A decorator for a rigid body. More...

#include <IMP/core/rigid_bodies.h>

Inheritance diagram for IMP::core::RigidBody:

Public Member Functions
	RigidBody (Model *m, ParticleIndex id)

	RigidBody (::IMP::kernel::Particle *p)

void	add_member (ParticleIndex p)

void	add_non_rigid_member (ParticleIndex pi)

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

const ParticleIndexes &	get_member_particle_indexes () const
	Return the members as particle pointers. More...

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 (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 ()
	Update the coordinates of the members.

Public Member Functions inherited from IMP::core::XYZ
	XYZ (Model *m, ParticleIndex id)

	XYZ (::IMP::kernel::Particle *p)

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	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. More...

static RigidBody	setup_particle (Particle *p, const 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 const FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...

static bool	particle_is_instance (Particle *p)

static bool	particle_is_instance (Model *m, ParticleIndex pi)

static XYZ	setup_particle (Model *m, ParticleIndex pi, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))

static XYZ	setup_particle (Particle *p, const algebra::Vector3D v=algebra::Vector3D(0, 0, 0))

Static Public Member Functions inherited from IMP::kernel::Decorator
static bool	particle_is_instance (Particle *p)
	Return true if the particle can be cast to the decorator. More...

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. More...

IMP::core::RigidBody	create_rigid_body (const Hierarchies &h, std::string name=std::string("created rigid body"))
	Rigidify a molecule or collection of molecules. More...

void	transform (RigidBody a, const algebra::Transformation3D &tr)
	Transform a rigid body. More...

Related Functions inherited from IMP::core::XYZ
double	get_dihedral (XYZ a, XYZ b, XYZ c, XYZ d)
	Compute the dihedral angle (in radians) between the four particles.

double	get_distance (XYZ a, XYZ b)
	Compute the distance between a pair of particles.

Additional Inherited Members
Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (Particle *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.Model()
 p = IMP.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 ( ParticleIndex p )

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

Definition at line 259 of file rigid_bodies.h.

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

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

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

This member function is here for efficiency.

Definition at line 95 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 221 of file rigid_bodies.h.

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void IMP::core::RigidBody::set_is_rigid_member	(	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 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	(	Particle *	p,
		const ParticlesTemp &	ps
	)

static

Parameters

[in]	p	The particle to make into a rigid body
[in]	ps	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.

Friends And Related Function Documentation

IMP::core::RigidBody create_compatible_rigid_body	(	Hierarchy	h,
		Hierarchy	reference
	)

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")`
	)

A name can be passed as it is not easy to automatically pick a decent name.

See Also: create_aligned_rigid_body()

void transform	(	RigidBody	a,
		const algebra::Transformation3D &	tr
	)

algebra::Transformation3D

Definition at line 479 of file rigid_bodies.h.

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

Public Member Functions

Static Public Member Functions

Related Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

Friends And Related Function Documentation