The RNA de novo structure modeling protocol. More...

#include <RNA_LoopCloser.hh>

Inheritance diagram for protocols::rna::movers::RNA_LoopCloser:

[legend]

Public Member Functions
	RNA_LoopCloser ()
	Construct the protocol object. More...

protocols::moves::MoverOP	clone () const override
	Clone this object. More...

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

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

void	apply (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections)
	Apply the loop-rebuild protocol to the input pose. More...

core::Real	apply (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections, core::Size const &cutpoint)
	Apply the loop-rebuild protocol to the input pose. More...

core::Real	apply (core::pose::Pose &pose, core::Size const &cutpoint)
	Apply the loop-rebuild protocol to the input pose. More...

void	apply (core::pose::Pose &pose, utility::vector1< core::Size > const &cutpoints)
	Apply the loop-rebuild protocol to the input pose. More...

void	fast_scan (bool const &setting)

bool	check_closure (core::pose::Pose const &pose, core::Size const i, core::Real ccd_tolerance=-1.0)

bool	check_closure (core::pose::Pose const &pose, core::Real ccd_tolerance=-1.0)

core::Real	get_dist_err (core::pose::Pose const &pose, core::Size const cutpoint) const

void	set_verbose (bool const setting)

void	set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapCOP setting)

utility::vector1< core::Size >	get_cutpoints_closed (core::pose::Pose const &pose) const

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...

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
bool	passes_fast_scan (core::pose::Pose &pose, core::Size const i) const

core::Real	rna_ccd_close (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections, core::Size const &cutpoint) const

core::Real	get_chainbreak_xyz (core::pose::Pose const &pose, core::Size const cutpoint, utility::vector1< core::Vector > &upstream_xyzs, utility::vector1< core::Vector > &downstream_xyzs, core::Size const cutpoint_next_input=0) const

core::Real	get_gap_distance (core::pose::Pose &pose, core::Size const cutpoint) const

Private Attributes
bool	verbose_

core::Size	NUM_ROUNDS_

bool	check_tolerance_

core::Real	ccd_tolerance_

core::Real	absolute_ccd_tolerance_

core::Real	attempt_closure_cutoff_

core::Real	gap_distance_cutoff_

bool	fast_scan_

core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map_

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNA_LoopCloser()

protocols::rna::movers::RNA_LoopCloser::RNA_LoopCloser ( )

Construct the protocol object.

Member Function Documentation

◆ apply() [1/5]

void protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Referenced by protocols::rna::denovo::movers::RNA_Minimizer::apply(), apply(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), and protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks().

◆ apply() [2/5]

Real protocols::rna::movers::RNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		core::Size const &	cutpoint
	)

Apply the loop-rebuild protocol to the input pose.

References rna_ccd_close(), protocols::rna::movers::TR(), and verbose_.

◆ apply() [3/5]

void protocols::rna::movers::RNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		std::map< core::Size, core::Size > const &	connections
	)

Apply the loop-rebuild protocol to the input pose.

Apply the RNA loop closer

References apply(), fast_scan_, get_cutpoints_closed(), and passes_fast_scan().

◆ apply() [4/5]

Real protocols::rna::movers::RNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		std::map< core::Size, core::Size > const &	connections,
		core::Size const &	cutpoint
	)

Apply the loop-rebuild protocol to the input pose.

References rna_ccd_close(), protocols::rna::movers::TR(), and verbose_.

◆ apply() [5/5]

void protocols::rna::movers::RNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	cutpoints
	)

Apply the loop-rebuild protocol to the input pose.

References apply().

◆ check_closure() [1/2]

bool protocols::rna::movers::RNA_LoopCloser::check_closure	(	core::pose::Pose const &	pose,
		core::Real	ccd_tolerance = `-1.0`
	)

References absolute_ccd_tolerance_, check_closure(), and get_cutpoints_closed().

◆ check_closure() [2/2]

bool protocols::rna::movers::RNA_LoopCloser::check_closure	(	core::pose::Pose const &	pose,
		core::Size const	i,
		core::Real	ccd_tolerance = `-1.0`
	)

References absolute_ccd_tolerance_, core::chemical::CUTPOINT_LOWER, get_dist_err(), core::chemical::ResidueTypeBase::has_variant_type(), and core::pose::Pose::residue_type().

Referenced by check_closure(), and protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_loop_closed().

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::RNA_LoopCloser::clone ( ) const

inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ fast_scan()

void protocols::rna::movers::RNA_LoopCloser::fast_scan ( bool const & setting )

inline

References fast_scan_.

◆ get_chainbreak_xyz()

Real protocols::rna::movers::RNA_LoopCloser::get_chainbreak_xyz	(	core::pose::Pose const &	pose,
		core::Size const	cutpoint,
		utility::vector1< core::Vector > &	upstream_xyzs,
		utility::vector1< core::Vector > &	downstream_xyzs,
		core::Size const	cutpoint_next_input = `0`
	)		const

private

References core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_dist_err(), and rna_ccd_close().

◆ get_cutpoints_closed()

utility::vector1< core::Size > protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed ( core::pose::Pose const & pose ) const

References atom_level_domain_map_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, and core::pose::Pose::size().

Referenced by apply(), and check_closure().

◆ get_dist_err()

Real protocols::rna::movers::RNA_LoopCloser::get_dist_err	(	core::pose::Pose const &	pose,
		core::Size const	cutpoint
	)		const

References get_chainbreak_xyz().

Referenced by check_closure(), and passes_fast_scan().

◆ get_gap_distance()

Real protocols::rna::movers::RNA_LoopCloser::get_gap_distance	(	core::pose::Pose &	pose,
		core::Size const	cutpoint
	)		const

private

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

Referenced by passes_fast_scan().

◆ get_name()

std::string protocols::rna::movers::RNA_LoopCloser::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ passes_fast_scan()

bool protocols::rna::movers::RNA_LoopCloser::passes_fast_scan	(	core::pose::Pose &	pose,
		core::Size const	i
	)		const

private

References absolute_ccd_tolerance_, attempt_closure_cutoff_, core::pose::Pose::conformation(), gap_distance_cutoff_, get_dist_err(), get_gap_distance(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), protocols::rna::movers::TR(), core::conformation::Conformation::update_domain_map(), and verbose_.

Referenced by apply().

◆ rna_ccd_close()

Real protocols::rna::movers::RNA_LoopCloser::rna_ccd_close	(	core::pose::Pose &	pose,
		std::map< core::Size, core::Size > const &	connections,
		core::Size const &	cutpoint
	)		const

private

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::BB, ccd_tolerance_, check_tolerance_, core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::declare_cutpoint_chemical_bond(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), get_chainbreak_xyz(), core::kinematics::tree::Atom::get_stub(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_NA(), core::kinematics::Stub::M, core::chemical::ResidueTypeBase::name(), core::kinematics::FoldTree::new_jump(), NUM_ROUNDS_, protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::pose::Pose::torsion(), protocols::rna::movers::TR(), verbose_, and core::kinematics::tree::Atom::xyz().

Referenced by apply().

◆ set_atom_level_domain_map()

void protocols::rna::movers::RNA_LoopCloser::set_atom_level_domain_map ( core::pose::toolbox::AtomLevelDomainMapCOP setting )

inline

References atom_level_domain_map_.

◆ set_verbose()

void protocols::rna::movers::RNA_LoopCloser::set_verbose ( bool const setting )

inline

References verbose_.

Member Data Documentation

◆ absolute_ccd_tolerance_

core::Real protocols::rna::movers::RNA_LoopCloser::absolute_ccd_tolerance_

private

Referenced by check_closure(), and passes_fast_scan().

◆ atom_level_domain_map_

core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::movers::RNA_LoopCloser::atom_level_domain_map_

private

Referenced by get_cutpoints_closed(), and set_atom_level_domain_map().

◆ attempt_closure_cutoff_

core::Real protocols::rna::movers::RNA_LoopCloser::attempt_closure_cutoff_

private

Referenced by passes_fast_scan().

◆ ccd_tolerance_

core::Real protocols::rna::movers::RNA_LoopCloser::ccd_tolerance_

private

Referenced by rna_ccd_close().

◆ check_tolerance_

bool protocols::rna::movers::RNA_LoopCloser::check_tolerance_

private

Referenced by rna_ccd_close().

◆ fast_scan_

bool protocols::rna::movers::RNA_LoopCloser::fast_scan_

private

Referenced by apply(), and fast_scan().

◆ gap_distance_cutoff_

core::Real protocols::rna::movers::RNA_LoopCloser::gap_distance_cutoff_

private

Referenced by passes_fast_scan().

◆ NUM_ROUNDS_

core::Size protocols::rna::movers::RNA_LoopCloser::NUM_ROUNDS_

private

Referenced by rna_ccd_close().

◆ verbose_

bool protocols::rna::movers::RNA_LoopCloser::verbose_

private

Referenced by apply(), passes_fast_scan(), rna_ccd_close(), and set_verbose().

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

src/protocols/rna/movers/RNA_LoopCloser.hh
src/protocols/rna/movers/RNA_LoopCloser.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNA_LoopCloser()

Member Function Documentation

◆ apply() [1/5]

◆ apply() [2/5]

◆ apply() [3/5]

◆ apply() [4/5]

◆ apply() [5/5]

◆ check_closure() [1/2]

◆ check_closure() [2/2]

◆ clone()

◆ fast_scan()

◆ get_chainbreak_xyz()

◆ get_cutpoints_closed()

◆ get_dist_err()

◆ get_gap_distance()

◆ get_name()

◆ passes_fast_scan()

◆ rna_ccd_close()

◆ set_atom_level_domain_map()

◆ set_verbose()

Member Data Documentation

◆ absolute_ccd_tolerance_

◆ atom_level_domain_map_

◆ attempt_closure_cutoff_

◆ ccd_tolerance_

◆ check_tolerance_

◆ fast_scan_

◆ gap_distance_cutoff_

◆ NUM_ROUNDS_

◆ verbose_