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:

Public Member Functions
	TorsionSweepingKinematicPerturber ()
	~TorsionSweepingKinematicPerturber () override
std::string	perturber_type () const 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
	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 override
void	set_nonpivot_res_to_sweep (utility::vector1< core::Size > const &resids)
void	set_nonpivot_bb_torsion_id (utility::vector1< core::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< core::Size > const &nsteps)
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 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...
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
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_

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.

Constructor & Destructor Documentation

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

(

)

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

overridedefault

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 > &    )

overridevirtual

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.

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

inlineoverridevirtual

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

References sweep_iterator_.

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

inlineoverridevirtual

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

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

(

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

bbtorids

)

References nonpivot_res_to_sweep_, and sweep_torsion_ids_.

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

(

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

resids

)

References nonpivot_res_to_sweep_, and core::select::resids().

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

(

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

nsteps

)

Initializes the LexicographicalIterator

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

)

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

)

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

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

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

Referenced by perturb_chain(), and set_sweep_start_angle().

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

private

Referenced by perturb_chain(), and set_sweep_step_size().

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

private

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