#include <RBSegmentRelax.hh>

Inheritance diagram for protocols::rbsegment_relax::RBSegmentRelax:

[legend]

Public Member Functions
	RBSegmentRelax ()

	RBSegmentRelax (core::scoring::ScoreFunctionOP scorefxn, utility::vector1< RBSegment > const &RBSegment_input, protocols::loops::Loops const &Loops_input)

	~RBSegmentRelax () override

void	initialize (utility::vector1< core::fragment::FragSetOP > const &frag_libs, core::Real rnd=0.0)
	setup_RBSegmentRelax; initialize movesets to defaults More...

void	apply (core::pose::Pose &pose) override
	apply method More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	add_helixMover (RBSegmentMoverOP newMover)

void	add_strandMover (RBSegmentMoverOP newMover)

void	add_genericRBMover (RBSegmentMoverOP newMover)

void	add_compositeSegmentMover (RBSegmentMoverOP newMover)

void	add_wholeStructureMover (protocols::moves::MoverOP newMover)

void	clear_movesets ()

void	set_temperature (core::Real start, core::Real final)

void	set_helicalMoveStepsize (core::Real onAxisTrans, core::Real onAxisRot, core::Real offAxisTrans, core::Real offAxisRot)

void	set_genericRBMoveStepsize (core::Real trans, core::Real rot)

void	set_ncycles (int ncycles)

void	set_cst_weight (core::Real wt)

void	set_cst_width (core::Real width)

void	set_randomize (core::Size rand)

void	set_bootstrap (bool boot)

void	set_skip_lr (bool skip)

void	set_fix_ligands (bool fix)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	set_default_movemap ()

Private Attributes
core::Real	cst_weight_

core::Real	cst_width_

core::Real	cst_stdev_

core::Size	cst_seqwidth_

core::scoring::ScoreFunctionOP	scorefxn_

protocols::moves::MonteCarloOP	mc_

core::Size	cycles_

core::Real	init_temp

core::Real	final_temp

core::Real	helical_sigT

core::Real	helical_sigR

core::Real	helical_sigOffAxisT

core::Real	helical_sigOffAxisR

core::Real	strand_sigT

core::Real	strand_sigR

core::Real	strand_sigOffAxisT

core::Real	strand_sigOffAxisR

core::Real	genericRB_sigT

core::Real	genericRB_sigR

core::Real	randomness_

core::Size	rand_

bool	no_lr_

bool	bootstrap_

bool	fix_ligands_

utility::vector1< RBSegment >	rbsegs_input_

utility::vector1< RBSegment >	rbsegs_remap_

protocols::loops::Loops	loops_input_

utility::vector1< core::fragment::FragSetOP >	frag_libs_

std::vector< protocols::moves::MoverOP >	WholeStructureMoveSet_

std::vector< RBSegmentMoverOP >	HelixMoveSet_

std::vector< RBSegmentMoverOP >	StrandMoveSet_

std::vector< RBSegmentMoverOP >	GenericRBMoveSet_

std::vector< RBSegmentMoverOP >	CompositeSegmentMoveSet_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

◆ RBSegmentRelax() [1/2]

protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax ( )

default

◆ RBSegmentRelax() [2/2]

protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax	(	core::scoring::ScoreFunctionOP	scorefxn,
		utility::vector1< RBSegment > const &	RBSegment_input,
		protocols::loops::Loops const &	Loops_input
	)

◆ ~RBSegmentRelax()

protocols::rbsegment_relax::RBSegmentRelax::~RBSegmentRelax ( )

overridedefault

Member Function Documentation

◆ add_compositeSegmentMover()

void protocols::rbsegment_relax::RBSegmentRelax::add_compositeSegmentMover ( RBSegmentMoverOP newMover )

References CompositeSegmentMoveSet_.

◆ add_genericRBMover()

void protocols::rbsegment_relax::RBSegmentRelax::add_genericRBMover ( RBSegmentMoverOP newMover )

References GenericRBMoveSet_.

◆ add_helixMover()

void protocols::rbsegment_relax::RBSegmentRelax::add_helixMover ( RBSegmentMoverOP newMover )

References HelixMoveSet_.

◆ add_strandMover()

void protocols::rbsegment_relax::RBSegmentRelax::add_strandMover ( RBSegmentMoverOP newMover )

References StrandMoveSet_.

◆ add_wholeStructureMover()

void protocols::rbsegment_relax::RBSegmentRelax::add_wholeStructureMover ( protocols::moves::MoverOP newMover )

References WholeStructureMoveSet_.

◆ apply()

void protocols::rbsegment_relax::RBSegmentRelax::apply ( core::pose::Pose & pose )

overridevirtual

apply method

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), bootstrap_, protocols::relax::loop::LoopRelaxMover::cmd_line_csts(), CompositeSegmentMoveSet_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_packer_task(), cst_seqwidth_, cst_stdev_, cst_weight_, cst_width_, cycles_, protocols::relax::loop::LoopRelaxMover::fa_scorefxn(), final_temp, fix_ligands_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::relax::loop::LoopRelaxMover::frag_libs(), frag_libs_, genericRB_sigR, genericRB_sigT, GenericRBMoveSet_, core::scoring::get_score_function(), HelixMoveSet_, protocols::loops::idealize_loop(), init_temp, protocols::relax::loop::LoopRelaxMover::intermedrelax(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_ligand(), protocols::relax::loop::LoopRelaxMover::loops(), loops_input_, mc_, no_lr_, core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), rand_, randomness_, rbsegs_input_, rbsegs_remap_, protocols::relax::loop::LoopRelaxMover::refine(), protocols::antibody::design::relax, protocols::relax::loop::LoopRelaxMover::relax(), protocols::rbsegment_relax::remap_rb_segments(), protocols::relax::loop::LoopRelaxMover::remodel(), core::pose::Pose::residue(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), core::optimization::AtomTreeMinimizer::run(), scorefxn_, core::pose::Pose::secstruct(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::rbsegment_relax::set_constraints(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::rbsegment_relax::set_rb_constraints(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), core::pose::Pose::size(), protocols::loops::Loops::size(), StrandMoveSet_, protocols::rbsegment_relax::TS(), and WholeStructureMoveSet_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

◆ clear_movesets()

void protocols::rbsegment_relax::RBSegmentRelax::clear_movesets ( )

References CompositeSegmentMoveSet_, GenericRBMoveSet_, HelixMoveSet_, StrandMoveSet_, and WholeStructureMoveSet_.

◆ get_name()

std::string protocols::rbsegment_relax::RBSegmentRelax::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ initialize()

void protocols::rbsegment_relax::RBSegmentRelax::initialize	(	utility::vector1< core::fragment::FragSetOP > const &	frag_libs,
		core::Real	rnd = `0.0`
	)

setup_RBSegmentRelax; initialize movesets to defaults

References CompositeSegmentMoveSet_, frag_libs_, genericRB_sigR, genericRB_sigT, GenericRBMoveSet_, helical_sigOffAxisR, helical_sigOffAxisT, helical_sigR, helical_sigT, HelixMoveSet_, randomness_, strand_sigOffAxisR, strand_sigOffAxisT, strand_sigR, strand_sigT, and StrandMoveSet_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

◆ set_bootstrap()

void protocols::rbsegment_relax::RBSegmentRelax::set_bootstrap ( bool boot )

inline

References bootstrap_.

◆ set_cst_weight()

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_weight ( core::Real wt )

References cst_weight_.

◆ set_cst_width()

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_width ( core::Real width )

References cst_width_.

◆ set_default_movemap()

void protocols::rbsegment_relax::RBSegmentRelax::set_default_movemap ( )

private

◆ set_fix_ligands()

void protocols::rbsegment_relax::RBSegmentRelax::set_fix_ligands ( bool fix )

inline

References fix_ligands_.

◆ set_genericRBMoveStepsize()

void protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize	(	core::Real	trans,
		core::Real	rot
	)

References genericRB_sigR, genericRB_sigT, rot(), and trans().

◆ set_helicalMoveStepsize()

void protocols::rbsegment_relax::RBSegmentRelax::set_helicalMoveStepsize	(	core::Real	onAxisTrans,
		core::Real	onAxisRot,
		core::Real	offAxisTrans,
		core::Real	offAxisRot
	)

References helical_sigOffAxisR, helical_sigOffAxisT, helical_sigR, and helical_sigT.

◆ set_ncycles()

void protocols::rbsegment_relax::RBSegmentRelax::set_ncycles ( int ncycles )

References cycles_.

◆ set_randomize()

void protocols::rbsegment_relax::RBSegmentRelax::set_randomize ( core::Size rand )

inline

References rand_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

◆ set_skip_lr()

void protocols::rbsegment_relax::RBSegmentRelax::set_skip_lr ( bool skip )

inline

References no_lr_.

◆ set_temperature()

void protocols::rbsegment_relax::RBSegmentRelax::set_temperature	(	core::Real	start,
		core::Real	final
	)

References final_temp, init_temp, and protocols::loops::start.

Member Data Documentation

◆ bootstrap_

bool protocols::rbsegment_relax::RBSegmentRelax::bootstrap_

private

Referenced by apply(), RBSegmentRelax(), and set_bootstrap().

◆ CompositeSegmentMoveSet_

std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::CompositeSegmentMoveSet_

private

Referenced by add_compositeSegmentMover(), apply(), clear_movesets(), and initialize().

◆ cst_seqwidth_

core::Size protocols::rbsegment_relax::RBSegmentRelax::cst_seqwidth_

private

Referenced by apply(), and RBSegmentRelax().

◆ cst_stdev_

core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_stdev_

private

Referenced by apply(), and RBSegmentRelax().

◆ cst_weight_

core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_weight_

private

Referenced by apply(), RBSegmentRelax(), and set_cst_weight().

◆ cst_width_

core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_width_

private

Referenced by apply(), RBSegmentRelax(), and set_cst_width().

◆ cycles_

core::Size protocols::rbsegment_relax::RBSegmentRelax::cycles_

private

Referenced by apply(), RBSegmentRelax(), and set_ncycles().

◆ final_temp

core::Real protocols::rbsegment_relax::RBSegmentRelax::final_temp

private

Referenced by apply(), RBSegmentRelax(), and set_temperature().

◆ fix_ligands_

bool protocols::rbsegment_relax::RBSegmentRelax::fix_ligands_

private

Referenced by apply(), and set_fix_ligands().

◆ frag_libs_

utility::vector1< core::fragment::FragSetOP > protocols::rbsegment_relax::RBSegmentRelax::frag_libs_

private

Referenced by apply(), and initialize().

◆ genericRB_sigR

core::Real protocols::rbsegment_relax::RBSegmentRelax::genericRB_sigR

private

Referenced by apply(), initialize(), RBSegmentRelax(), and set_genericRBMoveStepsize().

◆ genericRB_sigT

core::Real protocols::rbsegment_relax::RBSegmentRelax::genericRB_sigT

private

Referenced by apply(), initialize(), RBSegmentRelax(), and set_genericRBMoveStepsize().

◆ GenericRBMoveSet_

std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::GenericRBMoveSet_

private

Referenced by add_genericRBMover(), apply(), clear_movesets(), and initialize().

◆ helical_sigOffAxisR

core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigOffAxisR

private

Referenced by initialize(), RBSegmentRelax(), and set_helicalMoveStepsize().

◆ helical_sigOffAxisT

core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigOffAxisT

private

Referenced by initialize(), RBSegmentRelax(), and set_helicalMoveStepsize().

◆ helical_sigR

core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigR

private

Referenced by initialize(), RBSegmentRelax(), and set_helicalMoveStepsize().

◆ helical_sigT

core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigT

private

Referenced by initialize(), RBSegmentRelax(), and set_helicalMoveStepsize().

◆ HelixMoveSet_

std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::HelixMoveSet_

private

Referenced by add_helixMover(), apply(), clear_movesets(), and initialize().

◆ init_temp

core::Real protocols::rbsegment_relax::RBSegmentRelax::init_temp

private

Referenced by apply(), RBSegmentRelax(), and set_temperature().

◆ loops_input_

protocols::loops::Loops protocols::rbsegment_relax::RBSegmentRelax::loops_input_

private

Referenced by apply().

◆ mc_

protocols::moves::MonteCarloOP protocols::rbsegment_relax::RBSegmentRelax::mc_

private

Referenced by apply().

◆ no_lr_

bool protocols::rbsegment_relax::RBSegmentRelax::no_lr_

private

Referenced by apply(), RBSegmentRelax(), and set_skip_lr().

◆ rand_

core::Size protocols::rbsegment_relax::RBSegmentRelax::rand_

private

Referenced by apply(), RBSegmentRelax(), and set_randomize().

◆ randomness_

core::Real protocols::rbsegment_relax::RBSegmentRelax::randomness_

private

Referenced by apply(), and initialize().

◆ rbsegs_input_

utility::vector1< RBSegment > protocols::rbsegment_relax::RBSegmentRelax::rbsegs_input_

private

Referenced by apply().

◆ rbsegs_remap_

utility::vector1< RBSegment > protocols::rbsegment_relax::RBSegmentRelax::rbsegs_remap_

private

Referenced by apply().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rbsegment_relax::RBSegmentRelax::scorefxn_

private

Referenced by apply().

◆ strand_sigOffAxisR

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigOffAxisR

private

Referenced by initialize(), and RBSegmentRelax().

◆ strand_sigOffAxisT

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigOffAxisT

private

Referenced by initialize(), and RBSegmentRelax().

◆ strand_sigR

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigR

private

Referenced by initialize(), and RBSegmentRelax().

◆ strand_sigT

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigT

private

Referenced by initialize(), and RBSegmentRelax().

◆ StrandMoveSet_

std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::StrandMoveSet_

private

Referenced by add_strandMover(), apply(), clear_movesets(), and initialize().

◆ WholeStructureMoveSet_

std::vector< protocols::moves::MoverOP > protocols::rbsegment_relax::RBSegmentRelax::WholeStructureMoveSet_

private

Referenced by add_wholeStructureMover(), apply(), and clear_movesets().

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

src/protocols/rbsegment_relax/RBSegmentRelax.hh
src/protocols/rbsegment_relax/RBSegmentRelax.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RBSegmentRelax() [1/2]

◆ RBSegmentRelax() [2/2]

◆ ~RBSegmentRelax()

Member Function Documentation

◆ add_compositeSegmentMover()

◆ add_genericRBMover()

◆ add_helixMover()

◆ add_strandMover()

◆ add_wholeStructureMover()

◆ apply()

◆ clear_movesets()

◆ get_name()

◆ initialize()

◆ set_bootstrap()

◆ set_cst_weight()

◆ set_cst_width()

◆ set_default_movemap()

◆ set_fix_ligands()

◆ set_genericRBMoveStepsize()

◆ set_helicalMoveStepsize()

◆ set_ncycles()

◆ set_randomize()

◆ set_skip_lr()

◆ set_temperature()

Member Data Documentation

◆ bootstrap_

◆ CompositeSegmentMoveSet_

◆ cst_seqwidth_

◆ cst_stdev_

◆ cst_weight_

◆ cst_width_

◆ cycles_

◆ final_temp

◆ fix_ligands_

◆ frag_libs_

◆ genericRB_sigR

◆ genericRB_sigT

◆ GenericRBMoveSet_

◆ helical_sigOffAxisR

◆ helical_sigOffAxisT

◆ helical_sigR

◆ helical_sigT

◆ HelixMoveSet_

◆ init_temp

◆ loops_input_

◆ mc_

◆ no_lr_

◆ rand_

◆ randomness_

◆ rbsegs_input_

◆ rbsegs_remap_

◆ scorefxn_

◆ strand_sigOffAxisR

◆ strand_sigOffAxisT

◆ strand_sigR

◆ strand_sigT

◆ StrandMoveSet_

◆ WholeStructureMoveSet_