IMP Reference Guide
develop.4390929e3e,2024/11/12
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>
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.