IMP Reference Guide
develop.5ce362c3b9,2024/09/13
The Integrative Modeling Platform

Define and manipulate a kinematic structure over a model. More...
#include <IMP/kinematics/KinematicForest.h>
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.
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 () 
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
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
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)
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.
Joints IMP::kinematics::KinematicForest::get_ordered_joints  (  )  const 
return joints sorted by BFS traversal
Definition at line 143 of file KinematicForest.h.

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
rb  a rigid body that was previously added to the tree 
c  new coordinates 
Definition at line 203 of file KinematicForest.h.
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
rb  a rigid body that was previously added to the tree 
r  new reference frame 
Definition at line 251 of file KinematicForest.h.
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.
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.
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.