 |
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).
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: rigid bodies, rigid collisions, randomize rigid body, analyze convergence
Inheritance diagram for IMP::core::RigidBody:Public Member Functions | |
| RigidBody (::IMP::Particle *p) | |
| void | add_member (XYZ d) |
| Add a particle as a member. | |
| void | add_member (RigidBody o) |
| Add another rigid body. | |
| algebra::VectorD< 3 > | get_coordinates () const |
| Get the coordinates of the particle. | |
| bool | get_coordinates_are_optimized () const |
| RigidMember | get_member (unsigned int i) const |
| 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 RigidBody | setup_particle (Particle *p, const RigidBodies &o) |
| static RigidBody | setup_particle (Particle *p, RigidBody other, const RigidMembers &members) |
| Create a rigid body based on members of another one. | |
| static RigidBody | setup_particle (Particle *p, const XYZs &members, const algebra::ReferenceFrame3D &reference_frame) |
| Create a new rigid body from a set of particles, specifying the frame. | |
| static RigidBody | setup_particle (Particle *p, const XYZs &members) |
| Create a new rigid body from a set of particles. | |
| 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 | ( | RigidBody | o | ) |
Add another rigid body.
Rigid bodies can be tied together so that one updates the other.
| 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, |
| RigidBody | other, | ||
| const RigidMembers & | members | ||
| ) | [static] |
Create a rigid body based on members of another one.
This function creates a rigid body that is part of another one. The member particles passed must be part of the other rigid body and the created rigid body is added to that one as a member. The purpose of this method is to, for example, define a rigid body for part of a large molecule that is also rigid.
The passed members do not become members of this rigid body, as there would be no point.
| static RigidBody IMP::core::RigidBody::setup_particle | ( | Particle * | p, |
| const XYZs & | members | ||
| ) | [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 XYZs & | members, | ||
| const algebra::ReferenceFrame3D & | reference_frame | ||
| ) | [static] |
Create a new rigid body from a set of particles, specifying the frame.
| [in] | p | The particle to make into a rigid body |
| [in] | members | The particles to use as members of the rigid body |
| [in] | reference_frame | The reference frame to use |
The member particles do not already need to be RigidMember particles, only XYZ particles.
| static RigidBody IMP::core::RigidBody::setup_particle | ( | Particle * | p, |
| const RigidBodies & | o | ||
| ) | [static] |
Merge several rigid bodies into on.
| 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.
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().
