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

Public Member Functions
	CustomXYZR (const IMP::kernel::ParticleAdaptor &d, const FloatKey &tr=IMP::core::XYZR::get_radius_key())

	CustomXYZR (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id, const FloatKey &tr=IMP::core::XYZR::get_radius_key())

void	add_to_radius_derivative (double v, DerivativeAccumulator &d)

const DecoratorTraits &	get_decorator_traits () const

Float	get_radius () 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 (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)

	XYZ (const IMP::kernel::ParticleAdaptor &d)

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=IMP::core::XYZR::get_radius_key())

static const DecoratorTraits &	get_default_decorator_traits ()

static FloatKey	get_default_radius_key ()
	Get the default radius key.

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p, const FloatKey &tr=IMP::core::XYZR::get_radius_key())

static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex pi, FloatKey radius_key=get_default_radius_key())
	Check if the particle has the required attributes.

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi, const FloatKey &tr=IMP::core::XYZR::get_radius_key())

static bool	particle_is_instance (::IMP::kernel::Particle *p, const FloatKey &tr=IMP::core::XYZR::get_radius_key())

static CustomXYZR	setup_particle (IMP::kernel::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())

static CustomXYZR	setup_particle (kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())

static CustomXYZR	setup_particle (IMP::kernel::ParticleAdaptor d, double radius, DecoratorTraits tr=get_default_decorator_traits())

static CustomXYZR	setup_particle (kernel::Model *m, ParticleIndex pi, double radius, DecoratorTraits tr=get_default_decorator_traits())

static CustomXYZR	setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Sphere3D ball, DecoratorTraits tr=get_default_decorator_traits())

static CustomXYZR	setup_particle (IMP::kernel::ParticleAdaptor d, algebra::Sphere3D ball, DecoratorTraits tr=get_default_decorator_traits())

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 bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p)

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

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

static bool	particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)

static bool	particle_is_instance (::IMP::kernel::Particle *p)

static XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)

static XYZ	setup_particle (kernel::Model *m, ParticleIndex pi)

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

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

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	get_is_setup (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 (kernel::Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

Detailed Description

This is mostly just a sample decorator.

Definition at line 24 of file CustomXYZR.h.

Member Function Documentation

static CustomXYZR IMP::misc::CustomXYZR::decorate_particle	(	::IMP::kernel::Particle *	p,
		const FloatKey &	tr = `IMP::core::XYZR::get_radius_key()`
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 48 of file CustomXYZR.h.

static bool IMP::misc::CustomXYZR::particle_is_instance	(	::IMP::kernel::Particle *	p,
		const FloatKey &	tr = `IMP::core::XYZR::get_radius_key()`
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 48 of file CustomXYZR.h.

static bool IMP::misc::CustomXYZR::particle_is_instance	(	IMP::kernel::Model *	m,
		IMP::kernel::ParticleIndex	pi,
		const FloatKey &	tr = `IMP::core::XYZR::get_radius_key()`
	)

static

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 48 of file CustomXYZR.h.

static CustomXYZR IMP::misc::CustomXYZR::setup_particle	(	kernel::Model *	m,
		ParticleIndex	pi,
		DecoratorTraits	tr = `get_default_decorator_traits()`
	)

static

Setup the particle so it can be used with this decorator.

Definition at line 49 of file CustomXYZR.h.

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