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

#include <CoarseRNA_LoopCloser.hh>

Inheritance diagram for protocols::rna::denovo::coarse::CoarseRNA_LoopCloser:

[legend]

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

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

void	apply (core::pose::Pose &pose) override

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

bool	apply_after_jump_change (core::pose::Pose &pose, core::Size const &jumpno)

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

void	choose_best_solution_based_on_score_function (core::scoring::ScoreFunctionOP scorefxn)

void	choose_least_perturb_solution ()

void	get_all_solutions (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &pose_list)

void	set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map)

core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map ()

core::Size	nsol ()

utility::vector1< core::Size > const &	cutpos_list ()

ObjexxFCL::FArray1D< bool > const &	partition_definition ()

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	close_at_all_cutpoints (core::pose::Pose &pose)

void	figure_out_which_cutpoints_were_affected (core::pose::Pose const &pose)

bool	figure_out_pivots (core::pose::Pose const &pose)

void	remove_res (utility::vector1< core::Size > &res_vector, core::Size const &res)

void	backtrack (core::kinematics::tree::Atom const *current_atom, utility::vector1< core::Size > &upstream_res, utility::vector1< bool > &is_upstream_res, core::pose::Pose const &pose)

void	figure_out_forward_backward_res_by_backtracking (core::pose::Pose const &pose)

void	output_forward_backward_res ()

void	filter_path (utility::vector1< core::Size > &upstream_res, utility::vector1< bool > const &is_filter_res, core::pose::Pose const &pose)

void	figure_out_pivot_res_and_scratch_res ()

void	close_the_loop (core::pose::Pose &pose)

void	figure_out_dof_ids_and_offsets (core::pose::Pose const &pose, utility::vector1< core::Real > const &dt_ang)

void	figure_out_offset (core::pose::Pose const &pose, core::Size const &pivot, core::id::DOF_ID const &dof_id, core::Real const &original_torsion_value, utility::vector1< core::Real > &offset_save)

void	apply_solutions (core::pose::Pose &pose)

void	fill_solution (core::pose::Pose &pose, core::Size const n) const

void	output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) const

void	fill_chainTORS (core::pose::Pose const &pose, utility::vector1< core::id::NamedAtomID > const &atom_ids, utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len) const

Private Attributes
bool const	a_little_verbose_

bool const	verbose_

core::Size	seqpos_moved_

core::Size	cutpos_

utility::vector1< core::Size >	cutpos_list_

int	nsol_

core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map_

utility::vector1< core::Size >	backward_res_

utility::vector1< core::Size >	forward_res_

utility::vector1< core::Size >	pivot_res_

utility::vector1< core::Size >	scratch_res_

utility::vector1< core::Size >	pivot_to_scratch_res_

utility::vector1< bool >	is_backward_res_

utility::vector1< bool >	is_forward_res_

utility::vector1< bool >	is_pivot_res_

utility::vector1< bool >	is_scratch_res_

core::Size	which_scratch_res_is_cut_

core::scoring::ScoreFunctionOP	scorefxn_

utility::vector1< core::id::NamedAtomID >	atom_ids_

utility::vector1< core::Real >	offset_save1_

utility::vector1< core::Real >	offset_save2_

utility::vector1< core::id::DOF_ID >	dof_ids1_

utility::vector1< core::id::DOF_ID >	dof_ids2_

utility::vector1< utility::vector1< core::Real > >	t_ang_

utility::vector1< utility::vector1< core::Real > >	b_ang_

utility::vector1< utility::vector1< core::Real > >	b_len_

bool	choose_least_perturb_solution_

bool	choose_best_solution_

ObjexxFCL::FArray1D< bool >	partition_definition_

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

◆ CoarseRNA_LoopCloser()

protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::CoarseRNA_LoopCloser ( )

Construct the protocol object.

Member Function Documentation

◆ apply() [1/2]

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply ( core::pose::Pose & pose )

overridevirtual

Apply the RNA Loop Closer – currently specialized for coarse-grained RNA representation.

Implements protocols::moves::Mover.

◆ apply() [2/2]

bool protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		core::Size const &	seqpos_moved
	)

Apply the loop-rebuild protocol to the input pose.

