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protocols::loop_modeling::refiners Namespace Reference

Algorithms for lowering loop region scores during sampling. More...

Classes

class  MinimizationRefiner
 Refine sampled loops using gradient minimization. More...
 
class  MinimizationRefinerCreator
 
class  RepackingRefiner
 Refine sampled loops using sidechain repacking. More...
 
class  RepackingRefinerCreator
 
class  RotamerTrialsRefiner
 Refine sampled loops using rotamer trials. More...
 
class  RotamerTrialsRefinerCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< MinimizationRefiner
MinimizationRefinerOP
 
typedef
utility::pointer::shared_ptr
< MinimizationRefiner const > 
MinimizationRefinerCOP
 
typedef
utility::pointer::shared_ptr
< RepackingRefiner
RepackingRefinerOP
 
typedef
utility::pointer::shared_ptr
< RepackingRefiner const > 
RepackingRefinerCOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsRefiner
RotamerTrialsRefinerOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsRefiner const > 
RotamerTrialsRefinerCOP
 

Functions

template<typename PackingRefiner , typename PackingAlgorithm >
bool packing_helper (core::pose::Pose &pose, PackingRefiner *refiner, PackingAlgorithm packer)
 

Detailed Description

Algorithms for lowering loop region scores during sampling.

the classes in the namespace are broadly supposed to be responsible for lowering the score in loop regions sampled using the algorithms in the samplers namespace. The primary refinement algorithms are RepackingRefiner, RotamerTrialsRefiner, and MinimizationRefiner. These algorithms together account for the lion's share of the total running time in most loop modeling simulations.

Typedef Documentation

Function Documentation

template<typename PackingRefiner , typename PackingAlgorithm >
bool protocols::loop_modeling::refiners::packing_helper ( core::pose::Pose pose,
PackingRefiner *  refiner,
PackingAlgorithm  packer 
)