protocols::symmetry::SymmetrySlider Class Reference

#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

SymmetrySlider() [1/2]

protocols::symmetry::SymmetrySlider::SymmetrySlider

(

core::pose::Pose &

pose

)

SymmetrySlider() [2/2]

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.

~SymmetrySlider()

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

overridedefault

Member Function Documentation

allowed_current_slide()

bool protocols::symmetry::SymmetrySlider::allowed_current_slide

(

)

Referenced by slide().

apply()

void protocols::symmetry::SymmetrySlider::apply

(

core::pose::Pose &

pose

)

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

continue_slide()

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().

disallow_current_slide()

void protocols::symmetry::SymmetrySlider::disallow_current_slide

(

)

Referenced by slide().

dofmover_compresses()

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().

finished()

bool protocols::symmetry::SymmetrySlider::finished

(

)

get_allow_slide_jump_map()

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().

get_current_jump()

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

(

)

Referenced by slide().

get_slide_threshold()

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

(

)

rg()

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 core::conformation::Atom::xyz().

select_jump()

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

pure virtual

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

set_current_jump()

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().

set_slide_criteria()

void protocols::symmetry::SymmetrySlider::set_slide_criteria

(

std::string

SlideCriteria

)

set_slide_threshold()

void protocols::symmetry::SymmetrySlider::set_slide_threshold

(

std::string

threshold

)

setup()

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

slide()

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::rigid::RigidBodyDofTransMover::last_slide_good(), protocols::hybridization::score, core::pose::Pose::set_jump(), step_size(), protocols::rigid::RigidBodyDofTransMover::step_size(), protocols::symmetry::TR(), and protocols::rigid::RigidBodyDofTransMover::trans_axis().

slide_away()

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().

slide_score()

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().

step_size()

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

(

)

Referenced by slide().

very_far_away()

bool protocols::symmetry::SymmetrySlider::very_far_away

(

core::pose::Pose &

pose

)

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

Member Data Documentation

AllowSlideJumpMap_

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

private

current_jump_

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

private

dofs_

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

private

InitialJumps_

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

private

InvertJump_

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

private

reset_slide_

bool protocols::symmetry::SymmetrySlider::reset_slide_

private

scorefxn_

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

private

SlideCriteriaType_

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

private

SlideThreshold_

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

private

total_num_slides_

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