protocols::kinematic_closure Namespace Reference

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

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

Classes
class	BalancedKicMover
	Make a kinematic closure move that obeys detailed balance. More...
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...

Typedefs
typedef owning_ptr < BalancedKicMover >	BalancedKicMoverOP
typedef owning_ptr < BalancedKicMover const >	BalancedKicMoverCOP
typedef utility::pointer::owning_ptr < ClosureProblem >	ClosureProblemOP
typedef utility::pointer::owning_ptr < ClosureProblem const >	ClosureProblemCOP
typedef utility::pointer::owning_ptr < ClosureSolution >	ClosureSolutionOP
typedef utility::pointer::owning_ptr < ClosureSolution const >	ClosureSolutionCOP
typedef utility::vector1 < ClosureSolutionCOP >	SolutionList
typedef owning_ptr< KicMover >	KicMoverOP
typedef owning_ptr< KicMover const >	KicMoverCOP

Variables
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

typedef owning_ptr<BalancedKicMover const> protocols::kinematic_closure::BalancedKicMoverCOP

typedef owning_ptr<BalancedKicMover> protocols::kinematic_closure::BalancedKicMoverOP

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

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

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

typedef utility::pointer::owning_ptr<ClosureSolution> protocols::kinematic_closure::ClosureSolutionOP

typedef owning_ptr<KicMover const> protocols::kinematic_closure::KicMoverCOP

typedef owning_ptr<KicMover> protocols::kinematic_closure::KicMoverOP

typedef utility::vector1<ClosureSolutionCOP> protocols::kinematic_closure::SolutionList

Variable Documentation

Size protocols::kinematic_closure::num_bump_filter_fails = 0

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().

Size protocols::kinematic_closure::num_rama_filter_fails = 0

Referenced by protocols::kinematic_closure::ClosureSolution::apply_if_reasonable().