comprising the phi dihedral. If all atoms cannot be found, an empty list is returned.
Return the residue from the same chain with one lower index, or Hierarchy().
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Return the atoms comprising the psi dihedral. If all atoms cannot be found, an empty list is returned.