Functionality for dealing with kinematic mechanical structures. More...

Detailed Description

Functionality for dealing with kinematic mechanical structures.

Tools for handling the associated internal coordinates system are also provided.

Please note that this module is still at an experimental testing phase and should be used with caution.

Overview

This module provides a variety of functionality for defining and controlling kinematic structures (chains, trees and forests) over sets of rigid body particles. The IMP::kinematics::KinematicForest data structure provides the high-level interface to define the kinematic structure over a set of particles and to control their associated internal coordinates system. The basic building block of a kinematic structures is a kinematic joint (also known in the literature as a 'kinematic pair'), represented in the abstract class IMP::kinematics::Joint. A kinematic joint connects a pair of rigid bodies. See Wikipedia for some background theory about kinematic joints. The kinematics module supports differnt types of joints (prismatic / revolute / etc.) that differ in the constraints on the degrees of freedom of the joint. For instance, a prismatic joint or a slider (IMP::kinematics::PrismaticJoint) allows the two rigid bodies to slide along a shared axis among them (one degree of freedom), whereas a revolute joint (IMP::kinematics::RevoluteJoints) allows only rotation about the shared axis (one degree of freedom). The library also containes composite joints (IMP::kinematics::CompositeJoint) which allows composing several joints over the same pair of rigid bodies.

Conventions

The name "Joint" is used to refer to a kinematic pair between two rigid bodies.

rrt_sample

Sample protein conformations using rapidly exploring random tree (RRT).

For an example of using the rrt_sample command line tool, see the tutorial.

Info

Author(s): Dina Schneidman, Barak Raveh

Maintainer: duhovka, barakr

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Classes
class	BondAngleRevoluteJoint

class	CompositeJoint

class	DihedralAngleRevoluteJoint

class	DOF

class	DOFsSampler

class	Joint

class	KinematicForest

class	KinematicForestScoreState

class	KinematicNode

class	LocalPlanner

class	PathLocalPlanner

class	PrismaticJoint

class	ProteinKinematics

class	RevoluteJoint

class	RRT

class	TransformationJoint

class	UniformBackboneSampler

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < BondAngleRevoluteJoint > >	BondAngleRevolteJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < BondAngleRevoluteJoint > >	BondAngleRevolteJointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < CompositeJoint > >	CompositeJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < CompositeJoint > >	CompositeJointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < DihedralAngleRevoluteJoint > >	DihedralAngleRevoluteJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < DihedralAngleRevoluteJoint > >	DihedralAngleRevoluteJointsTemp

typedef IMP::base::Vector < DirectionalDOF >	DirectionalDOFs

typedef IMP::base::Vector < IMP::base::Pointer< DOF > >	DOFs

typedef IMP::base::Vector < IMP::base::Pointer < DOFsSampler > >	DOFsSamplers

typedef IMP::base::Vector < IMP::base::WeakPointer < DOFsSampler > >	DOFsSamplersTemp

typedef IMP::base::Vector < IMP::base::WeakPointer< DOF > >	DOFsTemp

typedef IMP::base::Vector < DOFValues >	DOFValuesList

typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS >	Graph

typedef IMP::base::Vector < IMP::base::Pointer< Joint > >	Joints

typedef IMP::base::Vector < IMP::base::WeakPointer < Joint > >	JointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < KinematicForest > >	KinematicForests

typedef IMP::base::Vector < IMP::base::WeakPointer < KinematicForest > >	KinematicForestsTemp

typedef IMP::base::Vector < KinematicNode >	KinematicNodes

typedef IMP::base::Vector < IMP::base::Pointer < LocalPlanner > >	LocalPlanners

typedef IMP::base::Vector < IMP::base::WeakPointer < LocalPlanner > >	LocalPlannersTemp

typedef IMP::base::Vector < IMP::base::Pointer < PathLocalPlanner > >	PathLocalPlanners

typedef IMP::base::Vector < IMP::base::WeakPointer < PathLocalPlanner > >	PathLocalPlannersTemp

typedef IMP::base::Vector < IMP::base::Pointer < PrismaticJoint > >	PrismaticJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < PrismaticJoint > >	PrismaticJointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < RevoluteJoint > >	RevoluteJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < RevoluteJoint > >	RevoluteJointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < TransformationJoint > >	TransformationJoints

typedef IMP::base::Vector < IMP::base::WeakPointer < TransformationJoint > >	TransformationJointsTemp

typedef IMP::base::Vector < IMP::base::Pointer < UniformBackboneSampler > >	UniformBackboneSamplers

typedef IMP::base::Vector < IMP::base::WeakPointer < UniformBackboneSampler > >	UniformBackboneSamplersTemp

Standard module functions
All `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< BondAngleRevoluteJoint > > IMP::kinematics::BondAngleRevolteJoints

Store a set of objects.

Definition at line 306 of file revolute_joints.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< BondAngleRevoluteJoint > > IMP::kinematics::BondAngleRevolteJointsTemp

Pass a set of objects.

See Also: BondAngleRevoluteJoint

Definition at line 307 of file revolute_joints.h.

typedef IMP::base::Vector<IMP::base::Pointer< CompositeJoint > > IMP::kinematics::CompositeJoints

Store a set of objects.

Definition at line 130 of file CompositeJoint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< CompositeJoint > > IMP::kinematics::CompositeJointsTemp

Pass a set of objects.

See Also: CompositeJoint

Definition at line 130 of file CompositeJoint.h.

typedef IMP::base::Vector<IMP::base::Pointer< DihedralAngleRevoluteJoint > > IMP::kinematics::DihedralAngleRevoluteJoints

Store a set of objects.

Definition at line 305 of file revolute_joints.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DihedralAngleRevoluteJoint > > IMP::kinematics::DihedralAngleRevoluteJointsTemp

Pass a set of objects.

See Also: DihedralAngleRevoluteJoint

Definition at line 306 of file revolute_joints.h.

typedef IMP::base::Vector< DirectionalDOF > IMP::kinematics::DirectionalDOFs

Pass or store a set of DirectionalDOF .

Definition at line 99 of file directional_DOFs.h.

typedef IMP::base::Vector<IMP::base::Pointer< DOF > > IMP::kinematics::DOFs

Store a set of objects.

Definition at line 70 of file DOF.h.

typedef IMP::base::Vector<IMP::base::Pointer< DOFsSampler > > IMP::kinematics::DOFsSamplers

Store a set of objects.

Definition at line 84 of file DOFsSampler.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DOFsSampler > > IMP::kinematics::DOFsSamplersTemp

Pass a set of objects.

See Also: DOFsSampler

Definition at line 84 of file DOFsSampler.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< DOF > > IMP::kinematics::DOFsTemp

Pass a set of objects.

See Also: DOF

Definition at line 70 of file DOF.h.

typedef IMP::base::Vector< DOFValues > IMP::kinematics::DOFValuesList

Pass or store a set of DOFValues .

Definition at line 87 of file DOFValues.h.

typedef IMP::base::Vector<IMP::base::Pointer< Joint > > IMP::kinematics::Joints

Store a set of objects.

Definition at line 130 of file Joint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Joint > > IMP::kinematics::JointsTemp

Pass a set of objects.

See Also: Joint

Definition at line 130 of file Joint.h.

typedef IMP::base::Vector<IMP::base::Pointer< KinematicForest > > IMP::kinematics::KinematicForests

Store a set of objects.

Definition at line 272 of file KinematicForest.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< KinematicForest > > IMP::kinematics::KinematicForestsTemp

Pass a set of objects.

See Also: KinematicForest

Definition at line 272 of file KinematicForest.h.

typedef IMP::base::Vector<IMP::base::Pointer< LocalPlanner > > IMP::kinematics::LocalPlanners

Store a set of objects.

Definition at line 83 of file local_planners.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< LocalPlanner > > IMP::kinematics::LocalPlannersTemp

Pass a set of objects.

See Also: LocalPlanner

Definition at line 83 of file local_planners.h.

typedef IMP::base::Vector<IMP::base::Pointer< PathLocalPlanner > > IMP::kinematics::PathLocalPlanners

Store a set of objects.

Definition at line 83 of file local_planners.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PathLocalPlanner > > IMP::kinematics::PathLocalPlannersTemp

Pass a set of objects.

See Also: PathLocalPlanner

Definition at line 84 of file local_planners.h.

typedef IMP::base::Vector<IMP::base::Pointer< PrismaticJoint > > IMP::kinematics::PrismaticJoints

Store a set of objects.

Definition at line 85 of file PrismaticJoint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< PrismaticJoint > > IMP::kinematics::PrismaticJointsTemp

Pass a set of objects.

See Also: PrismaticJoint

Definition at line 85 of file PrismaticJoint.h.

typedef IMP::base::Vector<IMP::base::Pointer< RevoluteJoint > > IMP::kinematics::RevoluteJoints

Store a set of objects.

Definition at line 305 of file revolute_joints.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< RevoluteJoint > > IMP::kinematics::RevoluteJointsTemp

Pass a set of objects.

See Also: RevoluteJoint

Definition at line 305 of file revolute_joints.h.

typedef IMP::base::Vector<IMP::base::Pointer< TransformationJoint > > IMP::kinematics::TransformationJoints

Store a set of objects.

Definition at line 44 of file TransformationJoint.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TransformationJoint > > IMP::kinematics::TransformationJointsTemp

Pass a set of objects.

See Also: TransformationJoint

Definition at line 44 of file TransformationJoint.h.

typedef IMP::base::Vector<IMP::base::Pointer< UniformBackboneSampler > > IMP::kinematics::UniformBackboneSamplers

Store a set of objects.

Definition at line 49 of file UniformBackboneSampler.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< UniformBackboneSampler > > IMP::kinematics::UniformBackboneSamplersTemp

Pass a set of objects.

See Also: UniformBackboneSampler

Definition at line 49 of file UniformBackboneSampler.h.

Function Documentation

std::string IMP::kinematics::get_data_path ( std::string file_name )

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

std::string IMP::kinematics::get_example_path ( std::string file_name )

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",

model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

Detailed Description

Overview

Conventions

rrt_sample

Info

Classes

Typedefs

Standard module functions

Typedef Documentation

Function Documentation