#include <SymDockingInitialPerturbation.hh>

Inheritance diagram for protocols::symmetry::SymmetrySlider:

Public Member Functions
	SymmetrySlider (core::pose::Pose &pose)

	SymmetrySlider (core::pose::Pose &pose, core::conformation::symmetry::SlideCriteriaType score_criteria, std::string SlideCriteriaVal="AUTOMATIC")

	~SymmetrySlider () override

void	setup (core::pose::Pose &pose)

virtual void	select_jump ()=0

core::Size	get_current_jump ()

core::Real	get_slide_threshold ()

std::map< core::Size, bool >	get_allow_slide_jump_map () const

void	set_current_jump (core::Size jump_nbr)

void	set_slide_criteria (std::string SlideCriteria)

void	set_slide_threshold (std::string threshold)

core::Real	slide_score (core::pose::Pose &pose)

void	slide_away (core::pose::Pose &pose)

core::Real	step_size ()

void	disallow_current_slide ()

bool	allowed_current_slide ()

bool	continue_slide (core::pose::Pose &pose)

bool	very_far_away (core::pose::Pose &pose)

bool	finished ()

void	slide (core::pose::Pose &pose)

void	apply (core::pose::Pose &pose)

core::Real	rg (core::pose::Pose const &pose)

bool	dofmover_compresses (core::pose::Pose &pose, protocols::rigid::RigidBodyDofTransMover &dofmover)

Private Attributes
std::map< core::Size, core::conformation::symmetry::SymDof >	dofs_

std::map< core::Size, bool >	AllowSlideJumpMap_

std::map< core::Size, core::kinematics::Jump >	InitialJumps_

std::map< core::Size, bool >	InvertJump_

core::conformation::symmetry::SlideCriteriaType	SlideCriteriaType_

core::scoring::ScoreFunctionOP	scorefxn_

std::string	SlideThreshold_

bool	reset_slide_

core::Size	total_num_slides_

core::Size	current_jump_

Constructor & Destructor Documentation

protocols::symmetry::SymmetrySlider::SymmetrySlider ( core::pose::Pose & pose )

protocols::symmetry::SymmetrySlider::SymmetrySlider	(	core::pose::Pose &	pose,
		core::conformation::symmetry::SlideCriteriaType	score_criteria,
		std::string	SlideCriteriaVal = `"AUTOMATIC"`
	)

References core::conformation::symmetry::CEN_DOCK_SCORE, core::scoring::CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::DOCK_LOW_PATCH, core::pose::Pose::energies(), core::scoring::fa_rep, core::conformation::symmetry::FA_REP_SCORE, protocols::symmetry::FaSymDockingSlideTogether::scorefxn_, core::scoring::Energies::total_energies(), and core::conformation::symmetry::TOTAL_NUM_CRITERIA.

protocols::symmetry::SymmetrySlider::~SymmetrySlider ( )

overridedefault

Member Function Documentation

bool protocols::symmetry::SymmetrySlider::allowed_current_slide ( )

Referenced by slide().

void protocols::symmetry::SymmetrySlider::apply ( core::pose::Pose & pose )

Referenced by protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), and protocols::symmetry::SymDockingInitialPerturbation::apply().

bool protocols::symmetry::SymmetrySlider::continue_slide ( core::pose::Pose & pose )

References core::conformation::symmetry::CEN_DOCK_SCORE, core::conformation::symmetry::FA_REP_SCORE, and protocols::symmetry::TR().

Referenced by slide().

void protocols::symmetry::SymmetrySlider::disallow_current_slide ( )

Referenced by slide().

bool protocols::symmetry::SymmetrySlider::dofmover_compresses	(	core::pose::Pose &	pose,
		protocols::rigid::RigidBodyDofTransMover &	dofmover
	)

References protocols::rigid::RigidBodyDofTransMover::apply(), core::scoring::rg, and protocols::rigid::RigidBodyDofTransMover::trans_axis().

bool protocols::symmetry::SymmetrySlider::finished ( )

std::map< core::Size, bool > protocols::symmetry::SymmetrySlider::get_allow_slide_jump_map ( ) const

Referenced by protocols::symmetry::SequentialSymmetrySlider::init(), protocols::symmetry::SequentialSymmetrySlider::select_jump(), protocols::symmetry::OrderedSequentialSymmetrySlider::select_jump(), and protocols::symmetry::RandomSymmetrySlider::select_jump().

