IMP::atom::RigidBodyDiffusion Class Reference
#include <IMP/atom/Diffusion.h>
Inheritance diagram for IMP::atom::RigidBodyDiffusion:Public Member Functions | |
| RigidBodyDiffusion (Model *m, ParticleIndex id) | |
| RigidBodyDiffusion (::IMP::kernel::Particle *p) | |
| 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 (Model *m, ParticleIndex id) | |
| Diffusion (::IMP::kernel::Particle *p) | |
| 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 (Model *m, ParticleIndex id) | |
| XYZ (::IMP::kernel::Particle *p) | |
| 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::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. | |
| 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 |
| Particle * | get_particle () const |
| Model * | get_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 FloatKey | get_rotational_diffusion_coefficient_key () |
| Get the D key. | |
| static bool | particle_is_instance (Particle *p) |
| Return true if the particle is an instance of an Diffusion. | |
| static bool | particle_is_instance (Model *m, ParticleIndex p) |
| Return true if the particle is an instance of an Diffusion. | |
| static RigidBodyDiffusion | setup_particle (Particle *p) |
| 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 | particle_is_instance (Particle *p) |
| Return true if the particle is an instance of an Diffusion. | |
| static bool | particle_is_instance (Model *m, ParticleIndex p) |
| Return true if the particle is an instance of an Diffusion. | |
| static Diffusion | setup_particle (Particle *p, const algebra::Vector3D &v, Float D) |
| static Diffusion | setup_particle (Particle *p, Float D) |
| static Diffusion | setup_particle (Particle *p) |
| 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 const FloatKeys & | get_xyz_keys () |
| Get a vector containing the keys for x,y,z. More... | |
| static bool | particle_is_instance (Particle *p) |
| static bool | particle_is_instance (Model *m, ParticleIndex pi) |
| static XYZ | setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0)) |
| static XYZ | setup_particle (Particle *p, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0)) |
| Static Public Member Functions inherited from IMP::kernel::Decorator | |
| static bool | particle_is_instance (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 (Model *m, ParticleIndex pi) | |
| Decorator (Particle *p) | |
| Related Functions inherited from IMP::core::XYZ | |
| double | get_dihedral (XYZ a, XYZ b, XYZ c, XYZ d) |
| Compute the dihedral angle (in radians) between the four particles. | |
| double | get_distance (XYZ a, XYZ b) |
| Compute the distance between a pair of particles. | |
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 105 of file Diffusion.h.
Member Function Documentation
|
static |
All diffusion coefficients are determined from the radius
The documentation for this class was generated from the following file: