IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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A decorator for a diffusing particle with a diffusion coefficient. More...
#include <IMP/atom/Diffusion.h>
A decorator for a diffusing particle with a diffusion coefficient.
Diffusion is used to decorate a particle with XYZ coordinates (since it inhertis from XYZ) and a translational diffusion coefficient D. D is specified in units of \(A^2/fs\), and it is used by eg IMP's Brownian dynamics simulator. It can be set explicitly or inferred implicitly from the radius.
Definition at line 36 of file Diffusion.h.
Public Member Functions | |
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::Vector3D & | get_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... | |
Model * | get_model () const |
Returns the Model containing the particle. More... | |
Particle * | get_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 | |
Particle * | operator-> () const |
Static Public Member Functions | |
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) |
Setup the particle with the specified diffusion coefficient. More... | |
static Diffusion | setup_particle (IMP::ParticleAdaptor pa, Float D) |
static Diffusion | setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v, Float D) |
static Diffusion | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v, Float D) |
Setup the particle with the specified coordinates and diffusion coefficient. More... | |
static Diffusion | setup_particle (Model *m, ParticleIndex pi) |
static Diffusion | setup_particle (IMP::ParticleAdaptor pa) |
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 FloatKeys & | get_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) | |
double IMP::atom::Diffusion::get_diffusion_coefficient | ( | ) | const |
get diffusion coefficient in \(A^2/fs\)
Definition at line 107 of file Diffusion.h.
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Get the D key.
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Return true if the particle is an instance of Diffusion.
Definition at line 97 of file Diffusion.h.
void IMP::atom::Diffusion::set_diffusion_coefficient | ( | double | d | ) |
set diffusion coefficient in \(A^2/fs\)
Definition at line 102 of file Diffusion.h.
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Definition at line 76 of file Diffusion.h.
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Setup the particle with the specified diffusion coefficient.
If the particle does not have coordinates, it is decorated as XYZ and its coordinates are set to [0,0,0], otherwise the coordinates remain the same.
Definition at line 76 of file Diffusion.h.
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Setup the particle with the specified coordinates and diffusion coefficient.
Definition at line 78 of file Diffusion.h.
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Definition at line 78 of file Diffusion.h.
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Definition at line 94 of file Diffusion.h.
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Setup the particle with a diffusion coefficient automatically inferred from its radius using the Stokes-Einstein equation. The diffusion coefficient is computed implicitly using the Stokes-Einstein equation by calling IMP::atom::get_einstein_diffusion_coefficient(R), where the Stokes radius R is core::XYZR::get_radius() and the temperature is the default IMP temperature of 297.15K.
Definition at line 94 of file Diffusion.h.