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

#include <IMP/core/XYZR.h>

Inheritance diagram for IMP::core::XYZR:

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.

void	set_radius (double r) const

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

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

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 ()

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

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

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 (IMP::kernel::ParticleAdaptor decorator, algebra::Sphere3D ball)

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

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

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.decorate_particle(p0)
 xd1 = IMP.core.XYZ.decorate_particle(p1)
 
 # distance without radii
 print IMP.core.get_distance(xd0, xd1)

Definition at line 27 of file XYZR.h.

Member Function Documentation

static XYZR IMP::core::XYZR::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 47 of file XYZR.h.

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

static

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.

static bool IMP::core::XYZR::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 47 of file XYZR.h.

static bool IMP::core::XYZR::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 47 of file XYZR.h.

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 it can be used with this decorator.

Definition at line 50 of file XYZR.h.

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

static

Setup the particle so 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

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation