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 (Model *m, ParticleIndex id)

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

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 (Model *m, ParticleIndex id)

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

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 FloatKey	get_radius_key ()
	Get the default radius key.

static bool	particle_is_instance (Particle *p)
	Check if the particle has the required attributes.

static XYZR	setup_particle (Particle *p)

static XYZR	setup_particle (Particle *p, Float radius)

static XYZR	setup_particle (Particle *p, const algebra::Sphere3D s)

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

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

static bool	particle_is_instance (Particle *p)

static bool	particle_is_instance (Model *m, ParticleIndex pi)

static XYZ	setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))

static XYZ	setup_particle (Particle *p, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	particle_is_instance (Particle *p)
	Return true if the particle can be cast to the decorator. More...

Related Functions
(Note that these are not member functions.)
XYZRs	create_xyzr_particles (Model *m, unsigned int num, Float radius, Float box_side=10)
	Create a set of particles with random coordinates. More...

double	get_distance (XYZR a, XYZR b)
	Compute the distance between a pair of particles.

algebra::Sphere3D	get_enclosing_sphere (const XYZs &v)
	Get a sphere enclosing the set of XYZRs. More...

void	set_enclosing_radius (XYZR b, const XYZs &v)
	Set the radius of the first to enclose the list. More...

void	set_enclosing_sphere (XYZR b, const XYZs &v, double slack=0)
	Set the coordinates and radius of the first to enclose the list. More...

Related Functions inherited from IMP::core::XYZ
double	get_dihedral (XYZ a, XYZ b, XYZ c, XYZ d)
	Compute the dihedral angle (in radians) between the four particles.

double	get_distance (XYZ a, XYZ b)
	Compute the distance between a pair of particles.

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

	Decorator (Particle *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.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.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::setup_particle ( Particle * p )

static

Create a decorator using radius_key to store the FloatKey.

Parameters

[in] p The particle to wrap.

Definition at line 36 of file XYZR.h.

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static XYZR IMP::core::XYZR::setup_particle	(	Particle *	p,
		Float	radius
	)

static

Create a decorator using radius_key to store the FloatKey. The particle should already be an XYZ particle.

Parameters

[in]	p	The particle to wrap.
[in]	radius	The radius to set initially

Definition at line 50 of file XYZR.h.

static XYZR IMP::core::XYZR::setup_particle	(	Particle *	p,
		const algebra::Sphere3D	s
	)

static

Create a decorator using radius_key to store the FloatKey.

Parameters

[in]	p	The particle to wrap.
[in]	s	The sphere to use to set the position and radius

Definition at line 60 of file XYZR.h.

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

static

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

Definition at line 70 of file XYZR.h.

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Friends And Related Function Documentation

XYZRs create_xyzr_particles	(	Model *	m,
		unsigned int	num,
		Float	radius,
		Float	box_side = `10`
	)

Parameters

[in]	m	The model to add them to.
[in]	num	The number of particles to create.
[in]	radius	The radius to give them.
[in]	box_side	The particles have coordinates from -box_side to box_side.

The particles coordinates are optimized.

algebra::Sphere3D get_enclosing_sphere ( const XYZs & v )

[in] v The one whose radius should be set Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

void set_enclosing_radius	(	XYZR	b,
		const XYZs &	v
	)

[in]	v	The vector of XYZ or XYZR particles to enclose
[out]	b	The one whose radius should be set Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

void set_enclosing_sphere	(	XYZR	b,
		const XYZs &	v,
		double	slack = `0`
	)

[in]	v	The vector of XYZ or XYZR particles to enclose
[out]	b	The one whose values should be set
[in]	slack	An amount to add to the radius. Any particle which does not have the attribute b.get_radius() is assumed to have a radius of 0.

Note: This function produces tighter bounds if the CGAL library is available.

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

XYZR.h

Public Member Functions

Static Public Member Functions

Related Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

Friends And Related Function Documentation