 |
|
IMP Reference Guide
2.18.0
The Integrative Modeling Platform
|
A decorator for a diffusing particle with a diffusion coefficient. More...
#include <IMP/atom/Diffusion.h>
Inheritance diagram for IMP::atom::Diffusion:A decorator for a diffusing particle with a diffusion coefficient.
Diffusion is used to decorate a diffusing particle with a diffusion coefficient D. D is assumed to be in units of \(A^2/fs\).
Definition at line 33 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) |
| 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 FloatKeys & | get_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) | |
| double IMP::atom::Diffusion::get_diffusion_coefficient | ( | ) | const |
get diffusion coefficient in \(A^2/fs\)
Definition at line 89 of file Diffusion.h.
Here is the call graph for this function:
|
static |
Get the D key.
|
static |
Return true if the particle is an instance of Diffusion.
Definition at line 80 of file Diffusion.h.
Here is the call graph for this function:| void IMP::atom::Diffusion::set_diffusion_coefficient | ( | double | d | ) |
set diffusion coefficient in \(A^2/fs\)
Definition at line 84 of file Diffusion.h.
Here is the call graph for this function:
|
static |
Definition at line 62 of file Diffusion.h.
|
static |
Decorates the particle as a Diffusion particle with a diffusion coefficient D.Setup the particle so that it can be used with this decorator
Definition at line 62 of file Diffusion.h.
|
static |
Decorates the particle as a core::XYZ particle with coordinates v and as a Diffusion particle with a diffusion coefficient D.Setup the particle so it can be used with this decorator.
Definition at line 68 of file Diffusion.h.
|
static |
Decorates the particle as a Diffusion particle with the diffusion coefficient of a particle with a stokes radius of core::XYZR(m, pi).get_radius() at the default IMP temperature (297.15K).
: It assumed particle is already a core::XYZR particle. Setup the particle so it can be used with this decorator.
Definition at line 77 of file Diffusion.h.