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)

Examples: XYZR Decorator, cover particles, symmetry, filter close pairs, initialize chains, merge tree, shared functions, dock with crosslinks, rigid brownian dynamics, profile fit, multiscale, local fitting, analyze convergence, nup84 cg, optimize balls, connectivity restraint

Inheritance diagram for IMP::core::XYZR:

List of all members.

Public Member Functions
	XYZR (Model *m, ParticleIndex id)
	XYZR (::IMP::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.
Static Public Member Functions
static XYZR	decorate_particle (::IMP::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)
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::Sphere3D	get_enclosing_sphere (const XYZs &v)
	Get a sphere enclosing the set of XYZRs.
void	set_enclosing_radius (XYZR b, const XYZs &v)
	Set the radius of the first to enclose the list.
void	set_enclosing_sphere (XYZR b, const XYZs &v, double slack=0)
	Set the coordinates and radius of the first to enclose the list.

Member Function Documentation

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

Get the default radius key.

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

Return a sphere object.

static bool IMP::core::XYZR::particle_is_instance ( Particle * p ) [static]

Check if the particle has the required attributes.

Reimplemented from IMP::core::XYZ.

Reimplemented in IMP::core::Cover, and IMP::atom::LennardJones.

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

Set the attributes from a sphere.

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.

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

Reimplemented in IMP::atom::LennardJones.

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

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.

double get_distance	(	XYZR	a,
		XYZR	b
	)		`[related]`

Compute the distance between a pair of particles.

algebra::Sphere3D get_enclosing_sphere ( const XYZs & v ) [related]

Get a sphere enclosing the set of XYZRs.

Parameters:

[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
	)		`[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 XYZs &	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 file:

XYZR.h

Detailed Description

Public Member Functions

Static Public Member Functions

Related Functions

Member Function Documentation

Friends And Related Function Documentation