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IMP Reference Guide  develop.f6c15b4169,2024/11/06
The Integrative Modeling Platform
IMP::atom::CHARMMAtom Class Reference

A decorator for an atom that has a defined CHARMM type. More...

#include <IMP/atom/CHARMMAtom.h>

+ Inheritance diagram for IMP::atom::CHARMMAtom:

Detailed Description

A decorator for an atom that has a defined CHARMM type.

Definition at line 24 of file CHARMMAtom.h.

Public Member Functions

 CHARMMAtom (::IMP::Model *m,::IMP::ParticleIndex id)
 
 CHARMMAtom (const IMP::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::Model *m,::IMP::ParticleIndex id)
 
 Atom (const IMP::ParticleAdaptor &d)
 
AtomType get_atom_type () const
 
Element get_element () const
 get element More...
 
double get_occupancy () const
 
double get_temperature_factor () const
 
void set_atom_type (AtomType t)
 Set the name and corresponding element and mass. More...
 
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 (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 >
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 DecoratorTraitsget_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...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_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
 
Particleoperator-> () const
 

Static Public Member Functions

static StringKey get_charmm_type_key ()
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 Return true if the particle is an instance of a CHARMMAtom. More...
 
static CHARMMAtom setup_particle (IMP::ParticleAdaptor pa, String charmm_type)
 
static CHARMMAtom setup_particle (Model *m, ParticleIndex pi, String charmm_type)
 Create a decorator with the passed CHARMM type. More...
 
- Static Public Member Functions inherited from IMP::atom::Atom
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 return true if the particle has the needed attributes More...
 
static Atom setup_particle (Model *m, ParticleIndex pi, Atom other)
 
static Atom setup_particle (IMP::ParticleAdaptor pa, Atom other)
 
static Atom setup_particle (Model *m, ParticleIndex pi, AtomType atom_type)
 Add the required attributes using the passed AtomType. More...
 
static Atom setup_particle (IMP::ParticleAdaptor pa, AtomType atom_type)
 
static IntKey get_atom_type_key ()
 
static IntKey get_element_key ()
 
static IntKey get_input_index_key ()
 
static FloatKey get_occupancy_key ()
 
static FloatKey get_temperature_factor_key ()
 
- 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 DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_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)
 

Member Function Documentation

String IMP::atom::CHARMMAtom::get_charmm_type ( ) const

returns the value of the charmm_type attribute

Definition at line 39 of file CHARMMAtom.h.

static bool IMP::atom::CHARMMAtom::get_is_setup ( Model m,
ParticleIndex  pi 
)
static

Return true if the particle is an instance of a CHARMMAtom.

Definition at line 42 of file CHARMMAtom.h.

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void IMP::atom::CHARMMAtom::set_charmm_type ( String  t)

sets the value of the charmm_type attribute to t

Definition at line 39 of file CHARMMAtom.h.

static CHARMMAtom IMP::atom::CHARMMAtom::setup_particle ( IMP::ParticleAdaptor  pa,
String  charmm_type 
)
static
Returns
a CHARMMAtom object that decorates the particle specified by pa
See Also
setup_particle(m, pi, charmm_type )

Definition at line 37 of file CHARMMAtom.h.

static CHARMMAtom IMP::atom::CHARMMAtom::setup_particle ( Model m,
ParticleIndex  pi,
String  charmm_type 
)
static

Create a decorator with the passed CHARMM type.

The particle is assumed to already have all atom attributes.

Returns
a CHARMMAtom object that decorates particle pi

Definition at line 37 of file CHARMMAtom.h.


The documentation for this class was generated from the following file: