protocols::loops::loop_closure::kinematic_closure Namespace Reference

Classes
class	BaseTabooPerturber
	Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials. More...
class	KinematicMover
	A mover class for performing kinematic loop closure on a peptide segment . More...
class	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	KinematicWrapper
class	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...
class	NeighborDependentTorsionSamplingKinematicPerturber
	neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup More...
class	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	TorsionRestrictedKinematicPerturber
	torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) More...
class	TorsionSamplingKinematicPerturber
	torsion sampling kinematic perturber More...
class	TorsionSweepingKinematicPerturber
	WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber. More...
class	VicinitySamplingKinematicPerturber
	vicinity sampling kinematic perturber More...

Typedefs
typedef utility::pointer::owning_ptr < KinematicMover >	KinematicMoverOP
typedef utility::pointer::owning_ptr < KinematicMover const >	KinematicMoverCOP
typedef utility::pointer::access_ptr < KinematicMover const >	KinematicMoverCAP
typedef utility::pointer::owning_ptr < KinematicPerturber >	KinematicPerturberOP
typedef utility::pointer::owning_ptr < KinematicPerturber const >	KinematicPerturberCOP
typedef utility::pointer::owning_ptr < TorsionSamplingKinematicPerturber >	TorsionSamplingKinematicPerturberOP
typedef utility::pointer::owning_ptr < TorsionSamplingKinematicPerturber const >	TorsionSamplingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < SmallMoveKinematicPerturber >	SmallMoveKinematicPerturberOP
typedef utility::pointer::owning_ptr < SmallMoveKinematicPerturber const >	SmallMoveKinematicPerturberCOP
typedef utility::pointer::owning_ptr < PivotBasedKinematicPerturber >	PivotBasedKinematicPerturberOP
typedef utility::pointer::owning_ptr < PivotBasedKinematicPerturber const >	PivotBasedKinematicPerturberCOP
typedef utility::pointer::owning_ptr < VicinitySamplingKinematicPerturber >	VicinitySamplingKinematicPerturberOP
typedef utility::pointer::owning_ptr < VicinitySamplingKinematicPerturber const >	VicinitySamplingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < TorsionSweepingKinematicPerturber >	TorsionSweepingKinematicPerturberOP
typedef utility::pointer::owning_ptr < TorsionSweepingKinematicPerturber const >	TorsionSweepingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < NeighborDependentTorsionSamplingKinematicPerturber >	NeighborDependentTorsionSamplingKinematicPerturberOP
typedef utility::pointer::owning_ptr < NeighborDependentTorsionSamplingKinematicPerturber const >	NeighborDependentTorsionSamplingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < NeighborDependentTabooSamplingKinematicPerturber >	NeighborDependentTabooSamplingKinematicPerturberOP
typedef utility::pointer::owning_ptr < NeighborDependentTabooSamplingKinematicPerturber const >	NeighborDependentTabooSamplingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < TorsionRestrictedKinematicPerturber >	TorsionRestrictedKinematicPerturberOP
typedef utility::pointer::owning_ptr < TorsionRestrictedKinematicPerturber const >	TorsionRestrictedKinematicPerturberCOP
typedef utility::pointer::owning_ptr < TabooSamplingKinematicPerturber >	TabooSamplingKinematicPerturberOP
typedef utility::pointer::owning_ptr < TabooSamplingKinematicPerturber const >	TabooSamplingKinematicPerturberCOP
typedef utility::pointer::owning_ptr < KinematicWrapper >	KinematicWrapperOP
typedef utility::pointer::owning_ptr < KinematicWrapper const >	KinematicWrapperCOP

Variables
static numeric::random::RandomGenerator	RG (43134)
static basic::Tracer	TR ("protocols.loops.loop_closure.kinematic_closure.KinematicPerturber")

Typedef Documentation

typedef utility::pointer::access_ptr< KinematicMover const > protocols::loops::loop_closure::kinematic_closure::KinematicMoverCAP

typedef utility::pointer::owning_ptr< KinematicMover const > protocols::loops::loop_closure::kinematic_closure::KinematicMoverCOP

typedef utility::pointer::owning_ptr< KinematicMover > protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP

typedef utility::pointer::owning_ptr< KinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::KinematicPerturberCOP

typedef utility::pointer::owning_ptr< KinematicPerturber > protocols::loops::loop_closure::kinematic_closure::KinematicPerturberOP

typedef utility::pointer::owning_ptr< KinematicWrapper const > protocols::loops::loop_closure::kinematic_closure::KinematicWrapperCOP

typedef utility::pointer::owning_ptr< KinematicWrapper > protocols::loops::loop_closure::kinematic_closure::KinematicWrapperOP

typedef utility::pointer::owning_ptr< NeighborDependentTabooSamplingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< NeighborDependentTabooSamplingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturberOP

typedef utility::pointer::owning_ptr< NeighborDependentTorsionSamplingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< NeighborDependentTorsionSamplingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturberOP

typedef utility::pointer::owning_ptr< PivotBasedKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::PivotBasedKinematicPerturberCOP

typedef utility::pointer::owning_ptr< PivotBasedKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::PivotBasedKinematicPerturberOP

typedef utility::pointer::owning_ptr< SmallMoveKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::SmallMoveKinematicPerturberCOP

typedef utility::pointer::owning_ptr< SmallMoveKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::SmallMoveKinematicPerturberOP

typedef utility::pointer::owning_ptr< TabooSamplingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< TabooSamplingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturberOP

typedef utility::pointer::owning_ptr< TorsionRestrictedKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturberCOP

typedef utility::pointer::owning_ptr< TorsionRestrictedKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturberOP

typedef utility::pointer::owning_ptr< TorsionSamplingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< TorsionSamplingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturberOP

typedef utility::pointer::owning_ptr< TorsionSweepingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< TorsionSweepingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturberOP

typedef utility::pointer::owning_ptr< VicinitySamplingKinematicPerturber const > protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturberCOP

typedef utility::pointer::owning_ptr< VicinitySamplingKinematicPerturber > protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturberOP

Variable Documentation

numeric::random::RandomGenerator protocols::loops::loop_closure::kinematic_closure::RG(43134)

static

Referenced by protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::check_rama(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_beta_residue(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain(), and protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::perturb_chain().

basic::Tracer protocols::loops::loop_closure::kinematic_closure::TR("protocols.loops.loop_closure.kinematic_closure.KinematicPerturber")

static

Referenced by protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::frequency_in_taboo_map(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::insert_sampled_torsion_string_into_taboo_map(), and protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::respect_this_movemap().