protocols::kinematic_closure::pivot_pickers Namespace Reference

Algorithms for choosing pivot residues. More...

Classes
class	EndToEndPivots
	Pick pivots that span the entire loop to sample. More...
class	FixedOffsetPivots
	Randomly pick pivots which are always offset by the same amount, but which can appear anywhere in the loop. More...
class	FixedPivots
	Use a fixed set of pivots specified in advance. More...
class	LoopPivots
	Use the start, stop, and cut points of the given loop as pivots. More...
class	PivotPicker
	Base class for all the pivot picking algorithms. More...
class	StandardPivots
	Randomly pick pivots in a way that may or may not span the whole loop. More...

Typedefs
typedef owning_ptr < EndToEndPivots >	EndToEndPivotsOP
typedef owning_ptr < EndToEndPivots const >	EndToEndPivotsCOP
typedef owning_ptr < FixedOffsetPivots >	FixedOffsetPivotsOP
typedef owning_ptr < FixedOffsetPivots const >	FixedOffsetPivotsCOP
typedef owning_ptr< FixedPivots >	FixedPivotsOP
typedef owning_ptr < FixedPivots const >	FixedPivotsCOP
typedef owning_ptr< LoopPivots >	LoopPivotsOP
typedef owning_ptr< LoopPivots const >	LoopPivotsCOP
typedef owning_ptr< PivotPicker >	PivotPickerOP
typedef owning_ptr < PivotPicker const >	PivotPickerCOP
typedef owning_ptr < StandardPivots >	StandardPivotsOP
typedef owning_ptr < StandardPivots const >	StandardPivotsCOP

Detailed Description

Algorithms for choosing pivot residues.

The pivot torsions are used by the kinematic closure algorithm to ensure that sampling doesn't cause the breaks in the backbone. The choice of pivots can be significant, because the pivot torsions are the most difficult degrees of freedom to control. In other words, since these DOFs are used to ensure that the backbone is closed, it is hard to impose other restraints on them. This is in contrast with the pivot torsions, which can be set arbitrarily. So if you're studying a loop and you know that some of the residues have really restrained torsions, it would be better to not represent these residues as pivots. This level of customization may require you to write a custom PivotPicker subclass, but it's not too hard.

Typedef Documentation

typedef owning_ptr<EndToEndPivots const> protocols::kinematic_closure::pivot_pickers::EndToEndPivotsCOP

typedef owning_ptr<EndToEndPivots> protocols::kinematic_closure::pivot_pickers::EndToEndPivotsOP

typedef owning_ptr<FixedOffsetPivots const> protocols::kinematic_closure::pivot_pickers::FixedOffsetPivotsCOP

typedef owning_ptr<FixedOffsetPivots> protocols::kinematic_closure::pivot_pickers::FixedOffsetPivotsOP

typedef owning_ptr<FixedPivots const> protocols::kinematic_closure::pivot_pickers::FixedPivotsCOP

typedef owning_ptr<FixedPivots> protocols::kinematic_closure::pivot_pickers::FixedPivotsOP

typedef owning_ptr<LoopPivots const> protocols::kinematic_closure::pivot_pickers::LoopPivotsCOP

typedef owning_ptr<LoopPivots> protocols::kinematic_closure::pivot_pickers::LoopPivotsOP

typedef owning_ptr<PivotPicker const> protocols::kinematic_closure::pivot_pickers::PivotPickerCOP

typedef owning_ptr<PivotPicker> protocols::kinematic_closure::pivot_pickers::PivotPickerOP

typedef owning_ptr<StandardPivots const> protocols::kinematic_closure::pivot_pickers::StandardPivotsCOP

typedef owning_ptr<StandardPivots> protocols::kinematic_closure::pivot_pickers::StandardPivotsOP