IMP
2.2.0
The Integrative Modeling Platform
|
A decorator for an atom that has a defined CHARMM type. More...
#include <IMP/atom/CHARMMAtom.h>
Public Member Functions | |
CHARMMAtom (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id) | |
CHARMMAtom (const IMP::kernel::ParticleAdaptor &d) | |
String | get_charmm_type () const |
void | set_charmm_type (String t) |
void | show (std::ostream &out=std::cout) const |
Public Member Functions inherited from IMP::atom::Atom | |
Atom (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id) | |
Atom (const IMP::kernel::ParticleAdaptor &d) | |
AtomType | get_atom_type () const |
Element | get_element () const |
get element | |
double | get_occupancy () const |
double | get_temperature_factor () const |
void | set_atom_type (AtomType t) |
Set the name and corresponding element and mass. | |
void | set_occupancy (double occupancy) |
void | set_temperature_factor (double tempFactor) |
void | show (std::ostream &out=std::cout) const |
Int | get_input_index () const |
void | set_input_index (Int t) |
Public Member Functions inherited from IMP::atom::Hierarchy | |
Hierarchy (kernel::Model *m, kernel::ParticleIndex pi) | |
Hierarchy (kernel::ParticleAdaptor 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 kernel::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 (const IMP::kernel::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits()) | |
Hierarchy (::IMP::kernel::Model *m,::IMP::kernel::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 |
kernel::ParticleIndex | get_child_index (unsigned int i) const |
int | get_child_index () const |
GenericHierarchies | get_children () const |
kernel::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::kernel::Decorator | |
Model * | get_model () const |
Returns the Model containing the particle. | |
Particle * | get_particle () const |
ParticleIndex | get_particle_index () const |
operator Particle * () const | |
operator ParticleIndex () const | |
Particle * | operator-> () const |
Additional Inherited Members | |
Public Types inherited from IMP::core::Hierarchy | |
typedef HierarchyTraits | DecoratorTraits |
Protected Member Functions inherited from IMP::kernel::Decorator | |
Decorator (Model *m, ParticleIndex pi) | |
Decorator (ParticleAdaptor p) | |
Definition at line 24 of file CHARMMAtom.h.
|
static |
Definition at line 33 of file CHARMMAtom.h.
|
static |
Create a decorator with the passed CHARMM type. The particle is assumed to already have all atom attributes.Setup the particle so that it can be used with this decorator
Definition at line 37 of file CHARMMAtom.h.
|
static |
Definition at line 37 of file CHARMMAtom.h.