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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...
 
class  KicMoverCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< BalancedKicMover
BalancedKicMoverOP
 
typedef
utility::pointer::shared_ptr
< BalancedKicMover const > 
BalancedKicMoverCOP
 
typedef
utility::pointer::shared_ptr
< ClosureProblem
ClosureProblemOP
 
typedef
utility::pointer::shared_ptr
< ClosureProblem const > 
ClosureProblemCOP
 
typedef
utility::pointer::shared_ptr
< ClosureSolution
ClosureSolutionOP
 
typedef
utility::pointer::shared_ptr
< ClosureSolution const > 
ClosureSolutionCOP
 
typedef utility::vector1
< ClosureSolutionCOP
SolutionList
 
typedef
utility::pointer::shared_ptr
< KicMover
KicMoverOP
 
typedef
utility::pointer::shared_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 utility::pointer::shared_ptr<BalancedKicMover const> protocols::kinematic_closure::BalancedKicMoverCOP
typedef utility::pointer::shared_ptr<ClosureProblem const> protocols::kinematic_closure::ClosureProblemCOP
typedef utility::pointer::shared_ptr<ClosureProblem> protocols::kinematic_closure::ClosureProblemOP
typedef utility::pointer::shared_ptr<ClosureSolution const> protocols::kinematic_closure::ClosureSolutionCOP
typedef utility::pointer::shared_ptr<KicMover const> protocols::kinematic_closure::KicMoverCOP
typedef utility::pointer::shared_ptr<KicMover> protocols::kinematic_closure::KicMoverOP

Variable Documentation

Size protocols::kinematic_closure::num_bump_filter_fails = 0
Size protocols::kinematic_closure::num_rama_filter_fails = 0