IMP
2.4.0
The Integrative Modeling Platform
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#include <IMP/core/Gaussian.h>
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::ParticleIndexes & | get_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::ParticleIndexes & | get_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::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. 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 |
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 |
Additional Inherited Members | |
Protected Member Functions inherited from IMP::kernel::Decorator | |
Decorator (Model *m, ParticleIndex pi) | |
Decorator (ParticleAdaptor p) | |
algebra::Gaussian3D IMP::core::Gaussian::get_gaussian | ( | ) | const |
create Gaussian3D from these attributes
Definition at line 87 of file Gaussian.h.
IMP_Eigen::Matrix3d IMP::core::Gaussian::get_global_covariance | ( | ) |
retrieve global covariance
Definition at line 76 of file Gaussian.h.
IMP_Eigen::Matrix3d IMP::core::Gaussian::get_local_covariance | ( | ) | const |
retrieve local covariance (as diagonal matrix)
Definition at line 59 of file Gaussian.h.
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 108 of file Gaussian.h.
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.
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 |
Setup the particle so it can be used with this decorator.
Definition at line 48 of file Gaussian.h.
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static |
Definition at line 49 of file Gaussian.h.
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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