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A decorator for a rigid body.
A rigid body particle describes a set of particles, known as the members, which move rigidly together. The rigid body is represented as an algebra::ReferenceFrame3D coupled with local coordinates (RigidMember::get_local_coordinates()) for the members expressed in that reference frame. The global coordinates of the members are accessed, as with other global coordinates, via the XYZ::get_coordinates().
Since the members are simply a set of particles which move together they don't (necessarily) define a shape. For example, the members of the rigid body made from a molecular hierarchy would include particles corresponding to intermediate levels of the hierarchy. As a result, methods that use rigid bodies also take a Refiner to map from the rigid body to the set of particles defining the geometry of interest.
The initial reference of the rigid body is computed from the coordinates, masses and radii of the particles passed to the constructor, based on diagonalizing the inertial tensor (which is not stored, currently).
RigidBodies can be nested (that is, a RigidBody can have another RigidBody as a member). This can be useful for organizational reasons as well as for accelerating computations since since operations are affected by the total number of children contained in the rigid body being operated on. Examples of this include collision detection where if you have multiple representations of geometry at different resolutions it is faster to put each of them in a separate rigid body and then creat one rigid body containing all of them.
It is often desirable to randomize the orientation of a rigid body:
# Assume p is a RigidBody Particle rbd= IMP.core.RigidBody(p) translation=IMP.algebra.get_random_vector_in(IMP.algebra.Vector3D(0,0,0), 10.0) # we don't yet have python code to generate a nearby rotation rotation= IMP.algebra.get_random_rotation_3d() transformation= IMP.algebra.Transformation3D(rotation, translation) # note, this overwrites the existing position # The True is to transform the members now rather than wait for a # score state rbd.set_transformation(transformation) # to instead perturb the existing transformation instead do rbd.set_transformation(IMP.algebra.compose(rbd.get_transformation(), transformation))
Examples: randomize rigid body, rigid collisions, dock with crosslinks, rigid brownian dynamics, analyze convergence
Inheritance diagram for IMP::core::RigidBody:Public Member Functions | |
| RigidBody (Model *m, ParticleIndex id) | |
| RigidBody (::IMP::Particle *p) | |
| void | add_member (Particle *p) |
| const ParticleIndexes & | get_body_member_particle_indexes () const |
| algebra::Vector3D | get_coordinates () const |
| Get the coordinates of the particle. | |
| bool | get_coordinates_are_optimized () const |
| Get whether the coordinates are optimized. | |
| RigidMember | get_member (unsigned int i) const |
| const ParticleIndexes & | get_member_particle_indexes () const |
| Return the members as particle pointers. | |
| RigidMembers | get_members () const |
| unsigned int | get_number_of_members () const |
| IMP::algebra::ReferenceFrame3D | get_reference_frame () const |
| Get the reference frame for the local coordinates. | |
| algebra::VectorD< 4 > | get_rotational_derivatives () const |
| Get the derivatives of the quaternion. | |
| void | normalize_rotation () |
| Normalized the quaternion. | |
| void | set_coordinates_are_optimized (bool tf) |
| Set whether the rigid body coordinates are optimized. | |
| void | set_reference_frame (const IMP::algebra::ReferenceFrame3D &tr) |
| Set the current reference frame. | |
| void | set_reference_frame_lazy (const IMP::algebra::ReferenceFrame3D &tr) |
| Change the reference, delay updating the members until evaluate. | |
| void | update_members () |
| Update the coordinates of the members. | |
Static Public Member Functions | |
| static RigidBody | decorate_particle (::IMP::Particle *p) |
| static bool | particle_is_instance (Particle *p) |
| Return true of the particle is a rigid body. | |
| static bool | particle_is_instance (Model *m, ParticleIndex pi) |
| Return true of the particle is a rigid body. | |
| static RigidBody | setup_particle (Particle *p, const ParticlesTemp &ps) |
| Create a new rigid body from a set of particles. | |
| static RigidBody | setup_particle (Particle *p, const algebra::ReferenceFrame3D &rf) |
| static void | teardown_particle (RigidBody rb) |
| Make the rigid body no longer rigid. | |
Related Functions | |
(Note that these are not member functions.) | |
| IMP::core::RigidBody | create_compatible_rigid_body (Hierarchy h, Hierarchy reference) |
| Rigidify a molecule or collection of molecules. | |
| IMP::core::RigidBody | create_rigid_body (const Hierarchies &h, std::string name=std::string("created rigid body")) |
| Rigidify a molecule or collection of molecules. | |
| void | transform (RigidBody a, const algebra::Transformation3D &tr) |
| Transform a rigid body. | |
| void IMP::core::RigidBody::add_member | ( | Particle * | p | ) |
Add a member, properly handle rigid bodies and XYZ particles.
| algebra::Vector3D IMP::core::RigidBody::get_coordinates | ( | ) | const |
Get the coordinates of the particle.
