Detailed Description

A decorator for a particle with x,y,z coordinates and a radius.

A simple example illustrating some of the functionality.

 ## \example core/XYZR_Decorator.py
 # This is a simple example using the XYZRDecorator to set the coordinates
 # and radius of a particle and compute distances between the resulting
 # spheres.
 
 import IMP
 import IMP.core
 import IMP.algebra
 
 m = IMP.kernel.Model()
 p0 = IMP.kernel.Particle(m)
 d0 = IMP.core.XYZR.setup_particle(
     p0, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(0, 1, 2),
                              1.0))
 p1 = IMP.kernel.Particle(m)
 d1 = IMP.core.XYZR.setup_particle(p1)
 d1.set_coordinates(IMP.algebra.Vector3D(3, 4, 5))
 d1.set_radius(2.0)
 
 print(IMP.core.get_distance(d0, d1))
 
 # use them as XYZ particles
 xd0 = IMP.core.XYZ(p0)
 xd1 = IMP.core.XYZ(p1)
 
 # distance without radii
 print(IMP.core.get_distance(xd0, xd1))

Definition at line 27 of file XYZR.h.

Public Member Functions
	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, 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 bool IMP::core::XYZR::get_is_setup	(	kernel::Model *	m,
		kernel::ParticleIndex	pi
	)

static

Check if the particle has the required attributes.

Add the coordinates and radius from the sphere to the particle.

Definition at line 57 of file XYZR.h.

static FloatKey IMP::core::XYZR::get_radius_key ( )

static

Get the key for the radius.

Definition at line 76 of file XYZR.h.

const algebra::Sphere3D& IMP::core::XYZR::get_sphere ( ) const

Return a sphere object.

Definition at line 67 of file XYZR.h.

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void IMP::core::XYZR::set_sphere ( const algebra::Sphere3D & s )

Set the attributes from a sphere.

Definition at line 72 of file XYZR.h.

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

static

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

Definition at line 48 of file XYZR.h.

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

static

Setup an XYZ particle as an XYZR particle. Setup the particle so that it can be used with this decorator

Definition at line 50 of file XYZR.h.

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

static

See Also: setup_particle(m, pi, radius )

Definition at line 50 of file XYZR.h.

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

static

See Also: setup_particle(m, pi, ball )

Definition at line 51 of file XYZR.h.

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

static

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

Definition at line 51 of file XYZR.h.

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

XYZR.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation