protocols::simple_moves::symmetry::SymmetrySlider Class Reference

#include <SymDockingInitialPerturbation.hh>

Inheritance diagram for protocols::simple_moves::symmetry::SymmetrySlider:

Collaboration diagram for protocols::simple_moves::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")
virtual	~SymmetrySlider ()
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< 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::symmetry::SymmetricScoreFunctionOP	scorefxn_
std::string	SlideThreshold_
bool	reset_slide_
core::Size	total_num_slides_
core::Size	current_jump_

Constructor & Destructor Documentation

protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider

(

core::pose::Pose &

pose)

protocols::simple_moves::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::simple_moves::symmetry::FaSymDockingSlideTogether::scorefxn_, core::scoring::Energies::total_energies(), and core::conformation::symmetry::TOTAL_NUM_CRITERIA.

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

virtual

Member Function Documentation

bool protocols::simple_moves::symmetry::SymmetrySlider::allowed_current_slide

(

)

Referenced by slide().

void protocols::simple_moves::symmetry::SymmetrySlider::apply

(

core::pose::Pose &

pose)

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

bool protocols::simple_moves::symmetry::SymmetrySlider::continue_slide

(

core::pose::Pose &

pose)

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

Referenced by slide().

void protocols::simple_moves::symmetry::SymmetrySlider::disallow_current_slide

(

)

Referenced by slide().

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

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

bool protocols::simple_moves::symmetry::SymmetrySlider::finished

(

)

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

(

)

const

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

core::Size protocols::simple_moves::symmetry::SymmetrySlider::get_current_jump

(

)

Referenced by slide().

core::Real protocols::simple_moves::symmetry::SymmetrySlider::get_slide_threshold

(

)

core::Real protocols::simple_moves::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(), protocols::simple_moves::rg(), core::pose::Pose::total_residue(), and protocols::kinmatch::xyz().

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

pure virtual

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

void protocols::simple_moves::symmetry::SymmetrySlider::set_current_jump

(

core::Size

jump_nbr)

References protocols::simple_moves::symmetry::TR().

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

void protocols::simple_moves::symmetry::SymmetrySlider::set_slide_criteria

(

std::string

SlideCriteria)

void protocols::simple_moves::symmetry::SymmetrySlider::set_slide_threshold

(

std::string

threshold)

void protocols::simple_moves::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::ScoreFunctionFactory::create_score_function(), core::scoring::DOCK_LOW_PATCH, core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::scorefxn_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and protocols::simple_moves::symmetry::TR().

void protocols::simple_moves::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(), core::pose::Pose::set_jump(), step_size(), protocols::rigid::RigidBodyDofTransMover::step_size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), protocols::simple_moves::symmetry::TR(), and protocols::rigid::RigidBodyDofTransMover::trans_axis().

void protocols::simple_moves::symmetry::SymmetrySlider::slide_away

(

core::pose::Pose &

pose)

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

core::Real protocols::simple_moves::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::simple_moves::symmetry::SymmetrySlider::step_size

(

)

Referenced by slide().

bool protocols::simple_moves::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(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), protocols::simple_moves::symmetry::TR(), and protocols::kinmatch::xyz().

Member Data Documentation

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

private

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

private

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

private

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

private

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

private

bool protocols::simple_moves::symmetry::SymmetrySlider::reset_slide_

private

core::scoring::symmetry::SymmetricScoreFunctionOP protocols::simple_moves::symmetry::SymmetrySlider::scorefxn_

private

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

private

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

private

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

private

---

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

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