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

#include <IMP/core/XYZ.h>

Inheritance diagram for IMP::core::XYZ:

Detailed Description

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

Using the decorator one can get and set coordinates and modify derivatives.

 ## \example core/XYZ_Decorator.py
 # This is a simple example using the XYZDecorator to set the coordinates
 # of some particles and compute the distance between them.
 
 import IMP
 import IMP.core
 import IMP.algebra
 
 m = IMP.kernel.Model()
 p0 = m.add_particle("xyz0")
 # add x,y,z coordinates to the particle
 d0 = IMP.core.XYZ.setup_particle(m, p0, IMP.algebra.Vector3D(0, 1, 2))
 p1 = m.add_particle("xyz1")
 # add slots for the coordinates, but leave them uninitialized
 d1 = IMP.core.XYZ.setup_particle(m, p1)
 # set the coordinate values
 d1.set_coordinates(IMP.algebra.Vector3D(3, 4, 5))
 
 # return the distance between the two points described by the decorated
 # particles
 print IMP.core.get_distance(d0, d1)

See Also: XYZR

Examples:: core/simple.cpp.

Definition at line 30 of file XYZ.h.

Public Member Functions
	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. More...

void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add something to the derivative of the coordinates. More...

Float	get_coordinate (int i) const
	Get the ith coordinate. More...

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. More...

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. More...

Float	get_x () const

Float	get_y () const

Float	get_z () const

void	set_coordinate (unsigned int i, Float v)
	set the ith coordinate More...

void	set_coordinates (const algebra::Vector3D &v)
	set all coordinates from a vector More...

void	set_coordinates_are_optimized (bool tf) const
	Set whether the coordinates are optimized. More...

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
bool	get_is_valid () const

Model *	get_model () const
	Returns the Model containing the particle. More...

Particle *	get_particle () const
	Returns the particle decorated by this decorator. More...

ParticleIndex	get_particle_index () const
	Returns the particle index decorated by this decorator. More...

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () const

Static Public Member Functions
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 XYZ	setup_particle (IMP::kernel::ParticleAdaptor decorator)

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

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

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

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

	Decorator (ParticleAdaptor p)

Member Function Documentation

void IMP::core::XYZ::add_to_derivative	(	int	i,
		Float	v,
		DerivativeAccumulator &	d
	)

Add something to the derivative of the ith coordinate.

Definition at line 75 of file XYZ.h.

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void IMP::core::XYZ::add_to_derivatives	(	const algebra::Vector3D &	v,
		DerivativeAccumulator &	d
	)

Add something to the derivative of the coordinates.

Definition at line 79 of file XYZ.h.

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Float IMP::core::XYZ::get_coordinate ( int i ) const

Get the ith coordinate.

Definition at line 69 of file XYZ.h.

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const algebra::Vector3D& IMP::core::XYZ::get_coordinates ( ) const

Convert it to a vector.

Somewhat suspect based on wanting a Point/Vector differentiation but we don't have points

Definition at line 107 of file XYZ.h.

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bool IMP::core::XYZ::get_coordinates_are_optimized ( ) const

Get whether the coordinates are optimized.

Returns: true only if all of them are optimized.

Definition at line 86 of file XYZ.h.

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Float IMP::core::XYZ::get_derivative ( int i ) const

Get the ith coordinate derivative.

Definition at line 73 of file XYZ.h.

algebra::Vector3D IMP::core::XYZ::get_derivatives ( ) const

Get the vector of derivatives.

Somewhat suspect based on wanting a Point/Vector differentiation but we don't have points

Definition at line 114 of file XYZ.h.

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algebra::Vector3D IMP::core::XYZ::get_vector_to ( const XYZ & b ) const

Get the vector from this particle to another.

Definition at line 99 of file XYZ.h.

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static const FloatKeys& IMP::core::XYZ::get_xyz_keys ( )

static

Get a vector containing the keys for x,y,z.

This is quite handy for initializing movers and things.

void IMP::core::XYZ::set_coordinate	(	unsigned int	i,
		Float	v
	)

set the ith coordinate

Definition at line 58 of file XYZ.h.

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void IMP::core::XYZ::set_coordinates ( const algebra::Vector3D & v )

set all coordinates from a vector

Examples:: core/simple.cpp.

Definition at line 62 of file XYZ.h.

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void IMP::core::XYZ::set_coordinates_are_optimized ( bool tf ) const

Set whether the coordinates are optimized.

Definition at line 92 of file XYZ.h.

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

static

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

Examples:: atom/dope_and_excluded_volume.cpp, and core/simple.cpp.

Definition at line 51 of file XYZ.h.

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

static

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

Definition at line 52 of file XYZ.h.

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

static

See Also: setup_particle(m, pi, v )

Definition at line 52 of file XYZ.h.

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

XYZ.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation