IMP
2.0.1
The Integrative Modeling Platform
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A decorator for a molecule.
#include <IMP/atom/Molecule.h>
Public Member Functions | |
Molecule (Model *m, ParticleIndex id) | |
Molecule (::IMP::kernel::Particle *p) | |
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. More... | |
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. More... | |
Hierarchy | get_parent () const |
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 |
Public Member Functions inherited from IMP::core::Hierarchy | |
Hierarchy (Model *m, ParticleIndex id, const HierarchyTraits &tr) | |
Hierarchy (::IMP::kernel::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 () |
Hierarchy | get_child (unsigned int i) const |
int | get_child_index () const |
GenericHierarchies | get_children () const |
const DecoratorTraits & | get_decorator_traits () const |
unsigned int | get_number_of_children () const |
Hierarchy | get_parent () const |
const HierarchyTraits & | get_traits () const |
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::kernel::Decorator | |
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 Molecule | decorate_particle (::IMP::kernel::Particle *p) |
static bool | particle_is_instance (Particle *p) |
static Molecule | setup_particle (Particle *p) |
Add the required attributes to the particle and create a Molecule. | |
static Molecule | setup_particle (Particle *p, Molecule) |
Copy data from the other Molecule to the particle p. | |
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 bool | particle_is_instance (Particle *p) |
static bool | particle_is_instance (Model *m, ParticleIndex p) |
static Hierarchy | setup_particle (Particle *p, const ParticlesTemp &children) |
static Hierarchy | setup_particle (Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp()) |
static Hierarchy | setup_particle (Particle *p) |
Static Public Member Functions inherited from IMP::core::Hierarchy | |
static Hierarchy | decorate_particle (::IMP::kernel::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. More... | |
Static Public Member Functions inherited from IMP::kernel::Decorator | |
static bool | particle_is_instance (Particle *p) |
Return true if the particle can be cast to the decorator. More... | |
Additional Inherited Members | |
Public Types inherited from IMP::core::Hierarchy | |
typedef HierarchyTraits | DecoratorTraits |
typedef Decorator | DecoratorTraitsBase |
Protected Member Functions inherited from IMP::kernel::Decorator | |
Decorator (Model *m, ParticleIndex pi) | |
Decorator (Particle *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... | |
Restraint * | create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1) |
Hierarchy | create_fragment (const Hierarchies &ps) |
Create a fragment containing the specified nodes. More... | |
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. More... | |
void | destroy (Hierarchy d) |
Delete the Hierarchy. More... | |
Atom | get_atom (Residue rd, AtomType at) |
Return a particle atom from the residue. More... | |
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 (const Selection &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. More... | |
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 | 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, PDBSelector *selector, bool select_first_model=true) |
Definition at line 25 of file Molecule.h.