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A decorator to associate a particle with a part of a protein/DNA/RNA.
The decorator stores an optional list of resdiue indexes.
Examples: rigid brownian dynamics, connectivity restraint
Inheritance diagram for IMP::atom::Fragment:Public Member Functions | |
| Fragment (::IMP::Particle *p) | |
| Fragment (Model *m, ParticleIndex id) | |
| bool | get_contains_residue (int rindex) const |
| Return true if this fragment contains a given residue. | |
| 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. | |
| 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. | |
| Hierarchy | get_parent () 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::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 () |
| int | get_child_index () const |
| const DecoratorTraits & | get_decorator_traits () const |
| unsigned int | get_number_of_children () const |
| const HierarchyTraits & | get_traits () const |
| void | remove_child (unsigned int i) |
| void | remove_child (Hierarchy h) |
| Public Member Functions inherited from IMP::Decorator | |
| std::size_t | __hash__ () const |
| 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::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 Hierarchy | setup_particle (Particle *p, const ParticlesTemp &children=ParticlesTemp()) |
| Static Public Member Functions inherited from IMP::core::Hierarchy | |
| static Hierarchy | decorate_particle (::IMP::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. | |
| static Decorator | setup_particle (Particle *p, extra_arguments) |
Additional Inherited Members | |
| Related Functions inherited from IMP::atom::Hierarchy | |
| Hierarchy | create_clone (Hierarchy d) |
| Clone the Hierarchy. | |
| Hierarchy | create_clone_one (Hierarchy d) |
| Clone the node in the Hierarchy. | |
| Restraint * | create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1) |
| Hierarchy | create_fragment (const Hierarchies &ps) |
| Create a fragment containing the specified nodes. | |
| 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. | |
| void | destroy (Hierarchy d) |
| Delete the Hierarchy. | |
| Atom | get_atom (Residue rd, AtomType at) |
| Return a particle atom from the residue. | |
| 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 (Hierarchy h) |
| Hierarchies | get_leaves (const Hierarchies &h) |
| Residue | get_residue (Atom d, bool nothrow=false) |
| Return the Residue containing this atom. | |
| Hierarchy | get_residue (Hierarchy mhd, unsigned int index) |
| Get the residue with the specified index. | |
| Hierarchy | get_root (Hierarchy h) |
| Return the root of the hierarchy. | |
| 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) |
| void | read_pdb (base::TextInput input, int model, Hierarchy h) |
| Hierarchy | read_pdb (base::TextInput input, Model *model, PDBSelector *selector, bool select_first_model=true) |
| Hierarchies | read_multimodel_pdb (base::TextInput input, Model *model, PDBSelector *selector) |
| Hierarchies | read_multimodel_pdb (base::TextInput input, Model *model) |
| void | write_pdb (Hierarchy mhd, base::TextOutput out, unsigned int model=0) |
| void | write_pdb (const Hierarchies &mhd, base::TextOutput out, unsigned int model=0) |
| void | write_multimodel_pdb (const Hierarchies &mhd, base::TextOutput out) |
| 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. | |
| 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. | |
| Hierarchy | get_root (Hierarchy h) |
| Return the root of the hierarchy. | |
| 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. | |
| template<class HD , class F > | |
| F | visit_breadth_first (HD d, F f) |
| Apply the visitor to each particle, breadth first. | |
| 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. | |
| template<class HD , class F > | |
| F | visit_depth_first (HD d, F f) |
| Apply functor F to each particle, traversing the hierarchy depth first. | |
| 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. | |
| bool IMP::atom::Fragment::get_contains_residue | ( | int | rindex | ) | const |
Return true if this fragment contains a given residue.
This could be made more efficient.
|
static |
Check if the particle has the needed attributes for a cast to succeed
Reimplemented from IMP::atom::Hierarchy.
| void IMP::atom::Fragment::set_residue_indexes | ( | Ints | o | ) |
Add the residues whose indexes are listed in the passed vector.
Create a domain by copying from o.
