IMP Reference Guide
2.6.1
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 diffusing particle with a diffusion coefficient D. D is assumed to be in units of \(A^2/fs\).
Definition at line 34 of file Diffusion.h.
Public Member Functions | |
Diffusion (::IMP::Model *m,::IMP::ParticleIndex id) | |
Diffusion (const IMP::ParticleAdaptor &d) | |
double | get_diffusion_coefficient () const |
void | set_diffusion_coefficient (double d) |
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) |
Add something to the derivative of the ith coordinate. More... | |
void | add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d) |
Add something to the derivative of the 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 |
Get the ith coordinate derivative. More... | |
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. 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 an 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) | |
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Get the D key.
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Return true if the particle is an instance of an Diffusion.
Definition at line 56 of file Diffusion.h.
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Definition at line 50 of file Diffusion.h.
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Setup the particle so that it can be used with this decorator
Definition at line 50 of file Diffusion.h.
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Setup the particle so it can be used with this decorator.
Definition at line 51 of file Diffusion.h.
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Assume particle is already a core::XYZR particle. Setup the particle so it can be used with this decorator.
Definition at line 53 of file Diffusion.h.