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>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::KinematicPerturber:

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Collaboration diagram for protocols::loops::loop_closure::kinematic_closure::KinematicPerturber:

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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 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 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 ()

Protected Attributes
KinematicMoverCAP	kinmover_

core::Size	max_sample_iterations_

Private Attributes
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.

Definition at line 45 of file KinematicPerturber.hh.

Constructor & Destructor Documentation

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

Definition at line 59 of file KinematicPerturber.cc.

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

virtual

Definition at line 63 of file KinematicPerturber.cc.

Member Function Documentation

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

inline

Definition at line 107 of file KinematicPerturber.hh.

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

Definition at line 67 of file KinematicPerturber.cc.

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(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::perturb_chain(), and protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::perturb_chain().

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

inline

Definition at line 104 of file KinematicPerturber.hh.

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::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.

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

inlinevirtual

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

Definition at line 96 of file KinematicPerturber.hh.

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

Definition at line 56 of file KinematicPerturber.hh.

References kinmover_.

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

inline

Definition at line 100 of file KinematicPerturber.hh.

References max_sample_iterations_.

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

Definition at line 65 of file KinematicPerturber.cc.

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::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::VicinitySamplingKinematicPerturber, and protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber.

Definition at line 70 of file KinematicPerturber.cc.

References kinmover_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and protocols::loops::start.

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