Reimplemented from IMP::core::XYZ.
| bool IMP::core::RigidBody::get_coordinates_are_optimized | ( | ) | const |
Get whether the coordinates are optimized.
Reimplemented from IMP::core::XYZ.
| const ParticleIndexes& IMP::core::RigidBody::get_member_particle_indexes | ( | ) | const |
Return the members as particle pointers.
This member function is here for efficiency.
| IMP::algebra::ReferenceFrame3D IMP::core::RigidBody::get_reference_frame | ( | ) | const |
Get the reference frame for the local coordinates.
| algebra::VectorD<4> IMP::core::RigidBody::get_rotational_derivatives | ( | ) | const |
Get the derivatives of the quaternion.
| void IMP::core::RigidBody::normalize_rotation | ( | ) |
Normalized the quaternion.
| static bool IMP::core::RigidBody::particle_is_instance | ( | Particle * | p | ) | [static] |
Return true of the particle is a rigid body.
Reimplemented from IMP::core::XYZ.
| static bool IMP::core::RigidBody::particle_is_instance | ( | Model * | m, |
| ParticleIndex | pi | ||
| ) | [static] |
Return true of the particle is a rigid body.
Reimplemented from IMP::core::XYZ.
| void IMP::core::RigidBody::set_coordinates_are_optimized | ( | bool | tf | ) |
Set whether the rigid body coordinates are optimized.
| void IMP::core::RigidBody::set_reference_frame | ( | const IMP::algebra::ReferenceFrame3D & | tr | ) |
Set the current reference frame.
All members of the rigid body will have their coordinates updated immediately.
| void IMP::core::RigidBody::set_reference_frame_lazy | ( | const IMP::algebra::ReferenceFrame3D & | tr | ) |
Change the reference, delay updating the members until evaluate.
See set_transformation()
| static RigidBody IMP::core::RigidBody::setup_particle | ( | Particle * | p, |
| const ParticlesTemp & | ps | ||
| ) | [static] |
Create a new rigid body from a set of particles.
| [in] | p | The particle to make into a rigid body |
| [in] | members | The particles to use as members of the rigid body |
The initial position and orientation of p is computed, as are the relative positions of the member particles. The member particles do not already need to be RigidMember particles, only XYZ particles.
| static RigidBody IMP::core::RigidBody::setup_particle | ( | Particle * | p, |
| const algebra::ReferenceFrame3D & | rf | ||
| ) | [static] |
Set it up with the provided initial reference frame.
| static void IMP::core::RigidBody::teardown_particle | ( | RigidBody | rb | ) | [static] |
Make the rigid body no longer rigid.
| void IMP::core::RigidBody::update_members | ( | ) |
Update the coordinates of the members.
| IMP::core::RigidBody create_compatible_rigid_body | ( | Hierarchy | h, |
| Hierarchy | reference | ||
| ) | [related] |
Rigidify a molecule or collection of molecules.
This method is identical to create_rigid_body() except that the chosen reference frame is aligned with that of reference (which must have exactly the same set of particles). This allows one to make sure the rigid body is equivalent when you have several copies of the same molecule.
| IMP::core::RigidBody create_rigid_body | ( | const Hierarchies & | h, |
| std::string | name = std::string("created rigid body") |
||
| ) | [related] |
Rigidify a molecule or collection of molecules.
The rigid body created has all the leaves as members and a member rigid body for each internal node in the tree. The particle created to be the rigid body is returned.
A name can be passed as it is not easy to automatically pick a decent name.
| void transform | ( | RigidBody | a, |
| const algebra::Transformation3D & | tr | ||
| ) | [related] |
Transform a rigid body.
The transformation is applied current conformation of the rigid body, as opposed to replacing the current conformation, as in RigidBody::set_transformation().
