Namespaces | Classes | Typedefs | Variables
protocols::kinematic_closure Namespace Reference

Implementation of the kinematic closure algorithm for sampling protein backbone conformations. More...


 Algorithms for sampling new backbone torsions.
 Algorithms for choosing pivot residues.
 Algorithms for picking one of the 0 to 16 solutions generated by kinematic closure.


class  BalancedKicMover
 Make a kinematic closure move that obeys detailed balance. More...
class  BalancedKicMoverCreator
class  ClosureProblem
 Represent and solve a kinematic closure problem. More...
class  ClosureSolution
 Represent a single solution to a kinematic closure problem. More...
class  KicMover
 Find a new backbone conformation for some region of a protein. More...
class  KicMoverCreator


typedef utility::pointer::shared_ptr< BalancedKicMoverBalancedKicMoverOP
typedef utility::pointer::shared_ptr< BalancedKicMover const > BalancedKicMoverCOP
typedef utility::pointer::shared_ptr< ClosureProblemClosureProblemOP
typedef utility::pointer::shared_ptr< ClosureProblem const > ClosureProblemCOP
typedef utility::pointer::shared_ptr< ClosureSolutionClosureSolutionOP
typedef utility::pointer::shared_ptr< ClosureSolution const > ClosureSolutionCOP
typedef utility::vector1< ClosureSolutionCOPSolutionList
typedef utility::pointer::shared_ptr< KicMoverKicMoverOP
typedef utility::pointer::shared_ptr< KicMover const > KicMoverCOP


Size num_rama_filter_fails = 0
Size num_bump_filter_fails = 0

Detailed Description

Implementation of the kinematic closure algorithm for sampling protein backbone conformations.

The most important classes in this namespace are KicMover, ClosureProblem, and ClosureSolution. KicMover is meant for use in other protocols, while ClosureProblem and ClosureSolution drive that kinematic closure algorithm under the hood.

KicMover objects are capable of sampling different backbone conformations in a pose. Exactly how these objects work can be heavily customized using the perturber and picker classes. Some of these classes are very general, while others are specific to certain applications. Feel free to create new sampler classes for your applications. For example, if you decide to write custom pivot picking and perturbing algorithms that are meant to be used together, make a new sampler class that wraps around KicMover and uses your custom algorithms by default.

The ClosureProblem and ClosureSolution classes are used by the KicMover as follows. First, a ClosureProblem object is created. This object is used to pick the pivot residues, to sample the nonpivot torsions, and to find backbone conformations consistent with all that. All possible solutions are found, and each solution is returned as ClosureSolution object. Then KicMover then picks a solution, using a handful of filters, and applies it to the pose.

Typedef Documentation

◆ BalancedKicMoverCOP

typedef utility::pointer::shared_ptr<BalancedKicMover const> protocols::kinematic_closure::BalancedKicMoverCOP

◆ BalancedKicMoverOP

◆ ClosureProblemCOP

typedef utility::pointer::shared_ptr<ClosureProblem const> protocols::kinematic_closure::ClosureProblemCOP

◆ ClosureProblemOP

typedef utility::pointer::shared_ptr<ClosureProblem> protocols::kinematic_closure::ClosureProblemOP

◆ ClosureSolutionCOP

typedef utility::pointer::shared_ptr<ClosureSolution const> protocols::kinematic_closure::ClosureSolutionCOP

◆ ClosureSolutionOP

◆ KicMoverCOP

typedef utility::pointer::shared_ptr<KicMover const> protocols::kinematic_closure::KicMoverCOP

◆ KicMoverOP

typedef utility::pointer::shared_ptr<KicMover> protocols::kinematic_closure::KicMoverOP

◆ SolutionList

Variable Documentation

◆ num_bump_filter_fails

Size protocols::kinematic_closure::num_bump_filter_fails = 0

◆ num_rama_filter_fails

Size protocols::kinematic_closure::num_rama_filter_fails = 0