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::ParticleIndexes &	get_body_member_particle_indexes () const

algebra::Vector3D	get_coordinates () const
	Get the coordinates of the particle.

bool	get_coordinates_are_optimized () const

const kernel::ParticleIndexes &	get_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::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.

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

Particle *	get_particle () const

Model *	get_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 FloatKeys &	get_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:

 ## \example core/randomize_rigid_body.py
 # This fragments shows how to either perturb or set the orientation of a rigid
 # body randomly.
 
 import IMP.core
 import IMP.algebra
 import IMP
 from IMP.algebra import ReferenceFrame3D
 from IMP.algebra import Transformation3D
 
 m = IMP.kernel.Model()
 p = IMP.kernel.Particle(m)
 rbd = IMP.core.RigidBody.setup_particle(p, ReferenceFrame3D())
 translation = IMP.algebra.get_random_vector_in(
     IMP.algebra.get_unit_bounding_box_3d())
 
 # we don't yet have python code to generate a nearby rotation
 rotation = IMP.algebra.get_random_rotation_3d()
 transformation = Transformation3D(rotation, translation)
 # Option 1:
 # note, this overwrites the existing position
 # The True is to transform the members now rather than wait for a
 # score state
 rbd.set_reference_frame(ReferenceFrame3D(transformation))
 # Option 2:
 # perturb the existing transformation
 composed_tr = IMP.algebra.compose \
     (rbd.get_reference_frame().get_transformation_to(),
      transformation)
 rbd.set_reference_frame(ReferenceFrame3D(composed_tr))
 # Alternative to Option 2:
 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 )

See set_reference_frame()

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:

rigid_bodies.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation