IMP  2.3.1
The Integrative Modeling Platform
IMP::core::Gaussian Class Reference

#include <IMP/core/Gaussian.h>

+ Inheritance diagram for IMP::core::Gaussian:

Detailed Description

A decorator for a particle storing a Gaussian.

Definition at line 40 of file Gaussian.h.

Public Member Functions

 Gaussian (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 Gaussian (const IMP::kernel::ParticleAdaptor &d)
 
algebra::Gaussian3D get_gaussian () const
 create Gaussian3D from these attributes More...
 
IMP_Eigen::Matrix3d get_global_covariance ()
 retrieve global covariance More...
 
IMP_Eigen::Matrix3d get_local_covariance () const
 retrieve local covariance (as diagonal matrix) More...
 
algebra::Vector3D get_variances () const
 retrieve local variances as Vector3D More...
 
void set_global_covariance (IMP_Eigen::Matrix3d covar)
 set the global-frame covariance. does NOT update local frame! More...
 
void set_local_covariance (const IMP_Eigen::Vector3d covar)
 set the local-frame covariance. More...
 
void set_variances (const algebra::Vector3D v)
 equivalent to set_local_covariance, used for backwards compatibility More...
 
void show (std::ostream &out=std::cout) const
 
void update_global_covariance ()
 update the global covariance More...
 
- Public Member Functions inherited from IMP::core::RigidBody
 RigidBody (const IMP::kernel::ParticleAdaptor &d)
 
 RigidBody (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
void add_member (kernel::ParticleIndexAdaptor p)
 
void add_non_rigid_member (kernel::ParticleIndexAdaptor p)
 
const kernel::ParticleIndexesget_body_member_particle_indexes () const
 
algebra::Vector3D get_coordinates () const
 Get the coordinates of the particle. More...
 
bool get_coordinates_are_optimized () const
 
kernel::ParticleIndexes get_member_indexes () const
 
const kernel::ParticleIndexesget_member_particle_indexes () const
 
RigidMembers get_members () const
 
IMP::algebra::ReferenceFrame3D get_reference_frame () const
 Get the reference frame for the local coordinates. More...
 
RigidMembers get_rigid_members () const
 
algebra::VectorD< 4 > get_rotational_derivatives () const
 Get the derivatives of the quaternion. More...
 
algebra::Vector3D get_torque () const
 
void normalize_rotation ()
 Normalize the quaternion. More...
 
void set_coordinates_are_optimized (bool tf)
 
void set_is_rigid_member (kernel::ParticleIndex pi, bool tf)
 
void set_reference_frame (const IMP::algebra::ReferenceFrame3D &tr)
 Set the current reference frame. More...
 
void set_reference_frame_from_members (const kernel::ParticleIndexes &members)
 
void set_reference_frame_lazy (const IMP::algebra::ReferenceFrame3D &tr)
 Change the reference, delay updating the members until evaluate. More...
 
void show (std::ostream &out=std::cout) const
 
void update_members ()
 
- 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. 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::kernel::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 ObjectKey get_global_covariance_key ()
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static ObjectKey get_local_covariance_key ()
 
static Gaussian setup_particle (kernel::Model *m, ParticleIndex pi)
 
static Gaussian setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static Gaussian setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Gaussian3D g)
 
static Gaussian setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Gaussian3D g)
 
- Static Public Member Functions inherited from IMP::core::RigidBody
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 Return true if the particle is a rigid body. More...
 
static RigidBody setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
 
static RigidBody setup_particle (IMP::kernel::ParticleAdaptor decorator, kernel::ParticleIndexesAdaptor ps)
 
static RigidBody setup_particle (kernel::Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf)
 
static RigidBody setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::ReferenceFrame3D rf)
 
static void teardown_particle (RigidBody rb)
 Make the rigid body no longer rigid. More...
 
- Static Public Member Functions inherited from IMP::core::XYZ
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 FloatKeysget_xyz_keys ()
 Get a vector containing the keys for x,y,z. More...
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi)
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)
 

Additional Inherited Members

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

Member Function Documentation

algebra::Gaussian3D IMP::core::Gaussian::get_gaussian ( ) const

create Gaussian3D from these attributes

Definition at line 87 of file Gaussian.h.

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IMP_Eigen::Matrix3d IMP::core::Gaussian::get_global_covariance ( )

retrieve global covariance

Definition at line 76 of file Gaussian.h.

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IMP_Eigen::Matrix3d IMP::core::Gaussian::get_local_covariance ( ) const

retrieve local covariance (as diagonal matrix)

Definition at line 59 of file Gaussian.h.

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algebra::Vector3D IMP::core::Gaussian::get_variances ( ) const

retrieve local variances as Vector3D

Definition at line 69 of file Gaussian.h.

void IMP::core::Gaussian::set_global_covariance ( IMP_Eigen::Matrix3d  covar)

set the global-frame covariance. does NOT update local frame!

Definition at line 112 of file Gaussian.h.

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void IMP::core::Gaussian::set_local_covariance ( const IMP_Eigen::Vector3d  covar)

set the local-frame covariance.

Definition at line 92 of file Gaussian.h.

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void IMP::core::Gaussian::set_variances ( const algebra::Vector3D  v)

equivalent to set_local_covariance, used for backwards compatibility

Definition at line 103 of file Gaussian.h.

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static Gaussian IMP::core::Gaussian::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 Gaussian.h.

static Gaussian IMP::core::Gaussian::setup_particle ( IMP::kernel::ParticleAdaptor  decorator,
algebra::Gaussian3D  g 
)
static
See Also
setup_particle(m, pi, g )

Definition at line 49 of file Gaussian.h.

static Gaussian IMP::core::Gaussian::setup_particle ( kernel::Model m,
ParticleIndex  pi,
algebra::Gaussian3D  g 
)
static

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

Definition at line 49 of file Gaussian.h.

void IMP::core::Gaussian::update_global_covariance ( )

update the global covariance


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