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IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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A decorator for keeping track of copies of a molecule. More...
#include <IMP/atom/Copy.h>
Inheritance diagram for IMP::atom::Copy:A decorator for keeping track of copies of a molecule.
This decorator is for differentiating and keeping track of identity when there are multiple copies of molecule in the system. It should only be applied to Molecule particles.
Public Member Functions | |
| Copy (::IMP::Model *m,::IMP::ParticleIndex id) | |
| Copy (const IMP::ParticleAdaptor &d) | |
| int | get_copy_index () const |
| void | show (std::ostream &out=std::cout) const |
| Public Member Functions inherited from IMP::atom::Molecule | |
| Molecule (::IMP::Model *m,::IMP::ParticleIndex id) | |
| Molecule (const IMP::ParticleAdaptor &d) | |
| 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 IntKey | get_copy_index_key () |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static Copy | setup_particle (Model *m, ParticleIndex pi, Int number) |
| static Copy | setup_particle (IMP::ParticleAdaptor decorator, Int number) |
| Static Public Member Functions inherited from IMP::atom::Molecule | |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static Molecule | setup_particle (Model *m, ParticleIndex pi) |
| static Molecule | setup_particle (IMP::ParticleAdaptor decorator) |
| static Molecule | setup_particle (Model *m, ParticleIndex pi, Molecule other) |
| static Molecule | setup_particle (IMP::ParticleAdaptor decorator, Molecule other) |
| 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 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... | |
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