#include <NearNativeLoopCloser.hh>

Inheritance diagram for protocols::pose_length_moves::NearNativeLoopCloser:

[legend]

Public Member Functions
	NearNativeLoopCloser ()

	NearNativeLoopCloser (int resAdjustmentStartLow, int resAdjustmentStartHigh, int resAdjustmentStopLow, int resAdjustmentStopHigh, int resAdjustmentStartLow_sheet, int resAdjustmentStartHigh_sheet, int resAdjustmentStopLow_sheet, int resAdjustmentStopHigh_sheet, core::Size loopLengthRangeLow, core::Size loopLengthRangeHigh, core::Size resBeforeLoop, core::Size resAfterLoop, char chainBeforeLoop, char chainAfterLoop, core::Real rmsThreshold, core::Real max_vdw_change, bool idealExtension, bool ideal, bool output_closed, std::string closure_type="lookback", std::string allowed_loop_abegos="", std::string label_loop="", std::string fragment_store_path="", std::string fragment_store_format="", std::string fragment_store_compression="", core::Size numb_stubs_to_consider=1)

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

core::Real	close_loop (Pose &pose)

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

void	combine_chains (Pose &pose)

void	switch_chain_order (Pose &pose, utility::vector1< core::Size > new_chain_order)

void	extendRegion (bool towardCTerm, core::Size resStart, char neighborResType, core::Size numberAddRes, core::pose::PoseOP &poseOP)

core::pose::PoseOP	create_maximum_length_pose (char resTypeBeforeLoop, char resTypeAfterLoop, core::pose::Pose pose)

utility::vector1< PossibleLoopOP >	create_potential_loops (core::pose::Pose pose)

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

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

core::pose::PoseOP	get_additional_output_with_rmsd (core::Real &return_rmsd)

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...

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...

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 Attributes
int	resAdjustmentStartLow_

int	resAdjustmentStartHigh_

int	resAdjustmentStopLow_

int	resAdjustmentStopHigh_

int	resAdjustmentStartLow_sheet_

int	resAdjustmentStartHigh_sheet_

int	resAdjustmentStopLow_sheet_

int	resAdjustmentStopHigh_sheet_

core::Size	loopLengthRangeLow_

core::Size	loopLengthRangeHigh_

core::Size	resBeforeLoop_

core::Size	resAfterLoop_

char	chainBeforeLoop_

char	chainAfterLoop_

core::Real	rmsThreshold_

bool	idealExtension_

bool	output_closed_

bool	output_all_

core::Size	numb_outputed_

core::Size	max_number_of_results_

bool	top_outputed_

core::Real	max_vdw_change_

bool	ideal_

std::string	closure_type_

std::string	pose_name_

std::string	label_loop_

protocols::indexed_structure_store::SSHashedFragmentStoreOP	SSHashedFragmentStoreOP_

utility::vector1< PossibleLoopOP >	possibleLoops_

std::string	allowed_loop_abegos_

std::string	fragment_store_path_

std::string	fragment_store_format_

std::string	fragment_store_compression_

core::Size	numb_stubs_to_consider_

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...

Constructor & Destructor Documentation

◆ NearNativeLoopCloser() [1/2]

protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser ( )

◆ NearNativeLoopCloser() [2/2]

protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser	(	int	resAdjustmentStartLow,
		int	resAdjustmentStartHigh,
		int	resAdjustmentStopLow,
		int	resAdjustmentStopHigh,
		int	resAdjustmentStartLow_sheet,
		int	resAdjustmentStartHigh_sheet,
		int	resAdjustmentStopLow_sheet,
		int	resAdjustmentStopHigh_sheet,
		core::Size	loopLengthRangeLow,
		core::Size	loopLengthRangeHigh,
		core::Size	resBeforeLoop,
		core::Size	resAfterLoop,
		char	chainBeforeLoop,
		char	chainAfterLoop,
		core::Real	rmsThreshold,
		core::Real	max_vdw_change,
		bool	idealExtension,
		bool	ideal,
		bool	output_closed,
		std::string	closure_type = `"lookback"`,
		std::string	allowed_loop_abegos = `""`,
		std::string	label_loop = `""`,
		std::string	fragment_store_path = `""`,
		std::string	fragment_store_format = `""`,
		std::string	fragment_store_compression = `""`,
		core::Size	numb_stubs_to_consider = `1`
	)

Member Function Documentation

◆ apply()

void protocols::pose_length_moves::NearNativeLoopCloser::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::conformation::Conformation::clear_parameters_set_list(), close_loop(), and core::pose::Pose::conformation().

◆ clone()

moves::MoverOP protocols::pose_length_moves::NearNativeLoopCloser::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ close_loop()

Real protocols::pose_length_moves::NearNativeLoopCloser::close_loop ( Pose & pose )

◆ combine_chains()

void protocols::pose_length_moves::NearNativeLoopCloser::combine_chains ( Pose & pose )

References core::pose::append_pose_to_pose(), chainAfterLoop_, chainBeforeLoop_, core::pose::get_chain_id_from_chain(), core::pose::get_chains(), core::pose::get_resnums_for_chain_id(), core::pose::has_chain(), core::pose::Pose::pdb_info(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::res_in_chain(), resAfterLoop_, resBeforeLoop_, core::pose::Pose::split_by_chain(), and switch_chain_order().

Referenced by close_loop().

◆ create_maximum_length_pose()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose	(	char	resTypeBeforeLoop,
		char	resTypeAfterLoop,
		core::pose::Pose	pose
	)

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::clone(), extendRegion(), core::pose::Pose::pdb_info(), core::kinematics::Edge::PEPTIDE, core::pose::renumber_pdbinfo_based_on_conf_chains(), resAdjustmentStartHigh_, resAdjustmentStopHigh_, resAfterLoop_, resBeforeLoop_, and core::pose::Pose::size().

Referenced by create_potential_loops().

◆ create_potential_loops()

vector1< PossibleLoopOP > protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops ( core::pose::Pose pose )

◆ extendRegion()

void protocols::pose_length_moves::NearNativeLoopCloser::extendRegion	(	bool	towardCTerm,
		core::Size	resStart,
		char	neighborResType,
		core::Size	numberAddRes,
		core::pose::PoseOP &	poseOP
	)

References core::chemical::aa_from_oneletter_code(), core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::conformation::ResidueFactory::create_residue(), idealExtension_, core::chemical::name_from_aa(), core::kinematics::Edge::PEPTIDE, and core::pose::renumber_pdbinfo_based_on_conf_chains().

Referenced by create_maximum_length_pose().

◆ get_additional_output()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output ( )

overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References get_additional_output_with_rmsd().

◆ get_additional_output_with_rmsd()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd ( core::Real & return_rmsd )

◆ get_name()

std::string protocols::pose_length_moves::NearNativeLoopCloser::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::pose_length_moves::NearNativeLoopCloser::mover_name ( )

static

Referenced by get_name(), protocols::pose_length_moves::NearNativeLoopCloserCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::pose_length_moves::NearNativeLoopCloser::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References allowed_loop_abegos_, chainAfterLoop_, chainBeforeLoop_, closure_type_, fragment_store_compression_, fragment_store_format_, fragment_store_path_, ideal_, idealExtension_, label_loop_, loopLengthRangeHigh_, loopLengthRangeLow_, max_number_of_results_, max_vdw_change_, numb_outputed_, numb_stubs_to_consider_, output_all_, output_closed_, resAdjustmentStartHigh_, resAdjustmentStartHigh_sheet_, resAdjustmentStartLow_, resAdjustmentStartLow_sheet_, resAdjustmentStopHigh_, resAdjustmentStopHigh_sheet_, resAdjustmentStopLow_, resAdjustmentStopLow_sheet_, resAfterLoop_, resBeforeLoop_, rmsThreshold_, SSHashedFragmentStoreOP_, top_outputed_, and protocols::TR().

◆ provide_xml_schema()

void protocols::pose_length_moves::NearNativeLoopCloser::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::pose_length_moves::NearNativeLoopCloserCreator::provide_xml_schema().

◆ switch_chain_order()

void protocols::pose_length_moves::NearNativeLoopCloser::switch_chain_order	(	Pose &	pose,
		utility::vector1< core::Size >	new_chain_order
	)

References core::pose::append_pose_to_pose(), core::conformation::Conformation::clear(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pose::Pose::pdb_info(), core::pose::renumber_pdbinfo_based_on_conf_chains(), and core::pose::Pose::split_by_chain().

Referenced by close_loop(), and combine_chains().

Member Data Documentation

◆ allowed_loop_abegos_

std::string protocols::pose_length_moves::NearNativeLoopCloser::allowed_loop_abegos_

private

Referenced by close_loop(), get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ chainAfterLoop_

char protocols::pose_length_moves::NearNativeLoopCloser::chainAfterLoop_

private

Referenced by close_loop(), combine_chains(), NearNativeLoopCloser(), and parse_my_tag().

◆ chainBeforeLoop_

char protocols::pose_length_moves::NearNativeLoopCloser::chainBeforeLoop_

private

Referenced by close_loop(), combine_chains(), NearNativeLoopCloser(), and parse_my_tag().

◆ closure_type_

std::string protocols::pose_length_moves::NearNativeLoopCloser::closure_type_

private

Referenced by close_loop(), NearNativeLoopCloser(), and parse_my_tag().

◆ fragment_store_compression_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_compression_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ fragment_store_format_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_format_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ fragment_store_path_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_path_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ ideal_

bool protocols::pose_length_moves::NearNativeLoopCloser::ideal_

private

Referenced by close_loop(), NearNativeLoopCloser(), and parse_my_tag().

◆ idealExtension_

bool protocols::pose_length_moves::NearNativeLoopCloser::idealExtension_

private

Referenced by extendRegion(), NearNativeLoopCloser(), and parse_my_tag().

◆ label_loop_

std::string protocols::pose_length_moves::NearNativeLoopCloser::label_loop_

private

Referenced by get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ loopLengthRangeHigh_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeHigh_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ loopLengthRangeLow_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeLow_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ max_number_of_results_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::max_number_of_results_

private

Referenced by get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ max_vdw_change_

core::Real protocols::pose_length_moves::NearNativeLoopCloser::max_vdw_change_

private

Referenced by NearNativeLoopCloser(), and parse_my_tag().

◆ numb_outputed_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::numb_outputed_

private

Referenced by get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ numb_stubs_to_consider_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::numb_stubs_to_consider_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ output_all_

bool protocols::pose_length_moves::NearNativeLoopCloser::output_all_

private

Referenced by get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ output_closed_

bool protocols::pose_length_moves::NearNativeLoopCloser::output_closed_

private

Referenced by close_loop(), get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ pose_name_

std::string protocols::pose_length_moves::NearNativeLoopCloser::pose_name_

private

Referenced by close_loop(), and get_additional_output_with_rmsd().

◆ possibleLoops_

utility::vector1<PossibleLoopOP> protocols::pose_length_moves::NearNativeLoopCloser::possibleLoops_

private

Referenced by close_loop(), and get_additional_output_with_rmsd().

◆ resAdjustmentStartHigh_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_

private

Referenced by create_maximum_length_pose(), create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStartHigh_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_sheet_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStartLow_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStartLow_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_sheet_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStopHigh_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_

private

Referenced by create_maximum_length_pose(), create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStopHigh_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_sheet_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStopLow_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAdjustmentStopLow_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_sheet_

private

Referenced by create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resAfterLoop_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::resAfterLoop_

private

Referenced by close_loop(), combine_chains(), create_maximum_length_pose(), create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ resBeforeLoop_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::resBeforeLoop_

private

Referenced by close_loop(), combine_chains(), create_maximum_length_pose(), create_potential_loops(), NearNativeLoopCloser(), and parse_my_tag().

◆ rmsThreshold_

core::Real protocols::pose_length_moves::NearNativeLoopCloser::rmsThreshold_

private

Referenced by close_loop(), get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

◆ SSHashedFragmentStoreOP_

protocols::indexed_structure_store::SSHashedFragmentStoreOP protocols::pose_length_moves::NearNativeLoopCloser::SSHashedFragmentStoreOP_

private

Referenced by NearNativeLoopCloser(), and parse_my_tag().

◆ top_outputed_

bool protocols::pose_length_moves::NearNativeLoopCloser::top_outputed_

private

Referenced by get_additional_output_with_rmsd(), NearNativeLoopCloser(), and parse_my_tag().

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

src/protocols/pose_length_moves/NearNativeLoopCloser.hh
src/protocols/pose_length_moves/NearNativeLoopCloser.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ NearNativeLoopCloser() [1/2]

◆ NearNativeLoopCloser() [2/2]

Member Function Documentation

◆ apply()

◆ clone()

◆ close_loop()

◆ combine_chains()

◆ create_maximum_length_pose()

◆ create_potential_loops()

◆ extendRegion()

◆ get_additional_output()

◆ get_additional_output_with_rmsd()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ switch_chain_order()

Member Data Documentation

◆ allowed_loop_abegos_

◆ chainAfterLoop_

◆ chainBeforeLoop_

◆ closure_type_

◆ fragment_store_compression_

◆ fragment_store_format_

◆ fragment_store_path_

◆ ideal_

◆ idealExtension_

◆ label_loop_

◆ loopLengthRangeHigh_

◆ loopLengthRangeLow_

◆ max_number_of_results_

◆ max_vdw_change_

◆ numb_outputed_

◆ numb_stubs_to_consider_

◆ output_all_

◆ output_closed_

◆ pose_name_

◆ possibleLoops_

◆ resAdjustmentStartHigh_

◆ resAdjustmentStartHigh_sheet_

◆ resAdjustmentStartLow_

◆ resAdjustmentStartLow_sheet_

◆ resAdjustmentStopHigh_

◆ resAdjustmentStopHigh_sheet_

◆ resAdjustmentStopLow_

◆ resAdjustmentStopLow_sheet_

◆ resAfterLoop_

◆ resBeforeLoop_

◆ rmsThreshold_

◆ SSHashedFragmentStoreOP_

◆ top_outputed_