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IMP
2.0.0
The Integrative Modeling Platform
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This is the complete list of members for IMP::atom::Atom, including all inherited members.
| add_child(Hierarchy o) | IMP::atom::Hierarchy | |
| add_child(Hierarchy h) const (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| add_child_at(Hierarchy h, unsigned int pos) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| Atom() (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| Atom(Model *m, ParticleIndex id) (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| Atom(::IMP::kernel::Particle *p) (defined in IMP::atom::Atom) | IMP::atom::Atom | explicit |
| clear_children() (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| create_clone(Hierarchy d) | IMP::atom::Hierarchy | related |
| create_clone_one(Hierarchy d) | IMP::atom::Hierarchy | related |
| create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1) | IMP::atom::Hierarchy | related |
| create_fragment(const Hierarchies &ps) | IMP::atom::Hierarchy | related |
| create_protein(Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1) | IMP::atom::Hierarchy | related |
| decorate_particle(::IMP::kernel::Particle *p) (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| IMP::atom::Hierarchy::decorate_particle(Particle *p) | IMP::atom::Hierarchy | static |
| decorate_particle(::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | static |
| Decorator(Model *m, ParticleIndex pi) (defined in IMP::kernel::Decorator) | IMP::kernel::Decorator | protected |
| Decorator(Particle *p) (defined in IMP::kernel::Decorator) | IMP::kernel::Decorator | protected |
| Decorator() (defined in IMP::kernel::Decorator) | IMP::kernel::Decorator | protected |
| Decorator(Particle *p) | IMP::kernel::Decorator | |
| Decorator() | IMP::kernel::Decorator | |
| DecoratorTraits typedef (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| DecoratorTraitsBase typedef (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| destroy(Hierarchy d) | IMP::atom::Hierarchy | related |
| find_breadth_first(HD h, F f) | IMP::core::Hierarchy | related |
| gather(H h, F f, Out out) | IMP::core::Hierarchy | related |
| gather_by_attribute(H h, K k, V v, Out out) | IMP::core::Hierarchy | related |
| gather_by_attributes(H h, K0 k0, V0 v0, K1 k1, V1 v1, Out out) | IMP::core::Hierarchy | related |
| gather_slice(H h, F f, Out out) | IMP::core::Hierarchy | related |
| get_all_descendants(Hierarchy mhd) | IMP::core::Hierarchy | related |
| get_as_atom() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_chain() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_domain() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_fragment() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_mass() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_molecule() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_residue() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_xyz() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_as_xyzr() const (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| get_atom(Residue rd, AtomType at) | IMP::atom::Hierarchy | related |
| get_atom_type() const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| get_atom_type_key() (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| get_bounding_sphere(const Hierarchy &h) | IMP::atom::Hierarchy | related |
| get_by_type(Hierarchy mhd, GetByType t) | IMP::atom::Hierarchy | related |
| get_child(unsigned int i) const | IMP::atom::Hierarchy | |
| get_child_index() const (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| get_children() const | IMP::atom::Hierarchy | |
| get_children() const | IMP::atom::Hierarchy | |
| get_decorator_traits() const (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| get_default_decorator_traits() (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | static |
| get_default_traits() | IMP::core::Hierarchy | static |
| get_element() const | IMP::atom::Atom | |
| get_element_key() (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| get_hierarchy_tree(Hierarchy h) | IMP::atom::Hierarchy | related |
| get_input_index() const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| get_input_index_key() (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| get_internal(Hierarchy mhd) | IMP::core::Hierarchy | related |
| get_is_valid(bool print_info) const | IMP::atom::Hierarchy | |
| get_leaves(Hierarchy h) | IMP::atom::Hierarchy | related |
| get_leaves(const Hierarchies &h) | IMP::atom::Hierarchy | related |
| get_leaves(const Selection &h) | IMP::atom::Hierarchy | related |
| IMP::core::Hierarchy::get_leaves(Hierarchy mhd) | IMP::core::Hierarchy | related |
| get_model() const | IMP::kernel::Decorator | |
| get_number_of_children() const (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| get_occupancy() const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| get_occupancy_key() (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| get_parent() const | IMP::atom::Hierarchy | |
| get_particle() const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| get_particle_index() const (defined in IMP::kernel::Decorator) | IMP::kernel::Decorator | |
| get_residue(Atom d, bool nothrow=false) | IMP::atom::Hierarchy | related |
| get_residue(Hierarchy mhd, unsigned int index) | IMP::atom::Hierarchy | related |
| get_root(Hierarchy h) | IMP::atom::Hierarchy | related |
| IMP::core::Hierarchy::get_root(Hierarchy h) | IMP::core::Hierarchy | related |
| get_temperature_factor() const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| get_temperature_factor_key() (defined in IMP::atom::Atom) | IMP::atom::Atom | static |
| get_traits() | IMP::atom::Hierarchy | static |
| get_traits() const (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| Hierarchy(Particle *p) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | explicit |
| Hierarchy(Model *m, ParticleIndex pi) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | |
| Hierarchy() | IMP::atom::Hierarchy | |
| Hierarchy(IMP::core::Hierarchy h) | IMP::atom::Hierarchy | explicit |
| Hierarchy(Model *m, ParticleIndex id, const HierarchyTraits &tr) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| Hierarchy(const HierarchyTraits &tr) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| Hierarchy(::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | explicit |
| particle_is_instance(Particle *p) | IMP::atom::Atom | static |
| particle_is_instance(Model *m, ParticleIndex p) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | static |
| IMP::core::Hierarchy::particle_is_instance(Particle *, HierarchyTraits=Hierarchy::get_default_traits()) | IMP::core::Hierarchy | static |
| read_pdb(base::TextInput input, Model *model, PDBSelector *selector, bool select_first_model=true) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | related |
| remove_child(unsigned int i) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| remove_child(Hierarchy h) (defined in IMP::core::Hierarchy) | IMP::core::Hierarchy | |
| set_atom_type(AtomType t) | IMP::atom::Atom | |
| set_input_index(Int t) (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| set_occupancy(double occupancy) (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| set_temperature_factor(double tempFactor) (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| setup_as_approximation(Hierarchy h) | IMP::atom::Hierarchy | related |
| setup_particle(Model *m, ParticleIndex pi, AtomType t) | IMP::atom::Atom | static |
| setup_particle(Particle *p, AtomType t) | IMP::atom::Atom | static |
| setup_particle(Particle *p, Atom o) | IMP::atom::Atom | static |
| setup_particle(Particle *p, const ParticlesTemp &children) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | static |
| IMP::atom::Hierarchy::setup_particle(Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp()) | IMP::atom::Hierarchy | static |
| setup_particle(Particle *p) (defined in IMP::atom::Hierarchy) | IMP::atom::Hierarchy | static |
| IMP::core::Hierarchy::setup_particle(Particle *p, HierarchyTraits traits=Hierarchy::get_default_traits()) | IMP::core::Hierarchy | static |
| IMP::core::Hierarchy::setup_particle(Particle *p, const Particles &children, HierarchyTraits traits=Hierarchy::get_default_traits()) | IMP::core::Hierarchy | static |
| show(std::ostream &out=std::cout) const (defined in IMP::atom::Atom) | IMP::atom::Atom | |
| IMP::atom::Hierarchy::show(Hierarchy h, std::ostream &out=std::cout) | IMP::atom::Hierarchy | related |
| IMP::core::Hierarchy::show(Hierarchy h, std::ostream &out=std::cout) | IMP::core::Hierarchy | related |
| Value() (defined in IMP::base::Value) | IMP::base::Value | protected |
| visit_breadth_first(HD d, F f) | IMP::core::Hierarchy | related |
| visit_breadth_first_with_data(HD d, F f, typename F::result_type i) | IMP::core::Hierarchy | related |
| visit_depth_first(HD d, F f) | IMP::core::Hierarchy | related |
| visit_depth_first_with_data(HD d, F f, typename F::result_type i) | IMP::core::Hierarchy | related |