#include <IMP/core/Gaussian.h>

Inheritance diagram for IMP::core::Gaussian:

Detailed Description

A decorator for a particle storing a Gaussian.

Definition at line 57 of file core/Gaussian.h.

Public Member Functions
	Gaussian (::IMP::Model *m,::IMP::ParticleIndex id)

	Gaussian (const IMP::ParticleAdaptor &d)

algebra::Gaussian3D	get_gaussian () const
	create Gaussian3D from these attributes More...

Eigen::Matrix3d	get_global_covariance ()
	retrieve global covariance More...

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_gaussian (const algebra::Gaussian3D &g)
	Get the covariance attributes from a Gaussian3D object. More...

void	set_global_covariance (Eigen::Matrix3d covar)
	set the global-frame covariance. does NOT update local frame! More...

void	set_local_covariance (const 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 (::IMP::Model *m,::IMP::ParticleIndex id)

	RigidBody (const IMP::ParticleAdaptor &d)

	RigidBody (const RigidBody &)=default

void	add_member (ParticleIndexAdaptor p)

void	add_non_rigid_member (ParticleIndexAdaptor p)

void	add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &local_location, DerivativeAccumulator &da)

void	add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &global_derivative, const algebra::Vector3D &local_location, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)

void	add_to_rotational_derivatives (const algebra::Vector4D &other_qderiv, const algebra::Rotation3D &rot_other_to_local, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)

void	add_to_rotational_derivatives (const algebra::Vector4D &qderiv, DerivativeAccumulator &da)

void	add_to_torque (const algebra::Vector3D &torque_local, DerivativeAccumulator &da)

const ParticleIndexes &	get_body_member_particle_indexes () const

algebra::Vector3D	get_coordinates () const

bool	get_coordinates_are_optimized () const

ParticleIndexes	get_member_indexes () const

const ParticleIndexes &	get_member_particle_indexes () const

IMP::algebra::ReferenceFrame3D	get_reference_frame () const

RigidMembers	get_rigid_members () const

IMP::algebra::Rotation3D	get_rotation () 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...

RigidBody &	operator= (const RigidBody &)=default

void	pull_back_body_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
	Pull back global adjoints from member that is also a rigid body. More...

void	pull_back_body_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &TA, algebra::Transformation3D &TB, algebra::Transformation3DAdjoint &DTC, algebra::Transformation3DAdjoint &DTA, algebra::Transformation3DAdjoint &DTB, algebra::Vector3D &betatorque, DerivativeAccumulator &da)

void	pull_back_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
	Pull back global adjoints from member that is a point. More...

void	pull_back_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &T, algebra::Vector3D &x, algebra::Vector3D &Dy, algebra::Vector3D &Dx, algebra::Transformation3DAdjoint &DT, algebra::Vector3D &xtorque, DerivativeAccumulator &da)

void	pull_back_members_adjoints (DerivativeAccumulator &da)
	Pull back global adjoints from members. More...

void	remove_member (ParticleIndexAdaptor p)
	Remove the member from this rigid body. More...

void	set_coordinates_are_optimized (bool tf)

void	set_is_rigid_member (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 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::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 ObjectKey	get_global_covariance_key ()

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

static bool	get_is_setup (Model *m, ParticleIndex pi)

static ObjectKey	get_local_covariance_key ()

static Gaussian	setup_particle (Model *m, ParticleIndex pi)

static Gaussian	setup_particle (IMP::ParticleAdaptor pa)

static Gaussian	setup_particle (Model *m, ParticleIndex pi, algebra::Gaussian3D g)

static Gaussian	setup_particle (IMP::ParticleAdaptor pa, algebra::Gaussian3D g)

Static Public Member Functions inherited from IMP::core::RigidBody
static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex pi)
	Return true if the particle is a rigid body. More...

static FloatKeys	get_rotation_keys ()
	Get keys for rotation quaternion. More...

static RigidBody	setup_particle (IMP::ParticleAdaptor pa, ParticleIndexesAdaptor ps)

static RigidBody	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)

static RigidBody	setup_particle (IMP::ParticleAdaptor pa, algebra::ReferenceFrame3D rf)

static RigidBody	setup_particle (Model *m, ParticleIndex pi, 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::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 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

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

create Gaussian3D from these attributes

Definition at line 104 of file core/Gaussian.h.

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

retrieve global covariance

Definition at line 93 of file core/Gaussian.h.

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

retrieve local covariance (as diagonal matrix)

Definition at line 76 of file core/Gaussian.h.

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

retrieve local variances as Vector3D

Definition at line 86 of file core/Gaussian.h.

void IMP::core::Gaussian::set_gaussian ( const algebra::Gaussian3D & g )

Get the covariance attributes from a Gaussian3D object.

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

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

Definition at line 128 of file core/Gaussian.h.

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

set the local-frame covariance.

Definition at line 112 of file core/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 123 of file core/Gaussian.h.

static Gaussian IMP::core::Gaussian::setup_particle ( IMP::ParticleAdaptor pa )

static

Returns: a Gaussian object that decorates the particle specified by pa

See Also: setup_particle(m, p)

Definition at line 65 of file core/Gaussian.h.

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

static

Returns: a Gaussian object that decorates particle pi

Definition at line 65 of file core/Gaussian.h.

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

static

Returns: a Gaussian object that decorates particle pi

Definition at line 66 of file core/Gaussian.h.

static Gaussian IMP::core::Gaussian::setup_particle	(	IMP::ParticleAdaptor	pa,
		algebra::Gaussian3D	g
	)

static

Returns: a Gaussian object that decorates the particle specified by pa

See Also: setup_particle(m, pi, g )

Definition at line 66 of file core/Gaussian.h.

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

update the global covariance

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

core/Gaussian.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation