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protocols::loops::loop_closure::kinematic_closure::KinematicPerturber Class Referenceabstract

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.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::KinematicPerturber ( )
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
core::Size protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::max_sample_iterations ( ) const
inline
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
virtual bool protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::perturber_exhausted ( ) const
inlinevirtual
virtual std::string protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::perturber_type ( ) const
pure virtual
void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_kinmover ( KinematicMoverCAP  kinmover)
inline
void protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_max_sample_iterations ( core::Size  sample_its)
inline
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::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.

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().

Member Data Documentation

KinematicMoverCAP protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_
protected

Referenced by protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::next_torsion_string(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::next_torsion_string(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::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(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::refill_torsion_string_vector(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::refill_torsion_string_vector(), set_kinmover(), set_pose_after_closure(), 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().

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::max_sample_iterations_
protected
core::kinematics::MoveMapCOP protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::movemap_
private

Referenced by get_movemap(), and set_movemap().


The documentation for this class was generated from the following files: