KinematicPerturber.hh File Reference

Header file for KinematicPerturbers used by the kineamtic mover. More...

#include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.fwd.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.fwd.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/ppo_torsion_bin.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/Ramachandran.fwd.hh>
#include <core/scoring/Ramachandran2B.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <utility/LexicographicalIterator.hh>
#include <utility/vector1.hh>
#include <utility/vector0.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <string>
#include <map>

Classes
class	protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
	pure virtual base class for KinematicPerturber. KinematicPerturbers determine HOW loops should be perturbed. The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity. More...
class	protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
	torsion sampling kinematic perturber More...
class	protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
	vicinity sampling kinematic perturber More...
class	protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
	WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber. More...
class	protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber
	neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup More...
class	protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
	torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) More...
class	protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
	Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials. More...
class	protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
	Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration) More...
class	protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
	Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) More...

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::loops
	protocols::loops::loop_closure
	protocols::loops::loop_closure::kinematic_closure

Detailed Description

Header file for KinematicPerturbers used by the kineamtic mover.

Author

Florian Richter, flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu, march 2009

Amelie Stein, ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu, October 2012 – refactoring vicinity sampling & new perturbers