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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  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.

Typedef Documentation

typedef utility::pointer::shared_ptr<FixedPivots const> protocols::kinematic_closure::pivot_pickers::FixedPivotsCOP
typedef utility::pointer::shared_ptr<LoopPivots const> protocols::kinematic_closure::pivot_pickers::LoopPivotsCOP
typedef utility::pointer::shared_ptr<PivotPicker const> protocols::kinematic_closure::pivot_pickers::PivotPickerCOP