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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< BondAnglePerturberBondAnglePerturberOP
 
typedef utility::pointer::shared_ptr< BondAnglePerturber const > BondAnglePerturberCOP
 
typedef utility::pointer::shared_ptr< FragmentPerturberFragmentPerturberOP
 
typedef utility::pointer::shared_ptr< FragmentPerturber const > FragmentPerturberCOP
 
typedef utility::pointer::shared_ptr< IdealizeNonPhiPsiIdealizeNonPhiPsiOP
 
typedef utility::pointer::shared_ptr< IdealizeNonPhiPsi const > IdealizeNonPhiPsiCOP
 
typedef utility::pointer::shared_ptr< LogFilePerturberLogFilePerturberOP
 
typedef utility::pointer::shared_ptr< LogFilePerturber const > LogFilePerturberCOP
 
typedef utility::pointer::shared_ptr< OmegaPerturberOmegaPerturberOP
 
typedef utility::pointer::shared_ptr< OmegaPerturber const > OmegaPerturberCOP
 
typedef utility::pointer::shared_ptr< PerturberPerturberOP
 
typedef utility::pointer::shared_ptr< Perturber const > PerturberCOP
 
typedef utility::pointer::shared_ptr< PerturberSetPerturberSetOP
 
typedef utility::pointer::shared_ptr< PerturberSet const > PerturberSetCOP
 
typedef utility::pointer::shared_ptr< Rama2bPerturberRama2bPerturberOP
 
typedef utility::pointer::shared_ptr< Rama2bPerturber const > Rama2bPerturberCOP
 
typedef utility::pointer::shared_ptr< RamaPerturberRamaPerturberOP
 
typedef utility::pointer::shared_ptr< RamaPerturber const > RamaPerturberCOP
 
typedef utility::pointer::shared_ptr< UniformPerturberUniformPerturberOP
 
typedef utility::pointer::shared_ptr< UniformPerturber const > UniformPerturberCOP
 
typedef utility::pointer::shared_ptr< VicinityPerturberVicinityPerturberOP
 
typedef utility::pointer::shared_ptr< VicinityPerturber const > VicinityPerturberCOP
 
typedef utility::pointer::shared_ptr< WalkingBondAnglePerturberWalkingBondAnglePerturberOP
 
typedef utility::pointer::shared_ptr< WalkingBondAnglePerturber const > WalkingBondAnglePerturberCOP
 
typedef utility::pointer::shared_ptr< WalkingPerturberWalkingPerturberOP
 
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

◆ BondAnglePerturberCOP

◆ BondAnglePerturberOP

◆ FragmentPerturberCOP

◆ FragmentPerturberOP

◆ IdealizeNonPhiPsiCOP

◆ IdealizeNonPhiPsiOP

◆ LogFilePerturberCOP

◆ LogFilePerturberOP

◆ OmegaPerturberCOP

◆ OmegaPerturberOP

◆ PerturberCOP

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

◆ PerturberOP

◆ PerturberSetCOP

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

◆ PerturberSetOP

◆ Rama2bPerturberCOP

◆ Rama2bPerturberOP

◆ RamaPerturberCOP

◆ RamaPerturberOP

◆ UniformPerturberCOP

◆ UniformPerturberOP

◆ VicinityPerturberCOP

◆ VicinityPerturberOP

◆ WalkingBondAnglePerturberCOP

◆ WalkingBondAnglePerturberOP

◆ WalkingPerturberCOP

◆ WalkingPerturberOP