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...

#include <KinematicPerturber.hh>

Public Member Functions
	KinematicPerturber ()

virtual	~KinematicPerturber ()

virtual std::string	perturber_type () const =0

void	set_kinmover (KinematicMoverCAP kinmover)

void	set_movemap (core::kinematics::MoveMapCOP mm)

core::kinematics::MoveMapCOP	get_movemap () const

virtual void	perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &bond_len)=0
	function that perturbs the chain, i.e. sets new values for the torsions, bond angles and bond lengths note: the torsions/angles/lengths that are input to this function will be identical to the ones in the pose, i.e. only the dof values that are explicitly set by this function plus the pivots will have changed after loop closure More...

virtual void	set_pose_after_closure (core::pose::Pose &pose, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &, utility::vector1< core::Real > const &, bool) const
	after the kinmover has closed the loop, the perturber needs to put the solutions into the pose note: the base class version of this function sets the torsions, so any KinematicPerturber that only changes the torsions will not have to implement this function More...

virtual bool	perturber_exhausted () const

void	set_max_sample_iterations (core::Size sample_its)

core::Size	max_sample_iterations () const

void	clear_torsion_string_stack ()

KinematicMoverCAP	kinmover () const

Private Attributes
KinematicMoverCAP	kinmover_

core::Size	max_sample_iterations_

core::kinematics::MoveMapCOP	movemap_

Detailed Description

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.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::KinematicPerturber ( )

References loops, max_kic_perturber_samples, option, and options.

protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::~KinematicPerturber ( )

virtual

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::clear_torsion_string_stack ( )

inline

core::kinematics::MoveMapCOP protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::get_movemap ( ) const

References movemap_.

Referenced by 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().

KinematicMoverCAP protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover ( ) const

References kinmover_.

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::max_sample_iterations ( ) const

inline

References max_sample_iterations_.

virtual void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::perturb_chain	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	torsions,
		utility::vector1< core::Real > &	bond_ang,
		utility::vector1< core::Real > &	bond_len
	)

pure virtual

function that perturbs the chain, i.e. sets new values for the torsions, bond angles and bond lengths note: the torsions/angles/lengths that are input to this function will be identical to the ones in the pose, i.e. only the dof values that are explicitly set by this function plus the pivots will have changed after loop closure

Implemented in protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber, protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber, and protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber.

virtual bool protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::perturber_exhausted ( ) const

inlinevirtual

Reimplemented in protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber.

virtual std::string protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::perturber_type ( ) const

pure virtual

Implemented in protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber, and protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber.

void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_kinmover ( KinematicMoverCAP kinmover )

inline

References kinmover(), and kinmover_.

Referenced by protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::BaseTabooPerturber(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::NeighborDependentTorsionSamplingKinematicPerturber(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::TorsionRestrictedKinematicPerturber(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::TorsionSamplingKinematicPerturber(), and protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::VicinitySamplingKinematicPerturber().

void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_max_sample_iterations ( core::Size sample_its )

inline

References max_sample_iterations_.

void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_movemap ( core::kinematics::MoveMapCOP mm )

References movemap_.

void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	,
		utility::vector1< core::Real > const &	,
		bool
	)		const

virtual

after the kinmover has closed the loop, the perturber needs to put the solutions into the pose note: the base class version of this function sets the torsions, so any KinematicPerturber that only changes the torsions will not have to implement this function

Reimplemented in protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber, protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber, protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber, and protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber.

References basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose, end, core::conformation::Residue::is_lower_terminus(), basic::options::OptionKeys::loops::kic_omega_sampling, kinmover_, basic::options::option, core::pose::Pose::residue(), basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string, basic::options::OptionKeys::loops::sample_omega_at_pre_prolines, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_torsion(), protocols::loops::start, core::pose::Pose::update_residue_neighbors(), and user.