IMP  2.1.1
The Integrative Modeling Platform
IMP::atom::RigidBodyDiffusion Class Reference

#include <IMP/atom/Diffusion.h>

+ Inheritance diagram for IMP::atom::RigidBodyDiffusion:

Public Member Functions

 RigidBodyDiffusion (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 RigidBodyDiffusion (const IMP::kernel::ParticleAdaptor &d)
 
double get_rotational_diffusion_coefficient () const
 
void set_rotational_diffusion_coefficient (double d) const
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::atom::Diffusion
 Diffusion (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Diffusion (const IMP::kernel::ParticleAdaptor &d)
 
double get_d () const
 
double get_diffusion_coefficient () const
 
void set_d (double d)
 
void set_diffusion_coefficient (double d)
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::core::XYZ
 XYZ (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 XYZ (const IMP::kernel::ParticleAdaptor &d)
 
void add_to_derivative (int i, Float v, DerivativeAccumulator &d)
 Add something to the derivative of the ith coordinate.
 
void add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
 Add something to the derivative of the coordinates.
 
Float get_coordinate (int i) const
 Get the ith coordinate.
 
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
 Get the ith coordinate derivative.
 
algebra::Vector3D get_derivatives () const
 Get the vector of derivatives. More...
 
algebra::Vector3D get_vector_to (const XYZ &b) const
 Get the vector from this particle to another.
 
Float get_x () const
 
Float get_y () const
 
Float get_z () const
 
void set_coordinate (unsigned int i, Float v)
 set the ith coordinate
 
void set_coordinates (const algebra::Vector3D &v)
 set all coordinates from a vector
 
void set_coordinates_are_optimized (bool tf) const
 Set whether the coordinates are optimized.
 
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::kernel::Decorator
ParticleIndex get_particle_index () const
 
Particleget_particle () const
 
Modelget_model () const
 Returns the Model containing the particle.
 
 Decorator (Particle *p)
 
 Decorator ()
 

Static Public Member Functions

static RigidBodyDiffusion decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex p)
 Return true if the particle is an instance of an Diffusion.
 
static FloatKey get_rotational_diffusion_coefficient_key ()
 Get the D key.
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static RigidBodyDiffusion setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static RigidBodyDiffusion setup_particle (kernel::Model *m, ParticleIndex pi)
 
- Static Public Member Functions inherited from IMP::atom::Diffusion
static Diffusion decorate_particle (::IMP::kernel::Particle *p)
 
static FloatKey get_diffusion_coefficient_key ()
 Get the D key.
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex p)
 Return true if the particle is an instance of an Diffusion.
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static Diffusion setup_particle (kernel::Model *m, ParticleIndex pi, Float D)
 
static Diffusion setup_particle (IMP::kernel::ParticleAdaptor decorator, Float D)
 
static Diffusion setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v, Float D)
 
static Diffusion setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v, Float D)
 
static Diffusion setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Diffusion setup_particle (kernel::Model *m, ParticleIndex pi)
 
- Static Public Member Functions inherited from IMP::core::XYZ
static XYZ decorate_particle (::IMP::kernel::Particle *p)
 
static FloatKey get_coordinate_key (unsigned int i)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static const FloatKeysget_xyz_keys ()
 Get a vector containing the keys for x,y,z. More...
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)
 
- Static Public Member Functions inherited from IMP::kernel::Decorator
static bool get_is_setup (Particle *p)
 Return true if the particle can be cast to the decorator. More...
 

Additional Inherited Members

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

Detailed Description

A rigid body that is diffusing, so it also has a rotation diffusion coefficient. The units on the rotational coefficient are \(radians^2/fs\).

Definition at line 80 of file Diffusion.h.

Member Function Documentation

static RigidBodyDiffusion IMP::atom::RigidBodyDiffusion::decorate_particle ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 84 of file Diffusion.h.

static bool IMP::atom::RigidBodyDiffusion::particle_is_instance ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 84 of file Diffusion.h.

static bool IMP::atom::RigidBodyDiffusion::particle_is_instance ( IMP::kernel::Model m,
IMP::kernel::ParticleIndex  pi 
)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 84 of file Diffusion.h.

static RigidBodyDiffusion IMP::atom::RigidBodyDiffusion::setup_particle ( kernel::Model m,
ParticleIndex  pi 
)
static

All diffusion coefficients are determined from the radius Setup the particle so it can be used with this decorator.

Definition at line 86 of file Diffusion.h.


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