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:

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
 import sys
 
 IMP.setup_from_argv(sys.argv, "XYZR decorator example")
 
 m = IMP.Model()
 p0 = IMP.Particle(m)
 d0 = IMP.core.XYZR.setup_particle(
     p0, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(0, 1, 2),
                              1.0))
 p1 = IMP.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::Model *m,::IMP::ParticleIndex id)

	XYZR (const IMP::ParticleAdaptor &d)

void	add_to_radius_derivative (double v, DerivativeAccumulator &d)
	add v to the derivative of the radius attribute More...

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::Model *m,::IMP::ParticleIndex id)

	XYZ (const IMP::ParticleAdaptor &d)

void	add_to_derivative (int i, Float v, DerivativeAccumulator &d)

void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add the vector v to the derivative vector of the x,y,z 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

algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_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::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...

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::ParticleAdaptor &p)

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

static XYZR	setup_particle (IMP::ParticleAdaptor pa)

static XYZR	setup_particle (IMP::ParticleAdaptor pa, Float radius)

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

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

static XYZR	setup_particle (IMP::ParticleAdaptor pa, 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::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)

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

static XYZ	setup_particle (IMP::ParticleAdaptor pa)

static XYZ	setup_particle (Model *m, ParticleIndex pi)

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

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

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

	Decorator (ParticleAdaptor p)

Member Function Documentation

void IMP::core::XYZR::add_to_radius_derivative	(	double	v,
		DerivativeAccumulator &	d
	)

add v to the derivative of the radius attribute

Definition at line 79 of file XYZR.h.

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static bool IMP::core::XYZR::get_is_setup	(	Model *	m,
		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.

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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 ( IMP::ParticleAdaptor pa )

static

Returns: a XYZR object that decorates the particle specified by pa

See Also: setup_particle(m, p)

Definition at line 48 of file XYZR.h.

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

static

Returns: a XYZR object that decorates particle pi

Definition at line 48 of file XYZR.h.

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

static

Setup an XYZ particle as an XYZR particle.

Returns: a XYZR object that decorates particle pi

Definition at line 50 of file XYZR.h.

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

static

Returns: a XYZR object that decorates the particle specified by pa

See Also: setup_particle(m, pi, radius )

Definition at line 50 of file XYZR.h.

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

static

Returns: a XYZR object that decorates the particle specified by pa

See Also: setup_particle(m, pi, ball )

Definition at line 51 of file XYZR.h.

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

static

Returns: a XYZR object that decorates particle pi

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