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IMP Reference Guide
2.5.0
The Integrative Modeling Platform
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A decorator for a molecule. More...
#include <IMP/atom/Molecule.h>
Inheritance diagram for IMP::atom::Molecule:A decorator for a molecule.
Definition at line 24 of file Molecule.h.
Public Member Functions | |
| 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) 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 |
| 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 |
| State | get_as_state () 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 |
| 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 (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) | |
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Mark the particle as denoting a molecule. Setup the particle so it can be used with this decorator.
Definition at line 37 of file Molecule.h.
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Definition at line 38 of file Molecule.h.
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Setup the particle so that it can be used with this decorator
Definition at line 38 of file Molecule.h.