References a_little_verbose_, close_at_all_cutpoints(), figure_out_which_cutpoints_were_affected(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_residue(), partition_definition_, seqpos_moved_, core::pose::Pose::size(), protocols::rna::denovo::TR(), and verbose_.

◆ apply_after_jump_change()

bool protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change	(	core::pose::Pose &	pose,
		core::Size const &	jumpno
	)

References a_little_verbose_, close_at_all_cutpoints(), figure_out_which_cutpoints_were_affected(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_jump(), partition_definition_, seqpos_moved_, core::pose::Pose::size(), protocols::rna::denovo::TR(), and verbose_.

◆ apply_solutions()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_solutions ( core::pose::Pose & pose )

private

References atom_ids_, b_ang_, b_len_, choose_best_solution_, choose_least_perturb_solution_, core::pose::Pose::dump_pdb(), fill_chainTORS(), fill_solution(), nsol_, output_chainTORS(), core::scoring::rg, protocols::hybridization::score, scorefxn_, core::pose::Pose::size(), t_ang_, verbose_, and core::pose::Pose::xyz().

Referenced by close_the_loop().

◆ atom_level_domain_map()

core::pose::toolbox::AtomLevelDomainMapOP protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::atom_level_domain_map ( )

References atom_level_domain_map_.

Referenced by set_atom_level_domain_map().

◆ backtrack()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::backtrack	(	core::kinematics::tree::Atom const *	current_atom,
		utility::vector1< core::Size > &	upstream_res,
		utility::vector1< bool > &	is_upstream_res,
		core::pose::Pose const &	pose
	)

private

References core::chemical::ResidueType::atom_name(), core::id::AtomID::atomno(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::parent(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

Referenced by figure_out_forward_backward_res_by_backtracking().

◆ choose_best_solution_based_on_score_function()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::choose_best_solution_based_on_score_function ( core::scoring::ScoreFunctionOP scorefxn )

References choose_best_solution_, choose_least_perturb_solution_, and scorefxn_.

◆ choose_least_perturb_solution()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::choose_least_perturb_solution ( )

References choose_best_solution_, and choose_least_perturb_solution_.

◆ clone()

protocols::moves::MoverOP protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::clone ( ) const

inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ close_at_all_cutpoints()

bool protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_at_all_cutpoints ( core::pose::Pose & pose )

private

References a_little_verbose_, close_the_loop(), cutpos_, cutpos_list_, figure_out_pivots(), nsol_, protocols::rna::denovo::TR(), and verbose_.

Referenced by apply(), and apply_after_jump_change().

◆ close_the_loop()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_the_loop ( core::pose::Pose & pose )

private

References a_little_verbose_, apply_solutions(), atom_ids_, b_ang_, b_len_, cutpos_, figure_out_dof_ids_and_offsets(), fill_chainTORS(), nsol_, protocols::forge::methods::order(), output_chainTORS(), pivot_to_scratch_res_, scratch_res_, t_ang_, protocols::rna::denovo::TR(), verbose_, which_scratch_res_is_cut_, and core::pose::Pose::xyz().

Referenced by close_at_all_cutpoints().

◆ cutpos_list()

utility::vector1< core::Size > const& protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::cutpos_list ( )

inline

References cutpos_list_.

◆ figure_out_dof_ids_and_offsets()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > const &	dt_ang
	)

private

References core::pose::Pose::atom_tree(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, dof_ids1_, dof_ids2_, figure_out_offset(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::named_atom_id_to_atom_id(), offset_save1_, offset_save2_, pivot_res_, pivot_to_scratch_res_, core::pose::Pose::residue_type(), and core::kinematics::AtomTree::torsion_angle_dof_id().

Referenced by close_the_loop().

◆ figure_out_forward_backward_res_by_backtracking()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking ( core::pose::Pose const & pose )

private

References core::kinematics::AtomTree::atom_dont_do_update(), core::pose::Pose::atom_tree(), backtrack(), backward_res_, cutpos_, filter_path(), forward_res_, is_backward_res_, is_forward_res_, core::conformation::named_atom_id_to_atom_id(), output_forward_backward_res(), core::pose::Pose::size(), and verbose_.

Referenced by figure_out_pivots().

◆ figure_out_offset()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_offset	(	core::pose::Pose const &	pose,
		core::Size const &	pivot,
		core::id::DOF_ID const &	dof_id,
		core::Real const &	original_torsion_value,
		utility::vector1< core::Real > &	offset_save
	)

private

References core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::dof(), and verbose_.

Referenced by figure_out_dof_ids_and_offsets().

◆ figure_out_pivot_res_and_scratch_res()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_pivot_res_and_scratch_res ( )

private

References a_little_verbose_, backward_res_, cutpos_, forward_res_, is_backward_res_, is_pivot_res_, is_scratch_res_, pivot_res_, pivot_to_scratch_res_, core::scoring::rg, scratch_res_, protocols::rna::denovo::TR(), verbose_, and which_scratch_res_is_cut_.

Referenced by figure_out_pivots().

◆ figure_out_pivots()

bool protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_pivots ( core::pose::Pose const & pose )

private

References atom_level_domain_map_, backward_res_, figure_out_forward_backward_res_by_backtracking(), figure_out_pivot_res_and_scratch_res(), forward_res_, output_forward_backward_res(), remove_res(), seqpos_moved_, and verbose_.

Referenced by close_at_all_cutpoints().

◆ figure_out_which_cutpoints_were_affected()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected ( core::pose::Pose const & pose )

private

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cutpos_, cutpos_list_, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), partition_definition_, core::pose::Pose::residue_type(), core::pose::Pose::size(), and verbose_.

Referenced by apply(), and apply_after_jump_change().

◆ fill_chainTORS()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::fill_chainTORS	(	core::pose::Pose const &	pose,
		utility::vector1< core::id::NamedAtomID > const &	atom_ids,
		utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &	atoms,
		utility::vector1< core::Real > &	dt_ang,
		utility::vector1< core::Real > &	db_ang,
		utility::vector1< core::Real > &	db_len
	)		const

private

References atom_ids_, and core::pose::Pose::xyz().

Referenced by apply_solutions(), and close_the_loop().

◆ fill_solution()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::fill_solution	(	core::pose::Pose &	pose,
		core::Size const	n
	)		const

private

References core::id::DOF_ID::BOGUS_DOF_ID(), dof_ids1_, dof_ids2_, offset_save1_, offset_save2_, pivot_to_scratch_res_, core::pose::Pose::set_dof(), and t_ang_.

Referenced by apply_solutions(), and get_all_solutions().

◆ filter_path()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::filter_path	(	utility::vector1< core::Size > &	upstream_res,
		utility::vector1< bool > const &	is_filter_res,
		core::pose::Pose const &	pose
	)

private

References atom_level_domain_map_, core::id::BB, and core::pose::Pose::conformation().

Referenced by figure_out_forward_backward_res_by_backtracking().

◆ get_all_solutions()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::get_all_solutions	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseOP > &	pose_list
	)

References core::pose::Pose::dump_pdb(), fill_solution(), nsol_, and verbose_.

◆ get_name()

std::string protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ nsol()

core::Size protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::nsol ( )

inline

References nsol_.

◆ output_chainTORS()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::output_chainTORS	(	utility::vector1< core::Real > const &	dt_ang,
		utility::vector1< core::Real > const &	db_ang,
		utility::vector1< core::Real > const &	db_len
	)		const

private

References core::chemical::element::F, and core::chemical::element::I.

Referenced by apply_solutions(), and close_the_loop().

◆ output_forward_backward_res()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::output_forward_backward_res ( )

private

References backward_res_, and forward_res_.

Referenced by figure_out_forward_backward_res_by_backtracking(), and figure_out_pivots().

◆ partition_definition()

ObjexxFCL::FArray1D< bool > const& protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::partition_definition ( )

inline

References partition_definition_.

◆ remove_res()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::remove_res	(	utility::vector1< core::Size > &	res_vector,
		core::Size const &	res
	)

private

Referenced by figure_out_pivots().

◆ set_atom_level_domain_map()

void protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::set_atom_level_domain_map ( core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map )

References atom_level_domain_map(), and atom_level_domain_map_.