IMP Reference Guide  2.5.0 The Integrative Modeling Platform
IMP::core::XYZR Class Reference

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

#include <IMP/core/XYZR.h>

Inheritance diagram for IMP::core::XYZR:

## Detailed Description

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

A simple example illustrating some of the functionality.

1 ## \example core/XYZR_Decorator.py
2 # This is a simple example using the XYZRDecorator to set the coordinates
3 # and radius of a particle and compute distances between the resulting
4 # spheres.
5
6 import IMP
7 import IMP.core
8 import IMP.algebra
9 import sys
10
11 IMP.setup_from_argv(sys.argv, "XYZR decorator example")
12
13 m = IMP.Model()
14 p0 = IMP.Particle(m)
17  1.0))
18 p1 = IMP.Particle(m)
20 d1.set_coordinates(IMP.algebra.Vector3D(3, 4, 5))
22
23 print(IMP.core.get_distance(d0, d1))
24
25 # use them as XYZ particles
26 xd0 = IMP.core.XYZ(p0)
27 xd1 = IMP.core.XYZ(p1)
28
30 print(IMP.core.get_distance(xd0, xd1))

Definition at line 27 of file XYZR.h.

## Public Member Functions

XYZR (::IMP::Model *m,::IMP::ParticleIndex id)

const algebra::Sphere3Dget_sphere () const
Return a sphere object. More...

void set_sphere (const algebra::Sphere3D &s)
Set the attributes from a sphere. More...

void show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::core::XYZ
XYZ (::IMP::Model *m,::IMP::ParticleIndex id)

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::Vector3Dget_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::Decorator
bool get_is_valid () const

Modelget_model () const
Returns the Model containing the particle. More...

Particleget_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

Particleoperator-> () const

## Static Public Member Functions

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

static bool get_is_setup (Model *m, ParticleIndex pi)
Check if the particle has the required attributes. More...

Get the key for the radius. More...

static XYZR setup_particle (Model *m, ParticleIndex pi)

static XYZR setup_particle (Model *m, ParticleIndex pi, Float radius)

static XYZR setup_particle (Model *m, ParticleIndex pi, algebra::Sphere3D ball)

static XYZR setup_particle (IMP::ParticleAdaptor decorator, algebra::Sphere3D ball)

Static Public Member Functions inherited from IMP::core::XYZ
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 FloatKeysget_xyz_keys ()
Get a vector containing the keys for x,y,z. More...

static XYZ setup_particle (Model *m, ParticleIndex pi)

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

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

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

## Member Function Documentation

 static bool IMP::core::XYZR::get_is_setup ( Model * m, ParticleIndex pi )
static

Check if the particle has the required attributes.

Definition at line 57 of file XYZR.h.

static

Get the key for the radius.

Definition at line 76 of file XYZR.h.

 const algebra::Sphere3D& IMP::core::XYZR::get_sphere ( ) const

Return a sphere object.

Definition at line 67 of file XYZR.h.

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 void IMP::core::XYZR::set_sphere ( const algebra::Sphere3D & s )

Set the attributes from a sphere.

Definition at line 72 of file XYZR.h.

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

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

Definition at line 48 of file XYZR.h.

 static XYZR IMP::core::XYZR::setup_particle ( Model * m, ParticleIndex pi, Float radius )
static

Setup an XYZ particle as an XYZR particle. Setup the particle so that it can be used with this decorator

Definition at line 50 of file XYZR.h.

static

Definition at line 50 of file XYZR.h.

 static XYZR IMP::core::XYZR::setup_particle ( IMP::ParticleAdaptor decorator, algebra::Sphere3D ball )
static