Adds constraints generated by ConstraintGenerators to a pose. More...

#include <NubInitioLoopClosureMover.hh>

Inheritance diagram for protocols::fold_from_loops::movers::NubInitioLoopClosureMover:

Public Member Functions
	NubInitioLoopClosureMover ()

	~NubInitioLoopClosureMover () override

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

core::scoring::ScoreFunctionOP	centroid_scorefxn () const
	centroid_score is provided to the CCDclosure to close the loop. More...

void	centroid_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

core::scoring::ScoreFunctionOP	fullatom_scorefxn () const
	fullatom_score is used to pack sidechains after the closure More...

void	fullatom_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

core::Size	break_side () const
	break_side defines how many residues in each side of the chainbreak are allowed to move (as long as they are not !FLEXIBLE+MOTIF labeled residues) More...

void	break_side (core::Real value)

bool	break_side_ramp () const
	when set to true, in each unsuccesfull closure try, it allows one more residue to move More...

void	break_side_ramp (bool pick)

void	max_trials (core::Size choice)
	set how many times we try to close the loops before accepting we cannot More...

core::Size	max_trials () const

std::string	fragments_id () const
	id of the fragments loaded into the DataMap More...

void	fragments_id (std::string const &name)

core::fragment::FragSetOP	fragments () const
	fragments More...

void	fragments (core::fragment::FragSetOP frags)

bool	trust () const
	if true, trust the residue variants to locate chain breaks; otherwise use the FoldTree More...

void	trust (bool pick)

bool	label () const
	if true, label the resiudes that have moved or been repacked during the Mover. More...

void	label (bool pick)

bool	centroid () const
	if true, assume input is centroid, and so should be the output. More...

void	centroid (bool pick)

bool	design () const
	if true, a part from repacking, also redesign the residues of the loop and around following FFL rules. More...

void	design (bool pick)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

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

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 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...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
void	repack (core::pose::Pose &pose)
	Repack sidechains without alter bb. More...

bool	is_cutpoint_close (core::pose::Pose const &pose, core::Size const &residue, bool by_variant=false) const
	Evaluate if the supossed cutpoint has already been fixed. It is assumed that one previously check if the residue is cutpoint. More...

core::kinematics::FoldTree	make_final_tree (core::pose::Pose const &pose) const
	Generates the expected final FoldTree that the Pose should have. More...

core::kinematics::MoveMapOP	loop_closure_movemap (core::pose::Pose const &pose)
	Generates the movemap for loop_closure. More...

core::select::residue_selector::ResidueSelectorOP	movable_residues () const
	Selector to pick residues labeled TEMPLATE or FLEXIBLE; the only ones that can be allowed to move. More...

bool	has_movable_residues (core::pose::Pose const &pose) const
	This mover works only when there are residues labeled TEMPLATE of FLEXIBLE. If there are no residues labeled like so, CCD closure will be unable to close and will end up reporting a failure. More...

core::select::residue_selector::ResidueSelectorOP	packable_residues () const
	Selector to pick residues labeled TEMPLATE, FLEXIBLE or COLDSPOT. More...

core::select::residue_selector::ResidueSelectorOP	active_movable_residues (core::pose::Pose const &pose)
	Selector to pick residues labeled TEMPLATE or FLEXIBLE; that are in the appropiate sequence distance of the cutpoints. More...

core::select::residue_selector::ResidueSelectorOP	active_packable_residues () const
	Selector to pick residues labeled TEMPLATE, FLEXIBLE or COLDSPOT; that are part of the moved loop. More...

bool	has_cutpoints (core::pose::Pose const &pose) const
	Check if there are cutpoints in the Pose. More...

void	apply_closure_trust (core::pose::Pose &pose, bool by_variant=false) const
	Checks if the residues still considered cutpoints have bee actually closed or not. More...

void	show_cutpoints (core::pose::Pose const &pose) const
	Show process. More...

void	make_cutpoints_coherent_to_foldtree (core::pose::Pose &pose) const
	Re-check the residue variant according to the FoldTree. More...

void	make_foldtree_coherent_to_cutpoints (core::pose::Pose &pose) const
	Re-check FoldTree according to residue variant. More...

Static Private Member Functions
static core::scoring::ScoreFunctionOP	default_centroid_scorefxn ()

static core::Real	default_centroid_chainclosure_weight ()

static core::scoring::ScoreFunctionOP	set_centroid_default_chainclosure_weight (core::scoring::ScoreFunctionOP const &scorefxn)

static core::scoring::ScoreFunctionOP	default_fullatom_scorefxn ()

static core::Size	default_break_side ()

static bool	default_break_side_ramp ()

static core::Size	default_max_trials ()

static bool	default_trust ()

static bool	default_label ()

static bool	default_centroid ()

static bool	default_design ()

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

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...

Detailed Description

Adds constraints generated by ConstraintGenerators to a pose.

Constructor & Destructor Documentation

protocols::fold_from_loops::movers::NubInitioLoopClosureMover::NubInitioLoopClosureMover ( )

protocols::fold_from_loops::movers::NubInitioLoopClosureMover::~NubInitioLoopClosureMover ( )

overridedefault

Member Function Documentation

core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::active_movable_residues ( core::pose::Pose const & pose )

private

Selector to pick residues labeled TEMPLATE or FLEXIBLE; that are in the appropiate sequence distance of the cutpoints.

References altered_residues_, break_side_, break_side_ramp_value_, movable_residues(), and core::select::residue_selector::ReturnResidueSubsetSelector::set_residue_subset().

Referenced by apply(), and loop_closure_movemap().

core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::active_packable_residues ( ) const

private

Selector to pick residues labeled TEMPLATE, FLEXIBLE or COLDSPOT; that are part of the moved loop.

References altered_residues_, core::select::residue_selector::ReturnResidueSubsetSelector::clone(), and packable_residues().

Referenced by repack().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References active_movable_residues(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), break_side_, break_side_ramp_, break_side_ramp_value_, core::chemical::CENTROID, centroid_, centroid_scorefxn_, protocols::jumping::close_chainbreaks(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::FA_STANDARD, protocols::moves::FAIL_BAD_INPUT, protocols::moves::FAIL_DO_NOT_RETRY, core::pose::Pose::fold_tree(), fragments_, get_name(), has_cutpoints(), has_movable_residues(), core::conformation::Residue::has_variant_type(), label_, loop_closure_movemap(), make_cutpoints_coherent_to_foldtree(), make_final_tree(), make_foldtree_coherent_to_cutpoints(), max_trials_, protocols::moves::MS_SUCCESS, core::pose::Pose::remove_constraints(), core::pose::remove_variant_type_from_pose_residue(), repack(), core::pose::Pose::replace_residue(), core::conformation::Conformation::residue(), set_centroid_default_chainclosure_weight(), protocols::moves::Mover::set_last_move_status(), core::pose::setPoseExtraScore(), show_cutpoints(), protocols::fold_from_loops::movers::TR(), trust_, core::pose::Pose::update_residue_neighbors(), and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::write().

Referenced by protocols::fold_from_loops::NubInitioMover::post_process().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust	(	core::pose::Pose &	pose,
		bool	by_variant = `false`
	)		const

private

Checks if the residues still considered cutpoints have bee actually closed or not.

References core::conformation::Residue::chain(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), is_cutpoint_close(), core::pose::remove_variant_type_from_pose_residue(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), show_cutpoints(), core::pose::Pose::size(), protocols::fold_from_loops::movers::TR(), and trust_.

Referenced by make_foldtree_coherent_to_cutpoints().

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side ( ) const

break_side defines how many residues in each side of the chainbreak are allowed to move (as long as they are not !FLEXIBLE+MOTIF labeled residues)

References break_side_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side ( core::Real value )

References break_side_.

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_ramp ( ) const

when set to true, in each unsuccesfull closure try, it allows one more residue to move

References break_side_ramp_.

Referenced by parse_my_tag(), and protocols::fold_from_loops::NubInitioMover::post_process().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_ramp ( bool pick )

References break_side_ramp_.

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid ( ) const

if true, assume input is centroid, and so should be the output.

References centroid_.

Referenced by protocols::fold_from_loops::NubInitioMover::post_process().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid ( bool pick )

References centroid_.

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid_scorefxn ( ) const

centroid_score is provided to the CCDclosure to close the loop.

References centroid_scorefxn_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References centroid_scorefxn_.

protocols::moves::MoverOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_break_side ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_break_side_ramp ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_centroid ( )

staticprivate

core::Real protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_centroid_chainclosure_weight ( )

staticprivate

Referenced by set_centroid_default_chainclosure_weight().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_centroid_scorefxn ( )

staticprivate

References core::scoring::ScoreFunctionFactory::create_score_function(), and set_centroid_default_chainclosure_weight().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_design ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_fullatom_scorefxn ( )

staticprivate

References core::scoring::get_score_function().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_label ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_max_trials ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_trust ( )

staticprivate

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::design ( ) const

if true, a part from repacking, also redesign the residues of the loop and around following FFL rules.

References design_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::design ( bool pick )

References design_.

core::fragment::FragSetOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments ( ) const

fragments

References fragments_.

Referenced by protocols::fold_from_loops::NubInitioMover::post_process().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments ( core::fragment::FragSetOP frags )

References fragments_.

std::string protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments_id ( ) const

id of the fragments loaded into the DataMap

References fragments_id_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments_id ( std::string const & name )

References fragments_id_, and protocols::moves::Mover::name().

protocols::moves::MoverOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fullatom_scorefxn ( ) const

fullatom_score is used to pack sidechains after the closure

References fullatom_scorefxn_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fullatom_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References fullatom_scorefxn_.

std::string protocols::fold_from_loops::movers::NubInitioLoopClosureMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by apply().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::has_cutpoints ( core::pose::Pose const & pose ) const

private

Check if there are cutpoints in the Pose.

References core::select::residue_selector::has_any_true_selection().

Referenced by apply().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::has_movable_residues ( core::pose::Pose const & pose ) const

private

This mover works only when there are residues labeled TEMPLATE of FLEXIBLE. If there are no residues labeled like so, CCD closure will be unable to close and will end up reporting a failure.

References core::select::residue_selector::has_any_true_selection(), and movable_residues().

Referenced by apply().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close	(	core::pose::Pose const &	pose,
		core::Size const &	residue,
		bool	by_variant = `false`
	)		const

private

Evaluate if the supossed cutpoint has already been fixed. It is assumed that one previously check if the residue is cutpoint.

References core::chemical::CUTPOINT_LOWER, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by apply_closure_trust().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::label ( ) const

if true, label the resiudes that have moved or been repacked during the Mover.

References label_.

Referenced by parse_my_tag(), and protocols::fold_from_loops::NubInitioMover::post_process().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::label ( bool pick )

References label_.

core::kinematics::MoveMapOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::loop_closure_movemap ( core::pose::Pose const & pose )

private

Generates the movemap for loop_closure.

References active_movable_residues(), and core::select::movemap::mm_enable.

Referenced by apply().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree ( core::pose::Pose & pose ) const

private

Re-check the residue variant according to the FoldTree.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::residue(), core::pose::Pose::size(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by apply().

core::kinematics::FoldTree protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree ( core::pose::Pose const & pose ) const

private

Generates the expected final FoldTree that the Pose should have.

References core::pose::Pose::fold_tree(), core::pose::Pose::residue(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and protocols::fold_from_loops::movers::TR().

Referenced by apply().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_foldtree_coherent_to_cutpoints ( core::pose::Pose & pose ) const

private

Re-check FoldTree according to residue variant.

References apply_closure_trust().

Referenced by apply().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::max_trials ( core::Size choice )

set how many times we try to close the loops before accepting we cannot

References max_trials_.

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::max_trials ( ) const

References max_trials_.

Referenced by parse_my_tag().

core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::movable_residues ( ) const

private

Selector to pick residues labeled TEMPLATE or FLEXIBLE; the only ones that can be allowed to move.

Referenced by active_movable_residues(), and has_movable_residues().

std::string protocols::fold_from_loops::movers::NubInitioLoopClosureMover::mover_name ( )

static

Referenced by get_name(), protocols::fold_from_loops::movers::NubInitioLoopClosureMoverCreator::keyname(), and provide_xml_schema().

core::select::residue_selector::ResidueSelectorOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::packable_residues ( ) const

private

Selector to pick residues labeled TEMPLATE, FLEXIBLE or COLDSPOT.

Referenced by active_packable_residues().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References break_side(), break_side_ramp(), centroid_scorefxn(), default_break_side(), default_break_side_ramp(), default_design(), default_label(), default_max_trials(), default_trust(), design(), fragments_, fragments_id(), fragments_id_, fullatom_scorefxn(), label(), max_trials(), core::scoring::parse_score_function(), protocols::fold_from_loops::movers::TR(), and trust().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function_w_description(), default_break_side(), default_break_side_ramp(), default_design(), default_label(), default_max_trials(), default_trust(), mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::fold_from_loops::movers::NubInitioLoopClosureMoverCreator::provide_xml_schema().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::repack ( core::pose::Pose & pose )

private

Repack sidechains without alter bb.

References active_packable_residues(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), core::pack::task::operation::DisallowIfNonnativeRLT::clone(), design_, core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), fullatom_scorefxn_, label_, and protocols::fold_from_loops::movers::TR().

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::set_centroid_default_chainclosure_weight ( core::scoring::ScoreFunctionOP const & scorefxn )

staticprivate

References core::scoring::chainbreak, default_centroid_chainclosure_weight(), core::scoring::linear_chainbreak, and core::scoring::overlap_chainbreak.

Referenced by apply(), and default_centroid_scorefxn().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::show_cutpoints ( core::pose::Pose const & pose ) const

private

Show process.

References core::pose::Pose::annotated_sequence(), core::pose::Pose::fold_tree(), core::select::residue_selector::represent_residue_selector(), core::select::residue_selector::selection_positions(), core::pose::Pose::sequence(), and protocols::fold_from_loops::movers::TR().

Referenced by apply(), and apply_closure_trust().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::trust ( ) const

if true, trust the residue variants to locate chain breaks; otherwise use the FoldTree

References trust_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::NubInitioLoopClosureMover::trust ( bool pick )

References trust_.

Member Data Documentation

core::select::residue_selector::ReturnResidueSubsetSelector protocols::fold_from_loops::movers::NubInitioLoopClosureMover::altered_residues_

private

Referenced by active_movable_residues(), and active_packable_residues().

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_

private

Referenced by active_movable_residues(), apply(), and break_side().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_ramp_

private

Referenced by apply(), and break_side_ramp().

core::Size protocols::fold_from_loops::movers::NubInitioLoopClosureMover::break_side_ramp_value_

private

Referenced by active_movable_residues(), and apply().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid_

private

Referenced by apply(), and centroid().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::centroid_scorefxn_

private

Referenced by apply(), and centroid_scorefxn().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::design_

private

Referenced by design(), and repack().

core::fragment::FragSetOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments_

private

Referenced by apply(), fragments(), and parse_my_tag().

std::string protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fragments_id_

private

Referenced by fragments_id(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::fold_from_loops::movers::NubInitioLoopClosureMover::fullatom_scorefxn_

private

Referenced by fullatom_scorefxn(), and repack().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::label_

private

Referenced by apply(), label(), and repack().

core::Real protocols::fold_from_loops::movers::NubInitioLoopClosureMover::max_trials_

private

Referenced by apply(), and max_trials().

bool protocols::fold_from_loops::movers::NubInitioLoopClosureMover::trust_

private

Referenced by apply(), apply_closure_trust(), and trust().

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

src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.hh
src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc

Private Attributes
core::scoring::ScoreFunctionOP	centroid_scorefxn_

core::scoring::ScoreFunctionOP	fullatom_scorefxn_

core::Size	break_side_

core::Size	break_side_ramp_value_

bool	break_side_ramp_

core::Real	max_trials_

std::string	fragments_id_

core::fragment::FragSetOP	fragments_

core::select::residue_selector::ReturnResidueSubsetSelector	altered_residues_

bool	trust_

bool	label_

bool	centroid_

bool	design_

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation