IMP::core::XYZR Class Reference

Detailed Description

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

A simple example illustrating some of the functionality.

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)

Inheritance diagram for IMP::core::XYZR:

[legend]


Public Member Functions
void	add_to_radius_derivative (double v, DerivativeAccumulator &d)
Float	get_radius () const
const FloatKey &	get_radius_key () const
algebra::SphereD< 3 >	get_sphere () const
	Return a sphere object.
void	set_radius (Float t)
void	set_sphere (const algebra::SphereD< 3 > &s)
	Set the attributes from a sphere.
	XYZR (::IMP::Particle *p, const FloatKey &tr=get_default_radius_key())
Static Public Member Functions
static XYZR	decorate_particle (::IMP::Particle *p, const FloatKey &tr=get_default_radius_key())
static FloatKey	get_default_radius_key ()
	Get the default radius key.
static bool	particle_is_instance (Particle *p, FloatKey radius_key=get_default_radius_key())
	Check if the particle has the required attributes.
static XYZR	setup_particle (Particle *p, const algebra::SphereD< 3 > &s, FloatKey radius_key=get_default_radius_key())
static XYZR	setup_particle (Particle *p, Float radius, FloatKey radius_key=get_default_radius_key())
static XYZR	setup_particle (Particle *p, FloatKey radius_key=get_default_radius_key())
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 which random coordinates.
double	get_distance (XYZR a, XYZR b)
	Compute the distance between a pair of particles.
algebra::SphereD< 3 >	get_enclosing_sphere (const XYZsTemp &v, FloatKey rk=XYZR::get_default_radius_key())
	Get a sphere enclosing the set of XYZRs.
void	set_enclosing_radius (XYZR b, const XYZsTemp &v)
	Set the radius of the first to enclose the list.
void	set_enclosing_sphere (XYZR b, const XYZsTemp &v, double slack=0)
	Set the coordinates and radius of the first to enclose the list.

Member Function Documentation

static XYZR IMP::core::XYZR::setup_particle	(	Particle *	p,
		const algebra::SphereD< 3 > &	s,
		FloatKey	radius_key = `get_default_radius_key()`
	)			`[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
`[in]`	radius_key	The (optional) key name to use. The default is "radius".

static XYZR IMP::core::XYZR::setup_particle	(	Particle *	p,
		Float	radius,
		FloatKey	radius_key = `get_default_radius_key()`
	)			`[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
`[in]`	radius_key	The (optional) key name to use. The default is "radius".

static XYZR IMP::core::XYZR::setup_particle	(	Particle *	p,
		FloatKey	radius_key = `get_default_radius_key()`
	)			`[static]`

Create a decorator using radius_key to store the FloatKey.

Parameters:

`[in]`	p	The particle to wrap.
`[in]`	radius_key	The (optional) key name to use. The default is "radius".

Friends And Related Function Documentation

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

Create a set of particles which random coordinates.

This function is mostly to be used to keep demo code brief.

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::SphereD< 3 > get_enclosing_sphere	(	const XYZsTemp &	v,
		FloatKey	rk = `XYZR::get_default_radius_key()`
	)			`[related]`

Get a sphere enclosing the set of XYZRs.

Parameters:

`[in]`	v	The one whose radius should be set
`[in]`	rk	The radius key to use 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 XYZsTemp &	v
	)			`[related]`

Set the radius of the first to enclose the list.

Parameters:

`[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 XYZsTemp &	v,
		double	slack = `0`
	)			`[related]`

Set the coordinates and radius of the first to enclose the list.

Parameters:

`[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 files:

XYZR.h
core/__init__.py

IMP::core::XYZR Class Reference

Detailed Description

Public Member Functions

Static Public Member Functions

Related Functions

Member Function Documentation

Friends And Related Function Documentation