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IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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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:A decorator to associate a particle with a part of a protein/DNA/RNA.
The decorator stores an optional list of residue indexes.
Definition at line 20 of file Fragment.h.
Public Member Functions | |
| Fragment (::IMP::Model *m,::IMP::ParticleIndex id) | |
| Fragment (const IMP::ParticleAdaptor &d) | |
| bool | get_contains_any_sorted_residue (const Ints &rinds) const |
| Return true if this fragment contains any of the sorted residues. More... | |
| bool | get_contains_residue (int rindex) const |
| Return true if this fragment contains a given residue. More... | |
| Ints | get_residue_indexes () const |
| void | set_residue_indexes (Ints o) |
| Add the residues whose indexes are listed in the passed vector. More... | |
| void | show (std::ostream &out=std::cout) const |
| Public Member Functions inherited from IMP::atom::Hierarchy | |
| Hierarchy (Model *m, ParticleIndex pi) | |
| Hierarchy (ParticleAdaptor pi) | |
| Hierarchy () | |
| Null constructor. More... | |
| Hierarchy (IMP::core::Hierarchy h) | |
| The traits must match. More... | |
| void | add_child (Hierarchy o) |
| Add a child and check that the types are appropriate. More... | |
| Hierarchy | get_child (unsigned int i) const |
| Get the ith child based on the order they were added. More... | |
| Hierarchies | get_children () const |
| Return the children in the order they were added. More... | |
| template<class C > | |
| C | get_children () const |
| Get the children in a container of your choosing, eg ParticlesTemp. More... | |
| bool | get_is_valid (bool print_info=false) const |
| Return true if the hierarchy is valid. More... | |
| Hierarchy | get_parent () const |
| Get the parent particle. More... | |
| void | show (std::ostream &out=std::cout) const |
| Public Member Functions inherited from IMP::core::Hierarchy | |
| Hierarchy (const IMP::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits()) | |
| Hierarchy (::IMP::Model *m,::IMP::ParticleIndex id, const HierarchyTraits &tr=get_default_traits()) | |
| 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 |
| ParticleIndex | get_child_index (unsigned int i) const |
| int | get_child_index () const |
Return i such that get_parent().get_child(i) == this More... | |
| GenericHierarchies | get_children () const |
| ParticleIndexes | get_children_indexes () const |
| const DecoratorTraits & | get_decorator_traits () const |
| unsigned int | get_number_of_children () const |
| Hierarchy | get_parent () const |
| HierarchyTraits | get_traits () |
| 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::Decorator | |
| bool | get_is_valid () const |
| Returns true if constructed with a non-default constructor. More... | |
| Model * | get_model () const |
| Returns the Model containing the particle. More... | |
| Particle * | get_particle () const |
| Returns the particle decorated by this decorator. More... | |
| ParticleIndex | get_particle_index () const |
| Returns the particle index decorated by this decorator. More... | |
| operator Particle * () const | |
| operator ParticleIndex () const | |
| Particle * | operator-> () const |
Static Public Member Functions | |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static Fragment | setup_particle (IMP::ParticleAdaptor pa) |
| static Fragment | setup_particle (Model *m, ParticleIndex pi) |
| static Fragment | setup_particle (Model *m, ParticleIndex pi, Fragment other) |
| static Fragment | setup_particle (IMP::ParticleAdaptor pa, Fragment other) |
| static Fragment | setup_particle (IMP::ParticleAdaptor pa, Ints residue_indexes) |
| static Fragment | setup_particle (Model *m, ParticleIndex pi, Ints residue_indexes) |
| Static Public Member Functions inherited from IMP::atom::Hierarchy | |
| static bool | get_is_setup (Model *m, ParticleIndex p) |
| Check if the particle has the needed attributes for a cast to succeed. More... | |
| static const IMP::core::HierarchyTraits & | get_traits () |
| Get the molecular hierarchy HierarchyTraits. More... | |
| static Hierarchy | setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor()) |
| Create a Hierarchy of level t by adding the needed attributes. More... | |
| Static Public Member Functions inherited from IMP::core::Hierarchy | |
| static TriggerKey | get_changed_key () |
| The key used to signal to the Model that the Hierarchy has changed. More... | |
| static const DecoratorTraits & | get_default_decorator_traits () |
| static const HierarchyTraits & | get_default_traits () |
| Get the default hierarchy traits. More... | |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits()) |
| static bool | get_is_setup (Model *, ParticleIndex, HierarchyTraits=Hierarchy::get_default_traits()) |
| static Hierarchy | setup_particle (IMP::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits()) |
| static Hierarchy | setup_particle (Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits()) |
| static Hierarchy | setup_particle (Model *m, ParticleIndex pi, ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits()) |
| static Hierarchy | setup_particle (IMP::ParticleAdaptor d, ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits()) |
| static Hierarchy | setup_particle (IMP::ParticleAdaptor d, ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits()) |
| static Hierarchy | setup_particle (Model *m, ParticleIndex pi, ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits()) |
Additional Inherited Members | |
| Public Types inherited from IMP::core::Hierarchy | |
| typedef HierarchyTraits | DecoratorTraits |
| Protected Member Functions inherited from IMP::Decorator | |
| Decorator (Model *m, ParticleIndex pi) | |
| Decorator (ParticleAdaptor 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... | |
| Hierarchy | create_fragment (const Hierarchies &ps) |
| Create a fragment containing the specified nodes. More... | |
| void | destroy (Hierarchy d) |
| Delete the Hierarchy. More... | |
| algebra::BoundingBoxD< 3 > | get_bounding_box (const Hierarchy &h) |
| Get a bounding box for the Hierarchy. More... | |
| algebra::Sphere3D | get_bounding_sphere (const Hierarchy &h) |
| Hierarchies | get_by_type (Hierarchy mhd, GetByType t) |
| Gather all the molecular particles of a certain level in the hierarchy. More... | |
| Bonds | get_internal_bonds (Hierarchy mhd) |
| Get the bonds internal to this tree. More... | |
| bool | get_is_heterogen (Hierarchy h) |
| Return true if the piece of hierarchy should be classified as a heterogen. More... | |
| Hierarchies | get_leaves (Hierarchy h) |
| Hierarchies | get_leaves (const Hierarchies &h) |
| 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 | show (Hierarchy h, std::ostream &out=std::cout) |
| Print out a molecular hierarchy. More... | |
| bool IMP::atom::Fragment::get_contains_any_sorted_residue | ( | const Ints & | rinds | ) | const |
Return true if this fragment contains any of the sorted residues.
The input list of residue indexes must be sorted.
| 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.
| void IMP::atom::Fragment::set_residue_indexes | ( | Ints | o | ) |
Add the residues whose indexes are listed in the passed vector.
Definition at line 52 of file Fragment.h.
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Definition at line 67 of file Fragment.h.
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Definition at line 67 of file Fragment.h.
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Definition at line 68 of file Fragment.h.
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Definition at line 68 of file Fragment.h.
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Setup a fragment with the passed residue indexes.
Definition at line 70 of file Fragment.h.
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Definition at line 70 of file Fragment.h.