IMP::atom::Fragment Class Reference
A decorator to associate a particle with a part of a protein/DNA/RNA. More...
#include <IMP/atom/Fragment.h>
Inheritance diagram for IMP::atom::Fragment:Public Member Functions | |
| Fragment (::IMP::kernel::Particle *p) | |
| Fragment (Model *m, ParticleIndex id) | |
| bool | get_contains_residue (int rindex) const |
| Return true if this fragment contains a given residue. More... | |
| IntPairs | get_residue_index_ranges () const |
| Ints | get_residue_indexes () const |
| void | set_residue_indexes (Ints o) |
| Add the residues whose indexes are listed in the passed vector. | |
| 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 Fragment | decorate_particle (::IMP::kernel::Particle *p) |
| static bool | particle_is_instance (Particle *p) |
| static Fragment | setup_particle (Particle *p, const Ints &ris=Ints()) |
| static Fragment | setup_particle (Particle *p, Fragment o) |
| Create a domain by copying from 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
The decorator stores an optional list of resdiue indexes.
Definition at line 20 of file Fragment.h.
Member Function Documentation
| bool IMP::atom::Fragment::get_contains_residue | ( | int | rindex | ) | const |
This could be made more efficient.
The documentation for this class was generated from the following file: