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 different 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 contains 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).

rrt_ccd

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

rmsd_cluster

RMSD based clustering of conformations

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

Info

Author(s): Dina Schneidman, Barak Raveh, Yannick Spill

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
	Joint that is parameterized as a bond angle between three particles. More...

class	CCDLoopClosure
	CCD loop closure. More...

class	CompositeJoint
	Joint that combines several inner joints, acting on the same rigid body pair. More...

class	DihedralAngleRevoluteJoint
	Joint that is parameterized as a dihedral angle between two planes. More...

class	DihedralMover
	Modify a set of joints using a normal distribution. More...

class	DirectionalDOF

class	DOF
	Representation of one degree of freedom (DOF). More...

class	DOFsSampler
	Base class for sampling certain combinations of degrees of freedom. More...

class	DOFValues
	A class that holds DOF values for DOFs. More...

class	FibrilSampler
	Simultaneous sampling of diheral angles and fibril symmetry operations. More...

class	Joint
	Base class for joints between rigid bodies in a kinematic tree. More...

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

class	KinematicForestScoreState

class	KinematicNode
	A rigid body that is connected by a joint to other rigid bodies. More...

class	LocalPlanner

class	PathLocalPlanner
	Local planner that samples conformations on a path between two nodes. More...

class	PrismaticJoint
	Joint in which two rigid bodies may slide along a line. More...

class	ProteinKinematics

class	RevoluteJoint
	Abstract class for all revolute joints. More...

class	RevoluteJointMover
	Modify a set of joints using a normal distribution. More...

class	RRT
	Simple implementation of the Rapidly-exploring Random Trees algorithm. More...

class	TransformationJoint

class	UniformBackboneSampler
	Sample uniformly over a set of backbone dihedral joints. More...

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

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

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

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

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

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

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

typedef IMP::Vector < IMP::WeakPointer < DirectionalDOF > >	DirectionalDOFsTemp

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

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

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

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

typedef IMP::Vector< DOFValues >	DOFValuesList

typedef IMP::Vector < IMP::Pointer< FibrilSampler > >	FibrilSamplers

typedef IMP::Vector < IMP::WeakPointer < FibrilSampler > >	FibrilSamplersTemp

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

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

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

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

typedef IMP::Vector < KinematicNode >	KinematicNodes

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

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

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

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

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

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

typedef IMP::Vector < IMP::Pointer < ProteinKinematics > >	ProteinKinematicsList

typedef IMP::Vector < IMP::WeakPointer < ProteinKinematics > >	ProteinKinematicsListTemp

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

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

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

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

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

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

Enumerations
enum	ProteinAngleType { PHI, PSI, CHI, CHI1, CHI2, CHI3, CHI4, CHI5, OTHER, OTHER2, OTHER3, OTHER4, OTHER5, TOTAL }

Functions
void	add_missing_bonds (IMP::ParticlesTemp &atoms, IMP::ParticlesTemp &bonds)

IMP::atom::Bond	create_bond (IMP::atom::Atoms &as)

IMP::atom::Atom	find_atom (const IMP::ParticlesTemp &atoms, int input_index)

IMP::atom::Residue	find_residue (const IMP::ParticlesTemp &residues, int res_index, std::string chain)

IMP::atom::Atom	get_ca_atom (const IMP::ParticlesTemp &atoms, int residue_index, std::string chain_id)

void	read_angle_file (const std::string &file_name, const IMP::ParticlesTemp &residues, const IMP::ParticlesTemp &atoms, IMP::atom::Residues &flexible_residues, std::vector< IMP::atom::Atoms > &dihedral_angles, std::vector< double > &range)

void	read_connect_chains_file (const std::string &file_name, const IMP::ParticlesTemp &atoms, std::vector< IMP::atom::Atoms > &connect_atoms)

unsigned int	rmsd_clustering (const std::vector< IMP::algebra::Vector3Ds > &coords_vec, std::vector< int > &out_cluster_numbers, float rmsd_thr, bool compute_trans)

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 ()
	Return the version of this module, as a string. More...

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...

std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Typedef Documentation

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

A vector of reference-counting object pointers.

Definition at line 308 of file revolute_joints.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: BondAngleRevoluteJoint

Definition at line 309 of file revolute_joints.h.

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

A vector of reference-counting object pointers.

Definition at line 117 of file CompositeJoint.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: CompositeJoint

Definition at line 117 of file CompositeJoint.h.

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

A vector of reference-counting object pointers.

Definition at line 307 of file revolute_joints.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: DihedralAngleRevoluteJoint

Definition at line 308 of file revolute_joints.h.

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

A vector of reference-counting object pointers.

Definition at line 97 of file directional_DOFs.h.

typedef IMP::Vector<IMP::WeakPointer< DirectionalDOF > > IMP::kinematics::DirectionalDOFsTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: DirectionalDOF

Definition at line 97 of file directional_DOFs.h.

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

A vector of reference-counting object pointers.

Definition at line 71 of file DOF.h.

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

A vector of reference-counting object pointers.

Definition at line 79 of file DOFsSampler.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: DOFsSampler

Definition at line 79 of file DOFsSampler.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: DOF

Definition at line 71 of file DOF.h.

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

Pass or store a set of DOFValues .

Definition at line 95 of file DOFValues.h.

typedef IMP::Vector<IMP::Pointer< FibrilSampler > > IMP::kinematics::FibrilSamplers

A vector of reference-counting object pointers.

Definition at line 55 of file FibrilSampler.h.

typedef IMP::Vector<IMP::WeakPointer< FibrilSampler > > IMP::kinematics::FibrilSamplersTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: FibrilSampler

Definition at line 55 of file FibrilSampler.h.

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

A vector of reference-counting object pointers.

Definition at line 125 of file Joint.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: Joint

Definition at line 125 of file Joint.h.

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

A vector of reference-counting object pointers.

Definition at line 303 of file KinematicForest.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: KinematicForest

Definition at line 303 of file KinematicForest.h.

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

A vector of reference-counting object pointers.

Definition at line 80 of file local_planners.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: LocalPlanner

Definition at line 80 of file local_planners.h.

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

A vector of reference-counting object pointers.

Definition at line 80 of file local_planners.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: PathLocalPlanner

Definition at line 81 of file local_planners.h.

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

A vector of reference-counting object pointers.

Definition at line 80 of file PrismaticJoint.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: PrismaticJoint

Definition at line 80 of file PrismaticJoint.h.

typedef IMP::Vector<IMP::Pointer< ProteinKinematics > > IMP::kinematics::ProteinKinematicsList

A vector of reference-counting object pointers.

Definition at line 356 of file ProteinKinematics.h.

typedef IMP::Vector<IMP::WeakPointer< ProteinKinematics > > IMP::kinematics::ProteinKinematicsListTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: ProteinKinematics

Definition at line 356 of file ProteinKinematics.h.

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

A vector of reference-counting object pointers.

Definition at line 307 of file revolute_joints.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: RevoluteJoint

Definition at line 307 of file revolute_joints.h.

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

A vector of reference-counting object pointers.

Definition at line 44 of file TransformationJoint.h.

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

A vector of weak (non reference-counting) pointers to specified objects.

See Also: TransformationJoint

Definition at line 44 of file TransformationJoint.h.

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

A vector of reference-counting object pointers.

Definition at line 49 of file UniformBackboneSampler.h.

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

A vector of weak (non reference-counting) pointers to specified 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 one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

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

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

Note: Each module has its own data directory, so be sure to use this function from the correct module.

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

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::kinematics::get_example_path("example_protein.pdb"));

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

Note: Each module has its own example directory, so be sure to use this function from the correct module.

std::string IMP::kinematics::get_module_version ( )

Return the version of this module, as a string.

Note: This function is only available in Python.

Definition at line 5 of file EMageFit/__init__.py.

Detailed Description

Overview

Conventions

rrt_sample

rrt_ccd

rmsd_cluster

Info

Classes

Typedefs

Enumerations

Functions

Standard module functions

Typedef Documentation

Function Documentation