IMP::core::XYZ Class Reference

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

#include <IMP/core/XYZ.h>

Inheritance diagram for IMP::core::XYZ:

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.
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 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

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 32 of file XYZ.h.

Member Function Documentation

static XYZ IMP::core::XYZ::decorate_particle ( ::IMP::kernel::Particle *  p )

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 51 of file XYZ.h.

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

(

)

const

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

Definition at line 109 of file XYZ.h.

Here is the call graph for this function:

bool IMP::core::XYZ::get_coordinates_are_optimized

(

)

const

Returns

true only if all of them are optimized.

Definition at line 88 of file XYZ.h.

Here is the call graph for this function:

algebra::Vector3D IMP::core::XYZ::get_derivatives

(

)

const

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

Definition at line 116 of file XYZ.h.

Here is the call graph for this function:

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

static

This is quite handy for initializing movers and things.

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

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 51 of file XYZ.h.

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

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 51 of file XYZ.h.

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 53 of file XYZ.h.

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

static

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

Definition at line 54 of file XYZ.h.

---

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

• XYZ.h