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protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber Class Reference

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...

#include <KinematicPerturber.hh>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber:
Inheritance graph
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Public Types

typedef BaseTabooPerturber parent
 
- Public Types inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
typedef KinematicPerturber parent
 

Public Member Functions

 TabooSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)
 
 ~TabooSamplingKinematicPerturber () override
 
std::string perturber_type () const override
 
- Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
 BaseTabooPerturber (KinematicMoverCAP kinmover_in)
 
 ~BaseTabooPerturber () override
 
void perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &) override
 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...
 
void set_pose_after_closure (core::pose::Pose &pose, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bond_ang, utility::vector1< core::Real > const &bond_len, bool closure_successful) const override
 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...
 
void set_vary_ca_bond_angles (bool vary_ca_bond_angles)
 
void clear_torsion_string_stack ()
 
core::Size num_strings () const
 
core::conformation::torsion_bin_string next_torsion_string ()
 
- Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
 KinematicPerturber ()
 
 ~KinematicPerturber () override
 
void set_kinmover (KinematicMoverCAP kinmover)
 
void set_movemap (core::kinematics::MoveMapCOP mm)
 
core::kinematics::MoveMapCOP get_movemap () const
 
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 Member Functions

void get_random_phi_psi_for_residue (core::pose::Pose const &pose, core::Size resid, core::conformation::ppo_torsion_bin torbin, core::Real &phi, core::Real &psi) const override
 
std::map
< core::conformation::ppo_torsion_bin,
core::Size
get_entries_per_torsion_bin (utility::vector1< core::chemical::AA > loop_seq, core::Size resid) const override
 This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector. More...
 

Private Attributes

core::scoring::Ramachandran const & rama_
 

Detailed Description

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)

Author
Amelie Stein

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::TabooSamplingKinematicPerturber ( KinematicMoverCAP  kinmover_in)
protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::~TabooSamplingKinematicPerturber ( )
overridedefault

Member Function Documentation

std::map< core::conformation::ppo_torsion_bin, core::Size > protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_entries_per_torsion_bin ( utility::vector1< core::chemical::AA loop_seq,
core::Size  resid 
) const
overrideprivatevirtual

This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector.

Implements protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber.

References core::scoring::Ramachandran::get_entries_per_torsion_bin(), and rama_.

void protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue ( core::pose::Pose const &  pose,
core::Size  resid,
core::conformation::ppo_torsion_bin  torbin,
core::Real phi,
core::Real psi 
) const
overrideprivatevirtual
std::string protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::perturber_type ( ) const
inlineoverridevirtual

Member Data Documentation

core::scoring::Ramachandran const& protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::rama_
private

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