IMP Reference Guide
2.12.0
The Integrative Modeling Platform
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A particle which covers a set of other particles. More...
#include <IMP/core/CoverRefined.h>
A particle which covers a set of other particles.
A decorator which sets up a particle to be a cover of a set of other particles. That is, the sphere defined by its XYZR decorator will always contain the passed particles.
Definition at line 72 of file CoverRefined.h.
Public Member Functions | |
Cover (const IMP::ParticleAdaptor &d) | |
Cover (::IMP::Model *m,::IMP::ParticleIndex id) | |
Constraint * | get_constraint () const |
void | show (std::ostream &out=std::cout) const |
Public Member Functions inherited from IMP::core::XYZR | |
XYZR (::IMP::Model *m,::IMP::ParticleIndex id) | |
XYZR (const IMP::ParticleAdaptor &d) | |
void | add_to_radius_derivative (double v, DerivativeAccumulator &d) |
add v to the derivative of the radius attribute More... | |
double | get_radius () const |
const algebra::Sphere3D & | get_sphere () const |
Return a sphere object. More... | |
void | set_radius (double r) const |
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::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 bool | get_is_setup (const IMP::ParticleAdaptor &p) |
static bool | get_is_setup (Model *m, ParticleIndex pi) |
static Cover | setup_particle (IMP::ParticleAdaptor decorator, Refiner *refiner) |
static Cover | setup_particle (Model *m, ParticleIndex pi, Refiner *refiner) |
static Cover | setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor members) |
static Cover | setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members) |
Static Public Member Functions inherited from IMP::core::XYZR | |
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... | |
static FloatKey | get_radius_key () |
Get the key for the radius. More... | |
static XYZR | setup_particle (Model *m, ParticleIndex pi) |
static XYZR | setup_particle (IMP::ParticleAdaptor decorator) |
static XYZR | setup_particle (IMP::ParticleAdaptor decorator, Float radius) |
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 FloatKeys & | get_xyz_keys () |
Get a vector containing the keys for x,y,z. More... | |
static XYZ | setup_particle (IMP::ParticleAdaptor decorator) |
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) |
Additional Inherited Members | |
Protected Member Functions inherited from IMP::Decorator | |
Decorator (Model *m, ParticleIndex pi) | |
Decorator (ParticleAdaptor p) | |
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Definition at line 72 of file CoverRefined.h.
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Definition at line 72 of file CoverRefined.h.
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Sets up Cover over members, and constrains Cover to be computed before model evaluation and to propagate derivatives following model evaluation. Setup the particle so that it can be used with this decorator
Definition at line 72 of file CoverRefined.h.
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Sets up Cover over particles passed by applying the refiner over the particle pi, and constrains Cover to be computed before model evaluation and to propagate derivatives following model evaluation. Setup the particle so that it can be used with this decorator
Definition at line 72 of file CoverRefined.h.