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

#include <RNA_AnalyticLoopCloser.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser:

Public Member Functions
	RNA_AnalyticLoopCloser (core::Size const moving_suite, core::Size const chainbreak_suite)
	Construct the protocol object. More...

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

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

void	apply (core::pose::Pose &pose) override
	Apply the loop-rebuild protocol to the input pose. 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)

Size	nsol ()

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

utility::vector1< core::Real >	get_torsions (core::Size const n)

utility::vector1 < utility::vector1< core::Real > >	get_torsions_for_all_solutions ()

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, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Private Member Functions
bool	close_at_cutpoint (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::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	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
core::Size const	moving_suite_

core::Size const	chainbreak_suite_

bool const	verbose_

int	nsol_

core::scoring::ScoreFunctionOP	scorefxn_

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

utility::vector1< core::Real >	offset_save_

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

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_

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 protocols::filters::Filters_map	Filters_map

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

protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::RNA_AnalyticLoopCloser	(	core::Size const	moving_suite,
		core::Size const	chainbreak_suite
	)

Construct the protocol object.

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply ( core::pose::Pose & pose )

overridevirtual

Apply the loop-rebuild protocol to the input pose.

Apply the RNA Loop Closer – set up for Full Atom Representation.

Implements protocols::moves::Mover.

References close_at_cutpoint().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::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_, protocols::TR(), verbose_, and core::pose::Pose::xyz().

Referenced by close_at_cutpoint().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_based_on_score_function ( core::scoring::ScoreFunctionOP scorefxn )

References choose_best_solution_, choose_least_perturb_solution_, and scorefxn_.

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution ( )

References choose_best_solution_, and choose_least_perturb_solution_.

protocols::moves::MoverOP protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::clone ( ) const

overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::close_at_cutpoint ( core::pose::Pose & pose )

private

References apply_solutions(), atom_ids_, b_ang_, b_len_, chainbreak_suite_, figure_out_dof_ids_and_offsets(), fill_chainTORS(), moving_suite_, nsol_, protocols::forge::methods::order(), output_chainTORS(), t_ang_, protocols::TR(), verbose_, and core::pose::Pose::xyz().

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > const &	dt_ang
	)

private

References core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), core::chemical::rna::RNA_Info::c3prime_atom_index(), core::chemical::rna::RNA_Info::c4prime_atom_index(), core::chemical::rna::RNA_Info::c5prime_atom_index(), chainbreak_suite_, dof_ids_, figure_out_offset(), moving_suite_, core::chemical::rna::RNA_Info::o3prime_atom_index(), core::chemical::rna::RNA_Info::o5prime_atom_index(), offset_save_, core::chemical::rna::RNA_Info::p_atom_index(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), and core::kinematics::AtomTree::torsion_angle_dof_id().

Referenced by close_at_cutpoint().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_offset	(	core::pose::Pose const &	pose,
		core::id::DOF_ID const &	dof_id,
		core::Real const &	original_torsion_value,
		utility::vector1< core::Real > &	offset_save
	)

private

References core::pose::Pose::dof(), dof_ids_, protocols::TR(), and verbose_.

Referenced by figure_out_dof_ids_and_offsets().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::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 core::pose::Pose::xyz().

Referenced by apply_solutions(), and close_at_cutpoint().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::fill_solution	(	core::pose::Pose &	pose,
		core::Size const	n
	)		const

References dof_ids_, offset_save_, core::pose::Pose::set_dof(), and t_ang_.

Referenced by apply_solutions(), and get_all_solutions().

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::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_.

std::string protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

utility::vector1< Real > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions ( core::Size const n )

References offset_save_, and t_ang_.

Referenced by get_torsions_for_all_solutions().

utility::vector1< utility::vector1< Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions_for_all_solutions ( )

References get_torsions(), and t_ang_.

Size protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::nsol ( )

inline

References nsol_.

void protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::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, core::chemical::element::I, and protocols::TR().

Referenced by apply_solutions(), and close_at_cutpoint().

Member Data Documentation

utility::vector1< core::id::NamedAtomID > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::atom_ids_

private

Referenced by apply_solutions(), and close_at_cutpoint().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::b_ang_

private

Referenced by apply_solutions(), and close_at_cutpoint().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::b_len_

private

Referenced by apply_solutions(), and close_at_cutpoint().

core::Size const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::chainbreak_suite_

private

Referenced by close_at_cutpoint(), and figure_out_dof_ids_and_offsets().

bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_

private

Referenced by apply_solutions(), choose_best_solution_based_on_score_function(), and choose_least_perturb_solution().

bool protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution_

private

Referenced by apply_solutions(), choose_best_solution_based_on_score_function(), and choose_least_perturb_solution().

utility::vector1< core::id::DOF_ID > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::dof_ids_

private

Referenced by figure_out_dof_ids_and_offsets(), figure_out_offset(), and fill_solution().

core::Size const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::moving_suite_

private

Referenced by close_at_cutpoint(), and figure_out_dof_ids_and_offsets().

int protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::nsol_

private

Referenced by apply_solutions(), close_at_cutpoint(), get_all_solutions(), and nsol().

utility::vector1< core::Real > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::offset_save_

private

Referenced by figure_out_dof_ids_and_offsets(), fill_solution(), and get_torsions().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::scorefxn_

private

Referenced by apply_solutions(), and choose_best_solution_based_on_score_function().

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::t_ang_

private

Referenced by apply_solutions(), close_at_cutpoint(), fill_solution(), get_torsions(), and get_torsions_for_all_solutions().

bool const protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::verbose_

private

Referenced by apply_solutions(), close_at_cutpoint(), figure_out_offset(), and get_all_solutions().

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

src/protocols/stepwise/legacy/modeler/rna/RNA_AnalyticLoopCloser.hh
src/protocols/stepwise/legacy/modeler/rna/RNA_AnalyticLoopCloser.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation