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IMP Reference Guide  develop.7cb8855c60,2024/10/04
The Integrative Modeling Platform
IMP::misc::CustomXYZR Class Reference

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

#include <IMP/misc/CustomXYZR.h>

+ Inheritance diagram for IMP::misc::CustomXYZR:

Detailed Description

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

This is mostly just a sample decorator.

Definition at line 24 of file CustomXYZR.h.

Public Types

typedef FloatKey DecoratorTraits
 

Public Member Functions

 CustomXYZR (const IMP::ParticleAdaptor &d, const FloatKey &tr=IMP::core::XYZR::get_radius_key())
 
 CustomXYZR (::IMP::Model *m,::IMP::ParticleIndex id, const FloatKey &tr=IMP::core::XYZR::get_radius_key())
 
void add_to_radius_derivative (double v, DerivativeAccumulator &d)
 
const DecoratorTraitsget_decorator_traits () const
 
Float get_radius () const
 
algebra::Sphere3D get_sphere () const
 Return a sphere object. More...
 
FloatKey get_traits ()
 
void set_radius (Float t)
 
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)
 
 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::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
 
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...
 
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 const DecoratorTraitsget_default_decorator_traits ()
 
static FloatKey get_default_radius_key ()
 Get the default radius key. More...
 
static bool get_is_setup (const IMP::ParticleAdaptor &p, const FloatKey &tr=IMP::core::XYZR::get_radius_key())
 
static bool get_is_setup (Model *m, ParticleIndex pi, FloatKey radius_key=get_default_radius_key())
 Check if the particle has the required attributes. More...
 
static CustomXYZR setup_particle (IMP::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())
 
static CustomXYZR setup_particle (Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())
 
static CustomXYZR setup_particle (Model *m, ParticleIndex pi, double radius, DecoratorTraits tr=get_default_decorator_traits())
 
static CustomXYZR setup_particle (IMP::ParticleAdaptor d, double radius, DecoratorTraits tr=get_default_decorator_traits())
 
static CustomXYZR setup_particle (IMP::ParticleAdaptor d, algebra::Sphere3D ball, DecoratorTraits tr=get_default_decorator_traits())
 
static CustomXYZR setup_particle (Model *m, ParticleIndex pi, algebra::Sphere3D ball, DecoratorTraits tr=get_default_decorator_traits())
 
- 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 (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

static FloatKey IMP::misc::CustomXYZR::get_default_radius_key ( )
static

Get the default radius key.

Definition at line 71 of file CustomXYZR.h.

static bool IMP::misc::CustomXYZR::get_is_setup ( Model m,
ParticleIndex  pi,
FloatKey  radius_key = get_default_radius_key() 
)
static

Check if the particle has the required attributes.

Definition at line 54 of file CustomXYZR.h.

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Float IMP::misc::CustomXYZR::get_radius ( ) const

returns the value of the radius attribute

Definition at line 58 of file CustomXYZR.h.

algebra::Sphere3D IMP::misc::CustomXYZR::get_sphere ( ) const

Return a sphere object.

Definition at line 61 of file CustomXYZR.h.

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void IMP::misc::CustomXYZR::set_radius ( Float  t)

sets the value of the radius attribute to t

Definition at line 58 of file CustomXYZR.h.

void IMP::misc::CustomXYZR::set_sphere ( const algebra::Sphere3D s)

Set the attributes from a sphere.

Definition at line 66 of file CustomXYZR.h.

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static CustomXYZR IMP::misc::CustomXYZR::setup_particle ( Model m,
ParticleIndex  pi,
DecoratorTraits  tr = get_default_decorator_traits() 
)
static
Returns
a CustomXYZR object that decorates particle pi

Definition at line 49 of file CustomXYZR.h.


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