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:

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 XYZ decorator to set the coordinates
# of some particles and compute the distance between them.

import IMP
import IMP.core
import IMP.algebra
import sys

IMP.setup_from_argv(sys.argv, "XYZ decorator example")

m = IMP.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::Model *m,::IMP::ParticleIndex id)
	XYZ (const IMP::ParticleAdaptor &d)
void	add_to_derivative (int i, Float v, DerivativeAccumulator &d)
void	add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
	Add the vector v to the derivative vector of the x,y,z 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
algebra::Vector3D	get_derivatives () const
	Get the vector of derivatives accumulated by add_to_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::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...
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::ParticleAdaptor &p)
static bool	get_is_setup (Model *m, ParticleIndex pi)
static const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...
static XYZ	setup_particle (IMP::ParticleAdaptor pa)
static XYZ	setup_particle (Model *m, ParticleIndex pi)
static XYZ	setup_particle (IMP::ParticleAdaptor pa, algebra::Vector3D v)
static XYZ	setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v)

Additional Inherited Members
Protected Member Functions inherited from IMP::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 v to the derivative of the ith coordinate, used by various

Definition at line 78 of file XYZ.h.

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

Add the vector v to the derivative vector of the x,y,z coordinates.

Definition at line 82 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 109 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 89 of file XYZ.h.

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Float IMP::core::XYZ::get_derivative

(

int

i

)

const

Get the derivative of the ith coordinate, as accumulated by add_to_derivative()

Definition at line 74 of file XYZ.h.

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

(

)

const

Get the vector of derivatives accumulated by add_to_derivatives().

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

Definition at line 116 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 102 of file XYZ.h.

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Float IMP::core::XYZ::get_x

(

)

const

returns the value of the x attribute

Definition at line 54 of file XYZ.h.

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.

Float IMP::core::XYZ::get_y

(

)

const

returns the value of the y attribute

Definition at line 55 of file XYZ.h.

Float IMP::core::XYZ::get_z

(

)

const

returns the value of the z attribute

Definition at line 56 of file XYZ.h.

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 95 of file XYZ.h.

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void IMP::core::XYZ::set_x

(

Float

t

)

sets the value of the x attribute to t

Definition at line 54 of file XYZ.h.

void IMP::core::XYZ::set_y

(

Float

t

)

sets the value of the y attribute to t

Definition at line 55 of file XYZ.h.

void IMP::core::XYZ::set_z

(

Float

t

)

sets the value of the z attribute to t

Definition at line 56 of file XYZ.h.

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

static

Setup the particle with unspecified coordinates.

Returns

a XYZ object that decorates particle pi

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 ( IMP::ParticleAdaptor  pa )

static

Returns

a XYZ object that decorates the particle specified by pa

See Also

setup_particle(m, p)

Definition at line 51 of file XYZ.h.

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

static

Returns

a XYZ object that decorates particle pi

Definition at line 52 of file XYZ.h.

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

static

Returns

a XYZ object that decorates the particle specified by pa

See Also

setup_particle(m, pi, v )

Definition at line 52 of file XYZ.h.

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

• XYZ.h