IMP  2.1.0
The Integrative Modeling Platform
IMP::core::RigidBody Class Reference

A decorator for a rigid body. More...

#include <IMP/core/rigid_bodies.h>

+ Inheritance diagram for IMP::core::RigidBody:

Public Member Functions

 RigidBody (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id)
 
 RigidBody (const IMP::kernel::ParticleAdaptor &d)
 
void add_member (kernel::ParticleIndexAdaptor p)
 
void add_non_rigid_member (kernel::ParticleIndex pi)
 
const kernel::ParticleIndexesget_body_member_particle_indexes () const
 
algebra::Vector3D get_coordinates () const
 Get the coordinates of the particle.
 
bool get_coordinates_are_optimized () const
 
const kernel::ParticleIndexesget_member_particle_indexes () const
 Return the members as particle pointers. More...
 
RigidMembers get_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.
 
algebra::Vector3D get_torque () const
 
void normalize_rotation ()
 Normalized the quaternion.
 
void set_coordinates_are_optimized (bool tf)
 Set whether the rigid body coordinates are optimized.
 
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 ()
 Update the coordinates of the 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.
 
void add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
 Add something to the derivative of the coordinates.
 
Float get_coordinate (int i) const
 Get the ith coordinate.
 
const algebra::Vector3Dget_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.
 
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.
 
Float get_x () const
 
Float get_y () const
 
Float get_z () const
 
void set_coordinate (unsigned int i, Float v)
 set the ith coordinate
 
void set_coordinates (const algebra::Vector3D &v)
 set all coordinates from a vector
 
void set_coordinates_are_optimized (bool tf) const
 Set whether the coordinates are optimized.
 
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
ParticleIndex get_particle_index () const
 
Particleget_particle () const
 
Modelget_model () const
 Returns the Model containing the particle.
 
 Decorator (Particle *p)
 
 Decorator ()
 

Static Public Member Functions

static RigidBody decorate_particle (::IMP::kernel::Particle *p)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static RigidBody setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
 
static RigidBody setup_particle (IMP::kernel::ParticleAdaptor decorator, kernel::ParticleIndexesAdaptor ps)
 
static RigidBody setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::ReferenceFrame3D rf)
 
static RigidBody setup_particle (kernel::Model *m, ParticleIndex pi, algebra::ReferenceFrame3D rf)
 
static void teardown_particle (RigidBody rb)
 Make the rigid body no longer rigid.
 
- Static Public Member Functions inherited from IMP::core::XYZ
static XYZ decorate_particle (::IMP::kernel::Particle *p)
 
static FloatKey get_coordinate_key (unsigned int i)
 
static bool get_is_setup (const IMP::kernel::ParticleAdaptor &p)
 
static bool get_is_setup (kernel::Model *m, kernel::ParticleIndex pi)
 
static const FloatKeysget_xyz_keys ()
 Get a vector containing the keys for x,y,z. More...
 
static bool particle_is_instance (IMP::kernel::Model *m, IMP::kernel::ParticleIndex pi)
 
static bool particle_is_instance (::IMP::kernel::Particle *p)
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi)
 
static XYZ setup_particle (kernel::Model *m, ParticleIndex pi, algebra::Vector3D v)
 
static XYZ setup_particle (IMP::kernel::ParticleAdaptor decorator, algebra::Vector3D v)
 
- Static Public Member Functions inherited from IMP::kernel::Decorator
static bool get_is_setup (Particle *p)
 Return true if the particle can be cast to the decorator. More...
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (kernel::Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Detailed Description

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_internal_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 usually should simply take the list of particles they are interested in and then check for rigid bodies internally.

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:

1 ## \example core/randomize_rigid_body.py
2 # This fragments shows how to either perturb or set the orientation of a rigid
3 # body randomly.
4 
5 import IMP.core
6 import IMP.algebra
7 import IMP
8 from IMP.algebra import ReferenceFrame3D
9 from IMP.algebra import Transformation3D
10 
11 m = IMP.kernel.Model()
13 rbd = IMP.core.RigidBody.setup_particle(p, ReferenceFrame3D())
15  IMP.algebra.get_unit_bounding_box_3d())
16 
17 # we don't yet have python code to generate a nearby rotation
19 transformation = Transformation3D(rotation, translation)
20 # Option 1:
21 # note, this overwrites the existing position
22 # The True is to transform the members now rather than wait for a
23 # score state
24 rbd.set_reference_frame(ReferenceFrame3D(transformation))
25 # Option 2:
26 # perturb the existing transformation
27 composed_tr = IMP.algebra.compose \
28  (rbd.get_reference_frame().get_transformation_to(),
29  transformation)
30 rbd.set_reference_frame(ReferenceFrame3D(composed_tr))
31 # Alternative to Option 2:
32 IMP.core.transform(rbd, transformation)
Note
The maintenance of the invariant is done by an associated IMP::Constraint. As a result, the state is only guaranteed to be correct either during model evaluation, or immediately following model evaluation before any particles have been changed.
See Also
RigidMember
RigidBodyMover
RigidClosePairsFinder
RigidBodyDistancePairScore

Definition at line 75 of file rigid_bodies.h.

Member Function Documentation

void IMP::core::RigidBody::add_member ( kernel::ParticleIndexAdaptor  p)

Add a member, properly handle rigid bodies and XYZ particles.

void IMP::core::RigidBody::add_non_rigid_member ( kernel::ParticleIndex  pi)

Add a NonRigidMember. Currently RigidBody non-rigid members are not handler properly.

static RigidBody IMP::core::RigidBody::decorate_particle ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Check explicitly instead.

Definition at line 124 of file rigid_bodies.h.

static bool IMP::core::RigidBody::get_is_setup ( kernel::Model m,
kernel::ParticleIndex  pi 
)
static

Return true of the particle is a rigid body

Definition at line 137 of file rigid_bodies.h.

const kernel::ParticleIndexes& IMP::core::RigidBody::get_member_particle_indexes ( ) const

This member function is here for efficiency.

Definition at line 102 of file rigid_bodies.h.

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algebra::Vector3D IMP::core::RigidBody::get_torque ( ) const

The units are kCal/Mol/Radian

Definition at line 210 of file rigid_bodies.h.

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static bool IMP::core::RigidBody::particle_is_instance ( ::IMP::kernel::Particle p)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 124 of file rigid_bodies.h.

static bool IMP::core::RigidBody::particle_is_instance ( IMP::kernel::Model m,
IMP::kernel::ParticleIndex  pi 
)
static
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_is_setup() instead.

Definition at line 124 of file rigid_bodies.h.

void IMP::core::RigidBody::set_is_rigid_member ( kernel::ParticleIndex  pi,
bool  tf 
)

Set whether a particular member is a rigid member or a non-rigid member.

void IMP::core::RigidBody::set_reference_frame ( const IMP::algebra::ReferenceFrame3D tr)

All members of the rigid body will have their coordinates updated immediately.

See Also
IMP::core::transform(RigidBody,const algebra::Transformation3D&)
lazy_set_reference_frame()
void IMP::core::RigidBody::set_reference_frame_from_members ( const kernel::ParticleIndexes members)

Update the reference frame of the rigid body based on the current coordinates of the passed members (nonpassed members are ignored). This can be used to update the rigid body after new coordinates were loaded for the members. The members are passed explictily since, typically, some are desired to just move along with the newly loaded rigid body.

Note
This requires at least three members that are not collinear to work.
void IMP::core::RigidBody::set_reference_frame_lazy ( const IMP::algebra::ReferenceFrame3D tr)
static RigidBody IMP::core::RigidBody::setup_particle ( kernel::Model m,
ParticleIndex  pi,
kernel::ParticleIndexesAdaptor  ps 
)
static

Setup the particle so it can be used with this decorator.

Definition at line 125 of file rigid_bodies.h.

static RigidBody IMP::core::RigidBody::setup_particle ( kernel::Model m,
ParticleIndex  pi,
algebra::ReferenceFrame3D  rf 
)
static

Create a rigid body with the passed reference frame as its initial position. Setup the particle so it can be used with this decorator.

Definition at line 128 of file rigid_bodies.h.


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