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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:
Inheritance graph
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Public Member Functions

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

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

References kinmover_.

Referenced by protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::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::BaseTabooPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::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(), and protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::set_pose_after_closure().

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

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
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::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 core::id::BB, core::sequence::end, core::conformation::Residue::is_lower_terminus(), kinmover(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_torsion(), protocols::loops::start, and core::pose::Pose::update_residue_neighbors().

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(), and protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::set_pose_after_closure().

Member Data Documentation

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

Referenced by kinmover(), and set_kinmover().

core::Size protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::max_sample_iterations_
private
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: