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	FixedOffsetsPivots
	Randomly pick pivots which are always offsets given in a list 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 utility::pointer::shared_ptr < EndToEndPivots >	EndToEndPivotsOP

typedef utility::pointer::shared_ptr < EndToEndPivots const >	EndToEndPivotsCOP

typedef utility::pointer::shared_ptr < FixedOffsetPivots >	FixedOffsetPivotsOP

typedef utility::pointer::shared_ptr < FixedOffsetPivots const >	FixedOffsetPivotsCOP

typedef utility::pointer::shared_ptr < FixedOffsetsPivots >	FixedOffsetsPivotsOP

typedef utility::pointer::shared_ptr < FixedOffsetsPivots const >	FixedOffsetsPivotsCOP

typedef utility::pointer::shared_ptr < FixedPivots >	FixedPivotsOP

typedef utility::pointer::shared_ptr < FixedPivots const >	FixedPivotsCOP

typedef utility::pointer::shared_ptr < LoopPivots >	LoopPivotsOP

typedef utility::pointer::shared_ptr < LoopPivots const >	LoopPivotsCOP

typedef utility::pointer::shared_ptr < PivotPicker >	PivotPickerOP

typedef utility::pointer::shared_ptr < PivotPicker const >	PivotPickerCOP

typedef utility::pointer::shared_ptr < StandardPivots >	StandardPivotsOP

typedef utility::pointer::shared_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.