core::Size protocols::symmetry::SymmetrySlider::get_current_jump ( )

Referenced by slide().

core::Real protocols::symmetry::SymmetrySlider::get_slide_threshold ( )

core::Real protocols::symmetry::SymmetrySlider::rg ( core::pose::Pose const & pose )

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::size(), and protocols::kinmatch::xyz().

virtual void protocols::symmetry::SymmetrySlider::select_jump ( )

pure virtual

Implemented in protocols::symmetry::RandomSymmetrySlider, protocols::symmetry::OrderedSequentialSymmetrySlider, and protocols::symmetry::SequentialSymmetrySlider.

void protocols::symmetry::SymmetrySlider::set_current_jump ( core::Size jump_nbr )

References protocols::symmetry::TR().

Referenced by protocols::symmetry::SequentialSymmetrySlider::select_jump(), protocols::symmetry::OrderedSequentialSymmetrySlider::select_jump(), and protocols::symmetry::RandomSymmetrySlider::select_jump().

void protocols::symmetry::SymmetrySlider::set_slide_criteria ( std::string SlideCriteria )

void protocols::symmetry::SymmetrySlider::set_slide_threshold ( std::string threshold )

void protocols::symmetry::SymmetrySlider::setup ( core::pose::Pose & pose )

References core::conformation::symmetry::SymDof::allow_dof(), core::conformation::symmetry::CEN_DOCK_SCORE, core::scoring::CENTROID_WTS, core::pose::Pose::conformation(), core::scoring::DOCK_LOW_PATCH, core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), protocols::symmetry::FaSymDockingSlideTogether::scorefxn_, and protocols::symmetry::TR().

void protocols::symmetry::SymmetrySlider::slide ( core::pose::Pose & pose )

References allowed_current_slide(), protocols::rigid::RigidBodyDofTransMover::apply(), core::pose::Pose::conformation(), continue_slide(), disallow_current_slide(), get_current_jump(), core::pose::symmetry::is_symmetric(), protocols::hybridization::score, core::pose::Pose::set_jump(), step_size(), protocols::rigid::RigidBodyDofTransMover::step_size(), protocols::symmetry::TR(), and protocols::rigid::RigidBodyDofTransMover::trans_axis().

void protocols::symmetry::SymmetrySlider::slide_away ( core::pose::Pose & pose )

References protocols::rigid::RigidBodyDofTransMover::apply(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), protocols::symmetry::TR(), and protocols::rigid::RigidBodyDofTransMover::trans_axis().

core::Real protocols::symmetry::SymmetrySlider::slide_score ( core::pose::Pose & pose )

References core::conformation::symmetry::CEN_DOCK_SCORE, core::pose::Pose::energies(), core::scoring::fa_rep, core::conformation::symmetry::FA_REP_SCORE, core::scoring::interchain_vdw, and core::scoring::Energies::total_energies().

core::Real protocols::symmetry::SymmetrySlider::step_size ( )

Referenced by slide().

bool protocols::symmetry::SymmetrySlider::very_far_away ( core::pose::Pose & pose )

References protocols::moves::Mover::clone(), core::pose::Pose::conformation(), core::sequence::end, core::pose::symmetry::find_symmetric_basejump_anchor(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), protocols::symmetry::TR(), and protocols::kinmatch::xyz().

Member Data Documentation

std::map< core::Size, bool > protocols::symmetry::SymmetrySlider::AllowSlideJumpMap_

private

core::Size protocols::symmetry::SymmetrySlider::current_jump_

private

std::map< core::Size, core::conformation::symmetry::SymDof > protocols::symmetry::SymmetrySlider::dofs_

private

std::map< core::Size, core::kinematics::Jump > protocols::symmetry::SymmetrySlider::InitialJumps_

private

std::map< core::Size, bool > protocols::symmetry::SymmetrySlider::InvertJump_

private

bool protocols::symmetry::SymmetrySlider::reset_slide_

private

core::scoring::ScoreFunctionOP protocols::symmetry::SymmetrySlider::scorefxn_

private

core::conformation::symmetry::SlideCriteriaType protocols::symmetry::SymmetrySlider::SlideCriteriaType_

private

std::string protocols::symmetry::SymmetrySlider::SlideThreshold_

private

core::Size protocols::symmetry::SymmetrySlider::total_num_slides_

private

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

src/protocols/symmetry/SymDockingInitialPerturbation.hh
src/protocols/symmetry/SymDockingInitialPerturbation.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation