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IMP Reference Guide  develop.d247202c1c,2019/10/23
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:

Detailed Description

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_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).

The rigid body radius is the farthest point of any of its members from the origin of its reference frame. For rigid body members, this takes into account the radius of the member.

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 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 create 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 fragment 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 import sys
9 
10 IMP.setup_from_argv(sys.argv, "randomize rigid body")
11 
12 m = IMP.Model()
13 p = IMP.Particle(m)
16  IMP.algebra.get_unit_bounding_box_3d())
17 
18 # we don't yet have python code to generate a nearby rotation
20 transformation = IMP.algebra.Transformation3D(rotation, translation)
21 # Option 1:
22 # note, this overwrites the existing position
23 rbd.set_reference_frame(IMP.algebra.ReferenceFrame3D(transformation))
24 # Option 2:
25 # perturb the existing transformation
26 composed_tr = IMP.algebra.compose \
27  (rbd.get_reference_frame().get_transformation_to(),
28  transformation)
29 rbd.set_reference_frame(IMP.algebra.ReferenceFrame3D(composed_tr))
30 # Alternative to Option 2:
31 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
NonRigidMember
RigidBodyMover
RigidClosePairsFinder
RigidBodyDistancePairScore

Definition at line 82 of file rigid_bodies.h.

Public Member Functions

 RigidBody (::IMP::Model *m,::IMP::ParticleIndex id)
 
 RigidBody (const IMP::ParticleAdaptor &d)
 
void add_member (ParticleIndexAdaptor p)
 
void add_non_rigid_member (ParticleIndexAdaptor p)
 
void add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &local_location, DerivativeAccumulator &da)
 
void add_to_derivatives (const algebra::Vector3D &local_derivative, const algebra::Vector3D &global_derivative, const algebra::Vector3D &local_location, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)
 
void add_to_rotational_derivatives (const algebra::Vector4D &other_qderiv, const algebra::Rotation3D &rot_other_to_local, const algebra::Rotation3D &rot_local_to_global, DerivativeAccumulator &da)
 
void add_to_rotational_derivatives (const algebra::Vector4D &qderiv, DerivativeAccumulator &da)
 
void add_to_torque (const algebra::Vector3D &torque_local, DerivativeAccumulator &da)
 
const ParticleIndexesget_body_member_particle_indexes () const
 
algebra::Vector3D get_coordinates () const
 
bool get_coordinates_are_optimized () const
 
ParticleIndexes get_member_indexes () const
 
const ParticleIndexesget_member_particle_indexes () const
 
IMP::algebra::ReferenceFrame3D get_reference_frame () const
 
RigidMembers get_rigid_members () const
 
IMP::algebra::Rotation3D get_rotation () const
 
algebra::VectorD< 4 > get_rotational_derivatives () const
 Get the derivatives of the quaternion. More...
 
algebra::Vector3D get_torque () const
 
void normalize_rotation ()
 Normalize the quaternion. More...
 
void pull_back_body_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
 Pull back global adjoints from member that is also a rigid body. More...
 
void pull_back_body_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &TA, algebra::Transformation3D &TB, algebra::Transformation3DAdjoint &DTC, algebra::Transformation3DAdjoint &DTA, algebra::Transformation3DAdjoint &DTB, algebra::Vector3D &betatorque, DerivativeAccumulator &da)
 
void pull_back_member_adjoints (ParticleIndex pi, DerivativeAccumulator &da)
 Pull back global adjoints from member that is a point. More...
 
void pull_back_member_adjoints (ParticleIndex pi, const algebra::Transformation3D &T, algebra::Vector3D &x, algebra::Vector3D &Dy, algebra::Vector3D &Dx, algebra::Transformation3DAdjoint &DT, algebra::Vector3D &xtorque, DerivativeAccumulator &da)
 
void pull_back_members_adjoints (DerivativeAccumulator &da)
 Pull back global adjoints from members. More...
 
void set_coordinates_are_optimized (bool tf)
 
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 ()
 
- Public Member Functions inherited from IMP::core::XYZ
 XYZ (::IMP::Model *m,::IMP::ParticleIndex id)
 
 XYZ (const IMP::ParticleAdaptor &d)
 
void add_to_derivative (int i, Float v, DerivativeAccumulator &d)
 
void add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d)
 Add the vector v to the derivative vector of the x,y,z coordinates. More...
 
Float get_coordinate (int i) const
 Get the ith coordinate. More...
 
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
 
algebra::Vector3D get_derivatives () const
 Get the vector of derivatives accumulated by add_to_derivatives(). More...
 
algebra::Vector3D get_vector_to (const XYZ &b) const
 Get the vector from this particle to another. More...
 
Float get_x () const
 
Float get_y () const
 
Float get_z () const
 
void set_coordinate (unsigned int i, Float v)
 set the ith coordinate More...
 
void set_coordinates (const algebra::Vector3D &v)
 set all coordinates from a vector More...
 
void set_coordinates_are_optimized (bool tf) const
 Set whether the coordinates are optimized. More...
 
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::Decorator
bool get_is_valid () const
 Returns true if constructed with a non-default constructor. More...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_particle () const
 Returns the particle decorated by this decorator. More...
 
ParticleIndex get_particle_index () const
 Returns the particle index decorated by this decorator. More...
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particleoperator-> () const
 

Static Public Member Functions

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

Additional Inherited Members

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

Member Function Documentation

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

Add a proper member that moves rigidly with this rigid body, properly handling rigid bodies and XYZ particles. Add p to the list of members. If p is a valid RigidBody, it is added as a rigid body member, otherwise it is added as a point member (for which the rotation is not tracked). By default, p is considered a strictly rigid member, in that its local coordinates are not expected to change independently.

The radius of the rigid body is updated to reflect the new member.

See Also
add_non_rigid_member
void IMP::core::RigidBody::add_non_rigid_member ( ParticleIndexAdaptor  p)

Add a non-rigid member, for which internal coordinates may change independently.

Note
Currently RigidBody non-rigid members are not handled properly.
void IMP::core::RigidBody::add_to_derivatives ( const algebra::Vector3D local_derivative,
const algebra::Vector3D local_location,
DerivativeAccumulator da 
)

Update the translational and rotational derivatives on the rigid body center of mass, using the Cartesian derivative vector at a speicified location (the point where the force is being applied).

Updates both the quaternion derivatives and the torque.

Parameters
local_derivativeThe derivative vector in local rigid body coordinates
local_locationThe location where the derivative is taken in local rigid body coordinates
daAccumulates the output derivative over the rigid body center of mass (translation and rotation torque, quaternion)
void IMP::core::RigidBody::add_to_derivatives ( const algebra::Vector3D local_derivative,
const algebra::Vector3D global_derivative,
const algebra::Vector3D local_location,
const algebra::Rotation3D rot_local_to_global,
DerivativeAccumulator da 
)

Faster version of the above, if all is cached.

Parameters
local_derivativeThe derivative vector in local rigid body coordinates
global_derivativeThe derivative vector in global coordinates
local_locationThe location where the derivative is taken in local rigid body coordinates
rot_local_to_globalRotation matrix from local rigid body to global coordinates
daAccumulates the output derivative over the rigid body center of mass (translation and rotation torque, quaternion)
void IMP::core::RigidBody::add_to_rotational_derivatives ( const algebra::Vector4D other_qderiv,
const algebra::Rotation3D rot_other_to_local,
const algebra::Rotation3D rot_local_to_global,
DerivativeAccumulator da 
)

Update the rotational derivatives from another body specified by the rotation from the other body's local coordinates to this body's local coordinates. The provided quaternion derivative on the other body are in the reference frame of the other body.

Updates only quaternion derivatives.

Parameters
other_qderivThe derivative on the quaternion taking the other body's local coordinates to global.
rot_other_to_localRotation taking the local coordinates of the other body to this body's local coordinates.
rot_local_to_globalRotation taking this rigid body's local coordinates to global coordinates.
daAccumulates the output derivatives.
void IMP::core::RigidBody::add_to_rotational_derivatives ( const algebra::Vector4D qderiv,
DerivativeAccumulator da 
)

Add to quaternion derivative of this rigid body Note that this method does not update the torque.

Parameters
qderivDerivative wrt to quaternion taking local coordinates to global.
daObject for accumulating derivatives
void IMP::core::RigidBody::add_to_torque ( const algebra::Vector3D torque_local,
DerivativeAccumulator da 
)

Add torque to derivative table of this rigid body Note that this method does not update the quaternion derivatives, so should be used by optimizers that rely on torque only (e.g. BrownianDynamics)

Parameters
torque_localTorque vector in local reference frame, in units of kCal/Mol/Radian
daObject for accumulating derivatives
const ParticleIndexes& IMP::core::RigidBody::get_body_member_particle_indexes ( ) const

Get all members that are themselves decorated as rigid bodies, as model particle indexes

Definition at line 146 of file rigid_bodies.h.

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

Get the coordinates of the particle (= translation from local to global rigid body coordinates)

Definition at line 196 of file rigid_bodies.h.

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bool IMP::core::RigidBody::get_coordinates_are_optimized ( ) const

Returns true if the rigid body coordinates are flagged as optimized for Optimizer objects

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

Return true if the particle is a rigid body.

Definition at line 189 of file rigid_bodies.h.

ParticleIndexes IMP::core::RigidBody::get_member_indexes ( ) const

Get the particle indexes of any member of this rigid body, regardless of whether it is itself a rigid body or not

Definition at line 159 of file rigid_bodies.h.

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

Returns a list of all members that are not themselves decorated as rigid bodies, in the form of particle indexes.

Definition at line 133 of file rigid_bodies.h.

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IMP::algebra::ReferenceFrame3D IMP::core::RigidBody::get_reference_frame ( ) const

Get the reference frame of this rigid body, which enables trnasformation between the local rigid body coordinates global coordinates

Definition at line 207 of file rigid_bodies.h.

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IMP::algebra::Rotation3D IMP::core::RigidBody::get_rotation ( ) const

returns the rotation of the particle (= rotation from local to global rigid body orientation)

Definition at line 200 of file rigid_bodies.h.

static FloatKeys IMP::core::RigidBody::get_rotation_keys ( )
static

Get keys for rotation quaternion.

Definition at line 127 of file rigid_bodies.h.

algebra::VectorD<4> IMP::core::RigidBody::get_rotational_derivatives ( ) const

Get the derivatives of the quaternion.

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

The units are kCal/Mol/Radian

Definition at line 470 of file rigid_bodies.h.

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void IMP::core::RigidBody::normalize_rotation ( )

Normalize the quaternion.

void IMP::core::RigidBody::pull_back_body_member_adjoints ( ParticleIndex  pi,
DerivativeAccumulator da 
)

Pull back global adjoints from member that is also a rigid body.

Parameters
piindex of member particle
daaccumulator for the adjoints
void IMP::core::RigidBody::pull_back_body_member_adjoints ( ParticleIndex  pi,
const algebra::Transformation3D TA,
algebra::Transformation3D TB,
algebra::Transformation3DAdjoint &  DTC,
algebra::Transformation3DAdjoint &  DTA,
algebra::Transformation3DAdjoint &  DTB,
algebra::Vector3D betatorque,
DerivativeAccumulator da 
)

Same as above, but uses fewer allocations.

Parameters
piindex of member particle
TAtransformation from this body's local coordinates to global
TBtransformation from member's local coordinates to this body's local coordinates
DTCadjoint on composition of TA and TB, which is the transformation from the member's local coordinates to global
DTAadjoint on TA
DTBadjoint on TB
betatorquetorque contribution from DTC in local coordinates at beta, the position of the member in local coordinates.
daaccumulator for the adjoints
void IMP::core::RigidBody::pull_back_member_adjoints ( ParticleIndex  pi,
DerivativeAccumulator da 
)

Pull back global adjoints from member that is a point.

Parameters
piindex of member particle
daaccumulator for the adjoints
void IMP::core::RigidBody::pull_back_member_adjoints ( ParticleIndex  pi,
const algebra::Transformation3D T,
algebra::Vector3D x,
algebra::Vector3D Dy,
algebra::Vector3D Dx,
algebra::Transformation3DAdjoint &  DT,
algebra::Vector3D xtorque,
DerivativeAccumulator da 
)

Same as above, but uses fewer allocations.

Parameters
piindex of member particle
Ttransformation from this body's local coordinates to global
xlocal coordinates of the member
Dyadjoint on the member's global coordinates
Dxadjoint on the member's local coordinates
DTadjoint on the transformation
xtorquetorque contribution from Dy in local coordinates
daaccumulator for the adjoints
void IMP::core::RigidBody::pull_back_members_adjoints ( DerivativeAccumulator da)

Pull back global adjoints from members.

Adjoints (reverse-mode sensitivities) are partial derivatives of the score with respect to intermediate values in the scoring function computation, such as the global coordinates of a bead within a rigid body or the global reference frame of a nested rigid body.

This function pulls back (back-propagates) global adjoints and local torque on all members to the global rotation, global coordinates, and local torque on this rigid body and the internal coordinates and rotation of any non-rigid members.

This is called by an internal score state after scoring function evaluation and is not meant to be called by the user.

void IMP::core::RigidBody::set_coordinates_are_optimized ( bool  tf)

Set whether the rigid body coordinates are flagged as optimized for Optimizer objects

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

Set whether a particular member is flagged as a rigid member or as a non-rigid member. This affects the way the rigid body updates the coordinates and / or reference frame of its members.

The radius of the rigid body is updated to reflect this change.

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.

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

Update the reference frame of the rigid body based on aligning the current global coordinates of the passed rigid body members onto their old local coordinates. Non-passed members are ignored.

This method is useful for updating the rigid body after new global coordinates were loaded for the members. The members are passed explicitly 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 colinear to work.
void IMP::core::RigidBody::set_reference_frame_lazy ( const IMP::algebra::ReferenceFrame3D tr)

Change the reference, delay updating the members until evaluate.

See Also
set_reference_frame()

Definition at line 242 of file rigid_bodies.h.

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static RigidBody IMP::core::RigidBody::setup_particle ( IMP::ParticleAdaptor  decorator,
ParticleIndexesAdaptor  ps 
)
static
See Also
setup_particle(m, pi, ps )

Definition at line 174 of file rigid_bodies.h.

static RigidBody IMP::core::RigidBody::setup_particle ( Model m,
ParticleIndex  pi,
ParticleIndexesAdaptor  ps 
)
static

Create a rigid body for pi with the particle indexes ps as its members. The coordinates of pi are set to the center of mass of ps and the rotation of its reference frame is based on the diagonalized inertia tensor of ps.

Note
If size(ps)=1, then its reference frame is copied if it is a rigid body, or its rotation is set to identity if it is not a rigid body.Setup the particle so that it can be used with this decorator

Definition at line 174 of file rigid_bodies.h.

static RigidBody IMP::core::RigidBody::setup_particle ( IMP::ParticleAdaptor  decorator,
algebra::ReferenceFrame3D  rf 
)
static
See Also
setup_particle(m, pi, rf )

Definition at line 180 of file rigid_bodies.h.

static RigidBody IMP::core::RigidBody::setup_particle ( 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 that it can be used with this decorator

Definition at line 180 of file rigid_bodies.h.

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 global coordinates of the members based on their local coordinates and this rigid body's reference frame


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