IMP  2.1.0
The Integrative Modeling Platform
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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:

Public Member Functions

 XYZR (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 XYZR (const IMP::kernel::ParticleAdaptor &d)
 
void add_to_radius_derivative (double v, DerivativeAccumulator &d)
 
double get_radius () const
 
const algebra::Sphere3D & get_sphere () const
 Return a sphere object.
 
void set_radius (double r) const
 
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 XYZR decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 Check if the particle has the required attributes. More...
 
static FloatKey get_radius_key ()
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static XYZR setup_particle (kernel::Model *m, ParticleIndex pi)
 
static XYZR setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static XYZR setup_particle (IMP::kernel::ParticleAdaptor decorator, Float radius)
 
static XYZR setup_particle (kernel::Model *m, ParticleIndex pi, Float radius)
 
static XYZR setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Sphere3D ball)
 
static XYZR setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Sphere3D ball)
 
- 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

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 
10 m = IMP.kernel.Model()
11 p0 = IMP.kernel.Particle(m)
12 d0 = IMP.core.XYZR.setup_particle(
13  p0, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(0, 1, 2),
14  1.0))
15 p1 = IMP.kernel.Particle(m)
16 d1 = IMP.core.XYZR.setup_particle(p1)
17 d1.set_coordinates(IMP.algebra.Vector3D(3, 4, 5))
18 d1.set_radius(2.0)
19 
20 print IMP.core.get_distance(d0, d1)
21 
22 # use them as XYZ particles
23 xd0 = IMP.core.XYZ.decorate_particle(p0)
24 xd1 = IMP.core.XYZ.decorate_particle(p1)
25 
26 # distance without radii
27 print IMP.core.get_distance(xd0, xd1)

Definition at line 27 of file XYZR.h.

Member Function Documentation

static XYZR IMP::core::XYZR::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 47 of file XYZR.h.

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

Add the coordinates and radius from the sphere to the particle.

Definition at line 57 of file XYZR.h.

static FloatKey IMP::core::XYZR::get_radius_key ( )
static

Get the key for the radius.

Definition at line 76 of file XYZR.h.

static bool IMP::core::XYZR::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 47 of file XYZR.h.

static bool IMP::core::XYZR::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 47 of file XYZR.h.

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

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

Definition at line 50 of file XYZR.h.

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

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

Definition at line 51 of file XYZR.h.

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