protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber Class Reference

WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber. More...

#include <KinematicPerturber.hh>

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

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

Public Member Functions
	TorsionSweepingKinematicPerturber ()
	~TorsionSweepingKinematicPerturber ()
std::string	perturber_type () const
void	perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &)
	movemap control NOT IMPLEMENTED in TorsionSweepingKP. It is also NOT NEEDED because you can use set_nonpivot_res_to_sweep instead. More...
bool	perturber_exhausted () const
void	set_nonpivot_res_to_sweep (utility::vector1< Size > const &resids)
void	set_nonpivot_bb_torsion_id (utility::vector1< Size > const &bbtorids)
void	set_sweep_start_angle (utility::vector1< core::Real > const &angles_in_degrees)
void	set_sweep_step_size (utility::vector1< core::Real > const &angle_steps_in_degrees)
void	set_sweep_nsteps (utility::vector1< Size > const &nsteps)
Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
	KinematicPerturber ()
virtual	~KinematicPerturber ()
void	set_kinmover (KinematicMoverCAP kinmover)
void	set_movemap (core::kinematics::MoveMapCOP mm)
core::kinematics::MoveMapCOP	get_movemap () const
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...
void	set_max_sample_iterations (core::Size sample_its)
core::Size	max_sample_iterations () const
void	clear_torsion_string_stack ()

Private Attributes
utility::vector1< core::Size >	nonpivot_res_to_sweep_
utility::vector1< core::Size >	sweep_torsion_ids_
utility::vector1< core::Real >	sweep_nonpivot_torsion_starts_
utility::vector1< core::Real >	sweep_step_sizes_
utility::LexicographicalIterator	sweep_iterator_

Additional Inherited Members
Protected Attributes inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
KinematicMoverCAP	kinmover_
core::Size	max_sample_iterations_

Detailed Description

WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber.

WARNING WARNING UNTESTED!!!! used to work in other implementation probably works now, but to make sure you shoud doublecheck

Here's some commentary on why the TorsionSweepingKinematicPerturber is Fun and Awesome to use! Basically, you take the loop as given and search for solutions nearby. Its purpose is not to produce large changes, but instead to produce small perturbations to find the bottom of the current energy well. It's not meant to be used for the original KIC protocol, in which the pivots are changed regularly: you can't sweep through nonpivot torsion space if the pivots don't stay the same.

Definition at line 228 of file KinematicPerturber.hh.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::TorsionSweepingKinematicPerturber

(

)

Definition at line 328 of file KinematicPerturber.cc.

protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::~TorsionSweepingKinematicPerturber

(

)

Definition at line 332 of file KinematicPerturber.cc.

Member Function Documentation

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

virtual

movemap control NOT IMPLEMENTED in TorsionSweepingKP. It is also NOT NEEDED because you can use set_nonpivot_res_to_sweep instead.

Implements protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

Definition at line 366 of file KinematicPerturber.cc.

References protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, nonpivot_res_to_sweep_, protocols::loops::start, sweep_iterator_, sweep_nonpivot_torsion_starts_, sweep_step_sizes_, and sweep_torsion_ids_.

bool protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::perturber_exhausted ( ) const

inlinevirtual

Reimplemented from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

Definition at line 247 of file KinematicPerturber.hh.

References sweep_iterator_.

std::string protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::perturber_type ( ) const

inlinevirtual

Implements protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

Definition at line 235 of file KinematicPerturber.hh.

void protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_nonpivot_bb_torsion_id

(

utility::vector1< Size > const &

bbtorids)

Definition at line 339 of file KinematicPerturber.cc.

References nonpivot_res_to_sweep_, and sweep_torsion_ids_.

void protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_nonpivot_res_to_sweep

(

utility::vector1< Size > const &

resids)

Definition at line 334 of file KinematicPerturber.cc.

References nonpivot_res_to_sweep_.

void protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_sweep_nsteps

(

utility::vector1< Size > const &

nsteps)

Initializes the LexicographicalIterator

Definition at line 358 of file KinematicPerturber.cc.

References nonpivot_res_to_sweep_, and sweep_iterator_.

void protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_sweep_start_angle

(

utility::vector1< core::Real > const &

angles_in_degrees)

Definition at line 345 of file KinematicPerturber.cc.

References nonpivot_res_to_sweep_, and sweep_nonpivot_torsion_starts_.

void protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_sweep_step_size

(

utility::vector1< core::Real > const &

angle_steps_in_degrees)

Definition at line 351 of file KinematicPerturber.cc.

References nonpivot_res_to_sweep_, and sweep_step_sizes_.

Member Data Documentation

utility::vector1< core::Size > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::nonpivot_res_to_sweep_

private

Definition at line 259 of file KinematicPerturber.hh.

Referenced by perturb_chain(), set_nonpivot_bb_torsion_id(), set_nonpivot_res_to_sweep(), set_sweep_nsteps(), set_sweep_start_angle(), and set_sweep_step_size().

utility::LexicographicalIterator protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::sweep_iterator_

mutableprivate

Definition at line 263 of file KinematicPerturber.hh.

Referenced by perturb_chain(), perturber_exhausted(), and set_sweep_nsteps().

utility::vector1< core::Real > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::sweep_nonpivot_torsion_starts_

private

Definition at line 261 of file KinematicPerturber.hh.

Referenced by perturb_chain(), and set_sweep_start_angle().

utility::vector1< core::Real > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::sweep_step_sizes_

private

Definition at line 262 of file KinematicPerturber.hh.

Referenced by perturb_chain(), and set_sweep_step_size().

utility::vector1< core::Size > protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::sweep_torsion_ids_

private

Definition at line 260 of file KinematicPerturber.hh.

Referenced by perturb_chain(), and set_nonpivot_bb_torsion_id().

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

• src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.hh
• src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc