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IMP Reference Guide
2.5.0
The Integrative Modeling Platform
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#include <IMP/core/Gaussian.h>
Inheritance diagram for IMP::core::Gaussian:A decorator for a particle storing a Gaussian.
Definition at line 40 of file 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... | |
| 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 (::IMP::Model *m,::IMP::ParticleIndex id) | |
| RigidBody (const IMP::ParticleAdaptor &d) | |
| void | add_member (ParticleIndexAdaptor p) |
| void | add_non_rigid_member (ParticleIndexAdaptor p) |
| const 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 |
| ParticleIndexes | get_member_indexes () const |
| const ParticleIndexes & | get_member_particle_indexes () 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 (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) |
| 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::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 |
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 decorator) |
| static Gaussian | setup_particle (Model *m, ParticleIndex pi, algebra::Gaussian3D g) |
| static Gaussian | setup_particle (IMP::ParticleAdaptor decorator, 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 RigidBody | setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps) |
| static RigidBody | setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor ps) |
| static RigidBody | setup_particle (Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf) |
| static RigidBody | setup_particle (IMP::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::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) | |
| algebra::Gaussian3D IMP::core::Gaussian::get_gaussian | ( | ) | const |
create Gaussian3D from these attributes
Definition at line 87 of file Gaussian.h.
Here is the call graph for this function:| IMP_Eigen::Matrix3d IMP::core::Gaussian::get_global_covariance | ( | ) |
retrieve global covariance
Definition at line 76 of file Gaussian.h.
Here is the call graph for this function:| IMP_Eigen::Matrix3d IMP::core::Gaussian::get_local_covariance | ( | ) | const |
retrieve local covariance (as diagonal matrix)
Definition at line 59 of file Gaussian.h.
Here is the call graph for this function:| 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.
Here is the call graph for this function:| 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.
Here is the call graph for this function:| 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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Setup the particle so it can be used with this decorator.
Definition at line 48 of file Gaussian.h.
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Definition at line 49 of file Gaussian.h.
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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