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

#include <IMP/misc/CustomXYZR.h>

Inheritance diagram for IMP::misc::CustomXYZR:

Public Types
typedef FloatKey	DecoratorTraits

typedef core::XYZ	DecoratorTraitsBase

Public Member Functions
	CustomXYZR (Model *m, ParticleIndex id, const FloatKey &tr)

	CustomXYZR (::IMP::kernel::Particle *p, const FloatKey &tr=get_default_radius_key())

	CustomXYZR (const FloatKey &tr)

void	add_to_radius_derivative (double v, DerivativeAccumulator &d)

const DecoratorTraits &	get_decorator_traits () const

Float	get_radius () const

const FloatKey &	get_radius_key () const

algebra::Sphere3D	get_sphere () const
	Return a sphere object.

FloatKey	get_traits ()

void	set_radius (Float t)

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 CustomXYZR	decorate_particle (::IMP::kernel::Particle *p, const FloatKey &tr=get_default_radius_key())

static const DecoratorTraits &	get_default_decorator_traits ()

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 CustomXYZR	setup_particle (Particle *p, FloatKey radius_key=get_default_radius_key())

static CustomXYZR	setup_particle (Particle *p, Float radius, FloatKey radius_key=get_default_radius_key())

static CustomXYZR	setup_particle (Particle *p, const algebra::Sphere3D &s, FloatKey radius_key=get_default_radius_key())

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...

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

	Decorator (Particle *p)

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.

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 CustomXYZR.h.

Member Function Documentation

static CustomXYZR IMP::misc::CustomXYZR::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".

Definition at line 39 of file CustomXYZR.h.

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static CustomXYZR IMP::misc::CustomXYZR::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".

Definition at line 56 of file CustomXYZR.h.

static CustomXYZR IMP::misc::CustomXYZR::setup_particle	(	Particle *	p,
		const algebra::Sphere3D &	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".

Definition at line 69 of file CustomXYZR.h.

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

CustomXYZR.h

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation