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IMP Reference Guide  develop.4390929e3e,2024/11/11
The Integrative Modeling Platform
IMP::atom::TAMDCentroid Class Reference

#include <IMP/atom/TAMDCentroid.h>

+ Inheritance diagram for IMP::atom::TAMDCentroid:

Detailed Description

A decorator for a center of mass particle that is part of a TAMD simulation (so simulators can recognize it as such)

See Also
BrownianDynamicsBarak

TAMDCentroid is almost identical to IMP::core::Centroid, used to decorate particles that represent centers of mass of their children. It also contains some flags that are useful for TAMD simulations (Temperature-Accelerated MD).

See Also
IMP::core::Centroid

Definition at line 38 of file TAMDCentroid.h.

Public Member Functions

 TAMDCentroid (::IMP::Model *m,::IMP::ParticleIndex id)
 
 TAMDCentroid (const IMP::ParticleAdaptor &d)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::core::Centroid
 Centroid (const IMP::ParticleAdaptor &d)
 
 Centroid (::IMP::Model *m,::IMP::ParticleIndex id)
 
Constraintget_constraint () const
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::core::XYZ
 XYZ (::IMP::Model *m,::IMP::ParticleIndex id)
 
 XYZ (const IMP::ParticleAdaptor &d)
 
void add_to_derivative (int i, Float v, DerivativeAccumulator &d)
 
void add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
 Add the vector v to the derivative vector of the x,y,z coordinates. More...
 
Float get_coordinate (int i) const
 Get the ith coordinate. More...
 
const algebra::Vector3Dget_coordinates () const
 Convert it to a vector. More...
 
bool get_coordinates_are_optimized () const
 Get whether the coordinates are optimized. More...
 
Float get_derivative (int i) const
 
algebra::Vector3D get_derivatives () const
 Get the vector of derivatives accumulated by add_to_derivatives(). More...
 
algebra::Vector3D get_vector_to (const XYZ &b) const
 Get the vector from this particle to another. More...
 
Float get_x () const
 
Float get_y () const
 
Float get_z () const
 
void set_coordinate (unsigned int i, Float v)
 set the ith coordinate More...
 
void set_coordinates (const algebra::Vector3D &v)
 set all coordinates from a vector More...
 
void set_coordinates_are_optimized (bool tf) const
 Set whether the coordinates are optimized. More...
 
void set_x (Float t)
 
void set_y (Float t)
 
void set_z (Float t)
 
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 bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static TAMDCentroid setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
 
static TAMDCentroid setup_particle (IMP::ParticleAdaptor pa, ParticleIndexesAdaptor members)
 
static TAMDCentroid setup_particle (Model *m, ParticleIndex pi, Refiner *refiner)
 
static TAMDCentroid setup_particle (IMP::ParticleAdaptor pa, Refiner *refiner)
 
- Static Public Member Functions inherited from IMP::core::Centroid
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static Centroid setup_particle (IMP::ParticleAdaptor pa, Refiner *refiner)
 
static Centroid setup_particle (Model *m, ParticleIndex pi, Refiner *refiner)
 
static Centroid setup_particle (IMP::ParticleAdaptor pa, ParticleIndexesAdaptor members)
 
static Centroid setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
 
- Static Public Member Functions inherited from IMP::core::XYZ
static FloatKey get_coordinate_key (unsigned int i)
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 
static const FloatKeysget_xyz_keys ()
 Get a vector containing the keys for x,y,z. More...
 
static XYZ setup_particle (IMP::ParticleAdaptor pa)
 
static XYZ setup_particle (Model *m, ParticleIndex pi)
 
static XYZ setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v)
 
static XYZ setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Member Function Documentation

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle ( IMP::ParticleAdaptor  pa,
ParticleIndexesAdaptor  members 
)
static
Returns
a TAMDCentroid object that decorates the particle specified by pa
See Also
setup_particle(m, pi, members )

Definition at line 63 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle ( Model m,
ParticleIndex  pi,
ParticleIndexesAdaptor  members 
)
static

Sets up TAMDCentroid over members, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDoc

Returns
a TAMDCentroid object that decorates particle pi

Definition at line 63 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle ( IMP::ParticleAdaptor  pa,
Refiner refiner 
)
static
Returns
a TAMDCentroid object that decorates the particle specified by pa
See Also
setup_particle(m, pi, refiner )

Definition at line 71 of file TAMDCentroid.h.

static TAMDCentroid IMP::atom::TAMDCentroid::setup_particle ( Model m,
ParticleIndex  pi,
Refiner refiner 
)
static

Sets up TAMDCentroid over particles passed by applying the refiner over the particle pi, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDoc

Returns
a TAMDCentroid object that decorates particle pi

Definition at line 71 of file TAMDCentroid.h.


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