Detailed Description

A decorator for a particle that is part of a rigid body but not rigid.

NonRigidMembers, like RigidMembers, have internal coordinates and move along with the rigid body. However, it is expected that their internal coordinates will change, and so they are not part of structures that assume rigidity.

See Also: RigidBody

Definition at line 768 of file rigid_bodies.h.

Public Member Functions
	NonRigidMember (::IMP::Model *m,::IMP::ParticleIndex id)

	NonRigidMember (const IMP::ParticleAdaptor &d)

	NonRigidMember (const NonRigidMember &)=default

void	add_to_internal_derivatives (const algebra::Vector3D &deriv_parent, DerivativeAccumulator &da)
	Add to derivatives of local coordinates. More...

void	add_to_internal_rotational_derivatives (const algebra::Vector4D &local_qderiv, const algebra::Rotation3D &rot_local_to_parent, const algebra::Rotation3D &rot_parent_to_global, DerivativeAccumulator &da)

void	add_to_internal_rotational_derivatives (const algebra::Vector4D &qderiv, DerivativeAccumulator &da)

algebra::Vector3D	get_internal_derivatives () const
	Get derivatives wrt translation component of internal transformation. More...

algebra::Vector4D	get_internal_rotational_derivatives () const
	Get derivatives wrt quaternion component of internal transformation. More...

NonRigidMember &	operator= (const NonRigidMember &)=default

void	show (std::ostream &out=std::cout) const

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

	RigidBodyMember (const IMP::ParticleAdaptor &d)

	RigidBodyMember (const RigidBodyMember &)=default

const algebra::Vector3D &	get_internal_coordinates () const
	Return the internal (local) coordinates of this member. More...

algebra::Transformation3D	get_internal_transformation () const

RigidBody	get_rigid_body () const

RigidBodyMember &	operator= (const RigidBodyMember &)=default

void	set_coordinates (const algebra::Vector3D &center)
	sets the global coordinates of this member using XYZ::set_coordinates() More...

void	set_internal_coordinates (const algebra::Vector3D &v) const
	set the internal (local) coordinates for this member More...

void	set_internal_transformation (const algebra::Transformation3D &v)

void	show (std::ostream &out=std::cout) const

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::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

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...

Model *	get_model () const
	Returns the Model containing the particle. More...

Particle *	get_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

Particle *	operator-> () const

Static Public Member Functions
static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndex p)
	return true if it is a rigid member More...

Static Public Member Functions inherited from IMP::core::RigidBodyMember
static FloatKeys	get_internal_coordinate_keys ()

static FloatKeys	get_internal_rotation_keys ()

static bool	get_is_setup (const IMP::ParticleAdaptor &p)

static bool	get_is_setup (Model *m, ParticleIndexAdaptor p)
	return true if it is a rigid member 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 FloatKeys &	get_xyz_keys ()
	Get a vector containing the keys for x,y,z. More...

static XYZ	setup_particle (IMP::ParticleAdaptor pa)

static XYZ	setup_particle (Model *m, ParticleIndex pi)

static XYZ	setup_particle (IMP::ParticleAdaptor pa, 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::NonRigidMember::add_to_internal_derivatives	(	const algebra::Vector3D &	deriv_parent,
		DerivativeAccumulator &	da
	)

Add to derivatives of local coordinates.

Parameters

deriv_parent	The derivative vector in local coordinates of the parent rigid body.
da	Accumulates the derivative over the local translation.

Definition at line 784 of file rigid_bodies.h.

Here is the call graph for this function:

void IMP::core::NonRigidMember::add_to_internal_rotational_derivatives	(	const algebra::Vector4D &	local_qderiv,
		const algebra::Rotation3D &	rot_local_to_parent,
		const algebra::Rotation3D &	rot_parent_to_global,
		DerivativeAccumulator &	da
	)

Update the rotational derivatives of the internal transformation.

Updates only local quaternion derivatives.

Parameters

local_qderiv	The derivative on the quaternion taking this non-rigid body's local coordinates to global.
rot_local_to_parent	Rotation taking the local coordinates of the non-rigid body to its parent's.
rot_parent_to_global	Rotation taking the parent rigid body's local coordinates to global coordinates.
da	Accumulates the output derivatives.

void IMP::core::NonRigidMember::add_to_internal_rotational_derivatives	(	const algebra::Vector4D &	qderiv,
		DerivativeAccumulator &	da
	)

Add to internal quaternion derivatives of this non-rigid body

Parameters

qderiv	Derivative wrt to quaternion taking local coordinates to parent.
da	Object for accumulating derivatives

Definition at line 817 of file rigid_bodies.h.

Here is the call graph for this function:

algebra::Vector3D IMP::core::NonRigidMember::get_internal_derivatives ( ) const

Get derivatives wrt translation component of internal transformation.

Definition at line 832 of file rigid_bodies.h.

Here is the call graph for this function:

algebra::Vector4D IMP::core::NonRigidMember::get_internal_rotational_derivatives ( ) const

Get derivatives wrt quaternion component of internal transformation.

Definition at line 842 of file rigid_bodies.h.

Here is the call graph for this function:

static bool IMP::core::NonRigidMember::get_is_setup	(	Model *	m,
		ParticleIndex	p
	)

static

return true if it is a rigid member

Definition at line 775 of file rigid_bodies.h.

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

rigid_bodies.h

Detailed Description

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Member Function Documentation