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

typedef utility::pointer::shared_ptr<MinimizationRefiner const> protocols::loop_modeling::refiners::MinimizationRefinerCOP

typedef utility::pointer::shared_ptr<MinimizationRefiner> protocols::loop_modeling::refiners::MinimizationRefinerOP

typedef utility::pointer::shared_ptr<RepackingRefiner const> protocols::loop_modeling::refiners::RepackingRefinerCOP

typedef utility::pointer::shared_ptr<RepackingRefiner> protocols::loop_modeling::refiners::RepackingRefinerOP

typedef utility::pointer::shared_ptr<RotamerTrialsRefiner const> protocols::loop_modeling::refiners::RotamerTrialsRefinerCOP

typedef utility::pointer::shared_ptr<RotamerTrialsRefiner> protocols::loop_modeling::refiners::RotamerTrialsRefinerOP

Function Documentation

template<typename PackingRefiner , typename PackingAlgorithm >

bool protocols::loop_modeling::refiners::packing_helper	(	core::pose::Pose &	pose,
		PackingRefiner *	refiner,
		PackingAlgorithm	packer
	)

References core::pose::Pose::update_residue_neighbors().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::do_apply(), and protocols::loop_modeling::refiners::RepackingRefiner::do_apply().