Detailed Description

A particle which covers a set of other particles.

A decorator which sets up a particle to be a cover of a set of other particles. That is, the sphere defined by its XYZR decorator will always contain the passed particles.

Note: The maintenance of the invariant is done by an associated IMP::Constraint. As a result, the state is only guaranteed to be correct either during model evaluation, or immediately following model evaluation before any particles have been changed.

Definition at line 72 of file CoverRefined.h.

Public Member Functions
	Cover (const IMP::kernel::ParticleAdaptor &d)

	Cover (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

Constraint *	get_constraint () const

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

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

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

void	add_to_radius_derivative (double v, DerivativeAccumulator &d)

double	get_radius () const

const algebra::Sphere3D &	get_sphere () const
	Return a sphere object. More...

void	set_radius (double r) const

void	set_sphere (const algebra::Sphere3D &s)
	Set the attributes from a sphere. More...

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. 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::kernel::Decorator
bool	get_is_valid () const

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

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

static Cover	setup_particle (IMP::kernel::ParticleAdaptor decorator, Refiner *refiner)

static Cover	setup_particle (kernel::Model m, ParticleIndex pi, Refiner refiner)

static Cover	setup_particle (IMP::kernel::ParticleAdaptor decorator, ParticleIndexesAdaptor members)

static Cover	setup_particle (kernel::Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)

Static Public Member Functions inherited from IMP::core::XYZR
static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
	Check if the particle has the required attributes. More...

static FloatKey	get_radius_key ()
	Get the key for the radius. More...

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

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

static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator, Float radius)

static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi, Float radius)

static XYZR	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Sphere3D ball)

static XYZR	setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Sphere3D ball)

Static Public Member Functions inherited from IMP::core::XYZ
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 XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)

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

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

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

Additional Inherited Members
Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

Member Function Documentation

static Cover IMP::core::Cover::setup_particle	(	IMP::kernel::ParticleAdaptor	decorator,
		Refiner *	refiner
	)

static

See Also: setup_particle(m, pi, refiner )

Definition at line 72 of file CoverRefined.h.

static Cover IMP::core::Cover::setup_particle	(	IMP::kernel::ParticleAdaptor	decorator,
		ParticleIndexesAdaptor	members
	)

static

See Also: setup_particle(m, pi, members )

Definition at line 72 of file CoverRefined.h.

static Cover IMP::core::Cover::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		ParticleIndexesAdaptor	members
	)

static

Sets up Cover over members, and constrains Cover to be computed before model evaluation and to propogate derivatives folllowing model evaulation. Setup the particle so that it can be used with this decorator

Definition at line 72 of file CoverRefined.h.

static Cover IMP::core::Cover::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		Refiner *	refiner
	)

static

Sets up Cover over particles passed by applying the refiner over the particle pi, and constrains Cover to be computed before model evaluation and to propogate derivatives following model evaluation. Setup the particle so that it can be used with this decorator

Definition at line 72 of file CoverRefined.h.

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

CoverRefined.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation