A decorator for a diffusing particle. More...

#include <IMP/atom/Diffusion.h>

Inheritance diagram for IMP::atom::Diffusion:

Public Member Functions
	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 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

See Also: BrownianDynamics

Warning: Diffusion has not been stabilized and is likely to change without notice. The name really should be fixed.

D is assumed to be in \(A^2/fs\)

Definition at line 31 of file Diffusion.h.

Member Function Documentation

static Diffusion IMP::atom::Diffusion::setup_particle	(	Particle *	p,
		const algebra::Vector3D &	v,
		Float	D
	)

static

Create a decorator with the passed coordinates and D.

Definition at line 39 of file Diffusion.h.

Here is the call graph for this function:

static Diffusion IMP::atom::Diffusion::setup_particle	(	Particle *	p,
		Float	D
	)

static

Create a decorator with the a given D. The particle is assumed to already have x,y,z attributes

Definition at line 51 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle ( Particle * p )

static

Create a decorator with the D determined from its radius.

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

Diffusion.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation