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IMP Reference Guide  2.17.0
The Integrative Modeling Platform
IMP::atom::RigidBodyDiffusion Class Reference

#include <IMP/atom/Diffusion.h>

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

Detailed Description

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

The translational and rotational diffusion coefficients are set automatically using IMP::atom::get_einstein_diffusion_coefficient(radius) and IMP::atom::get_einstein_rotational_diffusion_coefficient(radius) for radius IMP::core::XYZR(m, pi).get_radius().

Note that different translational and rotational coefficients should probably be set manually if the temperature is not the default IMP temperature.

Definition at line 97 of file Diffusion.h.

Public Member Functions

 RigidBodyDiffusion (::IMP::Model *m,::IMP::ParticleIndex id)
 
 RigidBodyDiffusion (const IMP::ParticleAdaptor &d)
 
double get_rotational_diffusion_coefficient () const
 returns the rotational diffusion coefficient in \(radians^2/fs\) More...
 
void set_rotational_diffusion_coefficient (double d) const
 sets the rotational diffusion coefficient in \(radians^2/fs\) More...
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::atom::Diffusion
 Diffusion (::IMP::Model *m,::IMP::ParticleIndex id)
 
 Diffusion (const IMP::ParticleAdaptor &d)
 
double get_diffusion_coefficient () const
 get diffusion coefficient in \(A^2/fs\) More...
 
void set_diffusion_coefficient (double d)
 set diffusion coefficient in \(A^2/fs\) More...
 
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 p)
 Return true if the particle is an instance of an Diffusion. More...
 
static FloatKey get_rotational_diffusion_coefficient_key ()
 Get the D key. More...
 
static RigidBodyDiffusion setup_particle (IMP::ParticleAdaptor decorator)
 
static RigidBodyDiffusion setup_particle (Model *m, ParticleIndex pi)
 All diffusion coefficients are determined from the radius. More...
 
- Static Public Member Functions inherited from IMP::atom::Diffusion
static FloatKey get_diffusion_coefficient_key ()
 Get the D key. More...
 
static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex p)
 Return true if the particle is an instance of Diffusion. More...
 
static Diffusion setup_particle (Model *m, ParticleIndex pi, Float D)
 
static Diffusion setup_particle (IMP::ParticleAdaptor decorator, Float D)
 
static Diffusion setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D v, Float D)
 
static Diffusion setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v, Float D)
 
static Diffusion setup_particle (Model *m, ParticleIndex pi)
 
static Diffusion setup_particle (IMP::ParticleAdaptor decorator)
 
- 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 decorator)
 
static XYZ setup_particle (Model *m, ParticleIndex pi)
 
static XYZ setup_particle (IMP::ParticleAdaptor decorator, 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 bool IMP::atom::RigidBodyDiffusion::get_is_setup ( Model m,
ParticleIndex  p 
)
static

Return true if the particle is an instance of an Diffusion.

Definition at line 120 of file Diffusion.h.

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double IMP::atom::RigidBodyDiffusion::get_rotational_diffusion_coefficient ( ) const

returns the rotational diffusion coefficient in \(radians^2/fs\)

Definition at line 106 of file Diffusion.h.

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static FloatKey IMP::atom::RigidBodyDiffusion::get_rotational_diffusion_coefficient_key ( )
static

Get the D key.

void IMP::atom::RigidBodyDiffusion::set_rotational_diffusion_coefficient ( double  d) const

sets the rotational diffusion coefficient in \(radians^2/fs\)

Definition at line 114 of file Diffusion.h.

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static RigidBodyDiffusion IMP::atom::RigidBodyDiffusion::setup_particle ( 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 103 of file Diffusion.h.


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