Define and manipulate a kinematic structure over a model. More...

#include <IMP/kinematics/KinematicForest.h>

Inheritance diagram for IMP::kinematics::KinematicForest:

Detailed Description

Define and manipulate a kinematic structure over a model.

The kinematic structure is defined as a forest over model particles at a certain hierarchy, such that a directed edge indicates the propagation of changes in internal coordinates (joint values) to values of external (Cartesian) coordinates.

See Also: Joint

Definition at line 39 of file KinematicForest.h.

Public Member Functions
	KinematicForest (Model *m)

	KinematicForest (Model *m, IMP::atom::Hierarchy hierarchy)

Joint *	add_edge (IMP::core::RigidBody parent, IMP::core::RigidBody child)

void	add_edge (Joint *joint)

void	add_rigid_bodies_in_chain (IMP::core::RigidBodies rbs)

void	apply_transform_safely (IMP::algebra::Transformation3D tr)
	apply a rigid body transformation to the entire forest safely More...

IMP::algebra::Vector3D	get_coordinates_safe (IMP::core::RigidBody rb) const

bool	get_is_member (IMP::core::RigidBody rb) const

Joints	get_ordered_joints () const
	return joints sorted by BFS traversal More...

IMP::algebra::ReferenceFrame3D	get_reference_frame_safe (IMP::core::RigidBody rb) const

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...

void	mark_external_coordinates_changed ()

void	mark_internal_coordinates_changed ()

void	reset_root (IMP::Particle *new_root)
	rebuild tree (same topology but change directionality) More...

void	set_coordinates_safe (IMP::core::RigidBody rb, IMP::algebra::Vector3D c)

void	set_reference_frame_safe (IMP::core::RigidBody rb, IMP::algebra::ReferenceFrame3D r)

void	transform_safe (IMP::algebra::Transformation3D tr)

void	update_all_external_coordinates ()

void	update_all_internal_coordinates ()

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

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

const std::string &	get_name () const

void	set_name (std::string name)

Friends
std::ostream &	operator<< (std::ostream &s, const KinematicForest &kt)

Additional Inherited Members
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::kinematics::KinematicForest::KinematicForest	(	Model *	m,
		IMP::atom::Hierarchy	hierarchy
	)

Builds a kinematic forest automatically from a hierarchy that contains rigid bodies and adds a ScoreState to the model, to make sure the internal and external coordinates are synced before model updating

Member Function Documentation

Joint* IMP::kinematics::KinematicForest::add_edge	(	IMP::core::RigidBody	parent,
		IMP::core::RigidBody	child
	)

Adds a kinematic edge between parent and child, using a TransformationJoint between them, and decorating them as KinematicNodes if needed.

Definition at line 63 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::add_edge ( Joint * joint )

Adds a kinematic edge between the joint parent and child rigid bodies, decorating them as KinematicNodes if needed. The joint becomes owned by this KinematicForest, such that changes to the joint are synchronized with the KinematicForest

Note: it is assumed that neither the joint or the rigid bodies in it were previously added to a kinematic forest (might change in future IMP versions)

void IMP::kinematics::KinematicForest::add_rigid_bodies_in_chain ( IMP::core::RigidBodies rbs )

adds edges between each pair of consecutive rigid bodies in the list rbs, using default TransformationJoint joints (transforming from one rigid body to the next)

Parameters

rbs	list of n consecutive rigid bodies

Definition at line 89 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::apply_transform_safely ( IMP::algebra::Transformation3D tr )

apply a rigid body transformation to the entire forest safely

Apply a rigid body transformation to the entire forest safely, such that the forest will return correct external and internal coordinates if queries through get_coordinates_safe() or get_reference_frame_safe(), or after updating with update_all_external_coordinates() or update_all_internal_coordinates(), respectively.

Definition at line 268 of file KinematicForest.h.

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Joints IMP::kinematics::KinematicForest::get_ordered_joints ( ) const

return joints sorted by BFS traversal

Definition at line 143 of file KinematicForest.h.

virtual ::IMP::VersionInfo IMP::kinematics::KinematicForest::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 43 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::mark_external_coordinates_changed ( )

notifies the tree that external Cartesian coordinates have changed and therefore internal (joint) coordinates are not up to date

Definition at line 191 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::mark_internal_coordinates_changed ( )

notifies the tree that joint (internal) coordinates have changed and therefore external coordinates are not up to date

Definition at line 182 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::reset_root ( IMP::Particle * new_root )

rebuild tree (same topology but change directionality)

Definition at line 96 of file KinematicForest.h.

void IMP::kinematics::KinematicForest::set_coordinates_safe	(	IMP::core::RigidBody	rb,
		IMP::algebra::Vector3D	c
	)

sets the coordinates of a particle, and makes sure that particles and joints in the tree will return correct external and internal coordinates

Parameters

rb	a rigid body that was previously added to the tree
c	new coordinates

Definition at line 203 of file KinematicForest.h.

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void IMP::kinematics::KinematicForest::set_reference_frame_safe	(	IMP::core::RigidBody	rb,
		IMP::algebra::ReferenceFrame3D	r
	)

sets the reference frame of a rigid body, and makes sure that particles and joints in the tree will return correct internal coordinates when queried directly through the KinematicForest

Parameters

rb	a rigid body that was previously added to the tree
r	new reference frame

Definition at line 251 of file KinematicForest.h.

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void IMP::kinematics::KinematicForest::transform_safe ( IMP::algebra::Transformation3D tr )

apply a rigid body transformation to the entire forest safelt, such that the forest will return correct external and internal coordinates if queries through get_coordinates_safe() or get_reference_frame_safe(), or after updating with update_all_external_coordinates() or update_all_internal_coordinates(), respectively.

Definition at line 170 of file KinematicForest.h.

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void IMP::kinematics::KinematicForest::update_all_external_coordinates ( )

update all external coordinates of particles in the forest based on their internal coordinates

Definition at line 118 of file KinematicForest.h.

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void IMP::kinematics::KinematicForest::update_all_internal_coordinates ( )

updated internal coordinates in the forest based on the current cartesian coordinates and the architecture of joints in the tree

Definition at line 104 of file KinematicForest.h.

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

KinematicForest.h

Detailed Description

Public Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation