A decorator for a diffusing particle. More...

#include <IMP/atom/Diffusion.h>

Inheritance diagram for IMP::atom::Diffusion:

Public Member Functions
	Diffusion (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	Diffusion (const IMP::kernel::ParticleAdaptor &d)

double	get_d () const

double	get_diffusion_coefficient () const

void	set_d (double d)

void	set_diffusion_coefficient (double d)

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::core::XYZ
	XYZ (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	XYZ (const IMP::kernel::ParticleAdaptor &d)

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	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex p)
	Return true if the particle is an instance of an Diffusion.

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static Diffusion	setup_particle (kernel::Model *m, ParticleIndex pi, Float D)

static Diffusion	setup_particle (IMP::kernel::ParticleAdaptor decorator, Float D)

static Diffusion	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v, Float D)

static Diffusion	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v, Float D)

static Diffusion	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static Diffusion	setup_particle (kernel::Model *m, ParticleIndex pi)

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 bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)

static const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi)

static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)

static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	get_is_setup (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 (kernel::Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

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::decorate_particle ( ::IMP::kernel::Particle * p )

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 46 of file Diffusion.h.

double IMP::atom::Diffusion::get_d ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_diffusion_coefficient().

static bool IMP::atom::Diffusion::particle_is_instance ( ::IMP::kernel::Particle * p )

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 46 of file Diffusion.h.

static bool IMP::atom::Diffusion::particle_is_instance	(	IMP::kernel::Model *	m,
		IMP::kernel::ParticleIndex	pi
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 46 of file Diffusion.h.

void IMP::atom::Diffusion::set_d ( double d )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use set_diffusion_coefficient().

static Diffusion IMP::atom::Diffusion::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		Float	D
	)

static

Setup the particle so it can be used with this decorator.

Definition at line 47 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		algebra::Vector3D	v,
		Float	D
	)

static

Setup the particle so it can be used with this decorator.

Definition at line 48 of file Diffusion.h.

static Diffusion IMP::atom::Diffusion::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi
	)

static

Assume particle is already a core::XYZR particle. Setup the particle so it can be used with this decorator.

Definition at line 50 of file Diffusion.h.

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