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Classes | Typedefs
protocols::kinematic_closure::perturbers Namespace Reference

Algorithms for sampling new backbone torsions. More...

Classes

class  BondAnglePerturber
 Resample each backbone bond angle from a gaussian distribution. More...
 
class  FragmentPerturber
 Pick phi/psi torsions from the given fragment library. More...
 
class  IdealizeNonPhiPsi
 Set all the non-phi/psi DOFs to ideal values. More...
 
class  LogFilePerturber
 Read torsion angles, bond angles, and bond lengths from a log file. More...
 
class  OmegaPerturber
 
class  Perturber
 Base class for all of the perturber algorithms. More...
 
class  PerturberSet
 Maintain a set of perturbers to be executed together. More...
 
class  Rama2bPerturber
 Pick phi/psi pairs from the neighbor-dependent rama distribution. More...
 
class  RamaPerturber
 Pick phi/psi pairs from the rama distribution. More...
 
class  UniformPerturber
 Sample backbone torsions from a uniform distribution. More...
 
class  VicinityPerturber
 Limit sampling to phi/psi pairs within some distance of a target loop. More...
 
class  WalkingBondAnglePerturber
 Resample each backbone bond angle from a gaussian distribution. More...
 
class  WalkingPerturber
 Make small perturbations to the previous backbone torsions. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< BondAnglePerturber
BondAnglePerturberOP
 
typedef
utility::pointer::shared_ptr
< BondAnglePerturber const > 
BondAnglePerturberCOP
 
typedef
utility::pointer::shared_ptr
< FragmentPerturber
FragmentPerturberOP
 
typedef
utility::pointer::shared_ptr
< FragmentPerturber const > 
FragmentPerturberCOP
 
typedef
utility::pointer::shared_ptr
< IdealizeNonPhiPsi
IdealizeNonPhiPsiOP
 
typedef
utility::pointer::shared_ptr
< IdealizeNonPhiPsi const > 
IdealizeNonPhiPsiCOP
 
typedef
utility::pointer::shared_ptr
< LogFilePerturber
LogFilePerturberOP
 
typedef
utility::pointer::shared_ptr
< LogFilePerturber const > 
LogFilePerturberCOP
 
typedef
utility::pointer::shared_ptr
< OmegaPerturber
OmegaPerturberOP
 
typedef
utility::pointer::shared_ptr
< OmegaPerturber const > 
OmegaPerturberCOP
 
typedef
utility::pointer::shared_ptr
< Perturber
PerturberOP
 
typedef
utility::pointer::shared_ptr
< Perturber const > 
PerturberCOP
 
typedef
utility::pointer::shared_ptr
< PerturberSet
PerturberSetOP
 
typedef
utility::pointer::shared_ptr
< PerturberSet const > 
PerturberSetCOP
 
typedef
utility::pointer::shared_ptr
< Rama2bPerturber
Rama2bPerturberOP
 
typedef
utility::pointer::shared_ptr
< Rama2bPerturber const > 
Rama2bPerturberCOP
 
typedef
utility::pointer::shared_ptr
< RamaPerturber
RamaPerturberOP
 
typedef
utility::pointer::shared_ptr
< RamaPerturber const > 
RamaPerturberCOP
 
typedef
utility::pointer::shared_ptr
< UniformPerturber
UniformPerturberOP
 
typedef
utility::pointer::shared_ptr
< UniformPerturber const > 
UniformPerturberCOP
 
typedef
utility::pointer::shared_ptr
< VicinityPerturber
VicinityPerturberOP
 
typedef
utility::pointer::shared_ptr
< VicinityPerturber const > 
VicinityPerturberCOP
 
typedef
utility::pointer::shared_ptr
< WalkingBondAnglePerturber
WalkingBondAnglePerturberOP
 
typedef
utility::pointer::shared_ptr
< WalkingBondAnglePerturber
const > 
WalkingBondAnglePerturberCOP
 
typedef
utility::pointer::shared_ptr
< WalkingPerturber
WalkingPerturberOP
 
typedef
utility::pointer::shared_ptr
< WalkingPerturber const > 
WalkingPerturberCOP
 

Detailed Description

Algorithms for sampling new backbone torsions.

The kinematic closure algorithm allows the non-pivot torsions to be set without any restrictions. The six pivot torsions are then used to ensure the backbone remains closed. There is a great deal of flexibility in how the non-pivot torsions are chosen. This namespace provides a number of different algorithms to sample these torsions. These algorithms can be mixed in matched in any way you'd like using samplers::KicMover.

Typedef Documentation

typedef utility::pointer::shared_ptr<Perturber const> protocols::kinematic_closure::perturbers::PerturberCOP
typedef utility::pointer::shared_ptr<PerturberSet const> protocols::kinematic_closure::perturbers::PerturberSetCOP