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

#include <RNA_AnalyticLoopCloser.hh>

Inheritance diagram for protocols::swa::rna::RNA_AnalyticLoopCloser:

Collaboration diagram for protocols::swa::rna::RNA_AnalyticLoopCloser:

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

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

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

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

void	choose_best_solution_based_on_score_function (scoring::ScoreFunctionOP scorefxn)

void	choose_least_perturb_solution ()

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

Size	nsol ()

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

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

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagPtr const tag, 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...

std::string	get_type () const

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...

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	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
bool	close_at_cutpoint (pose::Pose &pose)

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

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

void	apply_solutions (pose::Pose &pose)

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

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

Private Attributes
Size const	moving_suite_

Size const	chainbreak_suite_

bool const	verbose_

int	nsol_

scoring::ScoreFunctionOP	scorefxn_

utility::vector1< id::NamedAtomID >	atom_ids_

utility::vector1< Real >	offset_save_

utility::vector1< id::DOF_ID >	dof_ids_

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

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

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

bool	choose_least_perturb_solution_

bool	choose_best_solution_

bool	choose_random_solution_

bool	save_all_solutions_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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.

Definition at line 42 of file RNA_AnalyticLoopCloser.hh.

Constructor & Destructor Documentation

protocols::swa::rna::RNA_AnalyticLoopCloser::RNA_AnalyticLoopCloser	(	Size const	moving_suite,
		Size const	chainbreak_suite
	)

Construct the protocol object.

Definition at line 63 of file RNA_AnalyticLoopCloser.cc.

Referenced by clone().

Member Function Documentation

void protocols::swa::rna::RNA_AnalyticLoopCloser::apply ( pose::Pose & pose)

virtual

Apply the loop-rebuild protocol to the input pose.

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

Implements protocols::moves::Mover.

Definition at line 84 of file RNA_AnalyticLoopCloser.cc.

References close_at_cutpoint().

Referenced by protocols::swa::rna::RNA_LoopCloseSampler::apply().

void protocols::swa::rna::RNA_AnalyticLoopCloser::apply_solutions ( pose::Pose & pose)

private

Definition at line 282 of file RNA_AnalyticLoopCloser.cc.

References atom_ids_, b_ang_, b_len_, choose_best_solution_, choose_least_perturb_solution_, choose_random_solution_, core::pose::Pose::dump_pdb(), fill_chainTORS(), fill_solution(), nsol_, output_chainTORS(), protocols::RG(), scorefxn_, t_ang_, core::pose::Pose::total_residue(), verbose_, and core::pose::Pose::xyz().

Referenced by close_at_cutpoint().

void protocols::swa::rna::RNA_AnalyticLoopCloser::choose_best_solution_based_on_score_function ( scoring::ScoreFunctionOP scorefxn)

Definition at line 442 of file RNA_AnalyticLoopCloser.cc.

References choose_best_solution_, choose_least_perturb_solution_, and scorefxn_.

void protocols::swa::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution ( )

Definition at line 450 of file RNA_AnalyticLoopCloser.cc.

References choose_best_solution_, and choose_least_perturb_solution_.

protocols::moves::MoverOP protocols::swa::rna::RNA_AnalyticLoopCloser::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

Definition at line 76 of file RNA_AnalyticLoopCloser.cc.

References RNA_AnalyticLoopCloser().

bool protocols::swa::rna::RNA_AnalyticLoopCloser::close_at_cutpoint ( pose::Pose & pose)

private

Definition at line 91 of file RNA_AnalyticLoopCloser.cc.

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_, verbose_, and core::pose::Pose::xyz().

Referenced by apply().

void protocols::swa::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets	(	pose::Pose const &	pose,
		utility::vector1< Real > const &	dt_ang
	)

private

Definition at line 195 of file RNA_AnalyticLoopCloser.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), chainbreak_suite_, dof_ids_, figure_out_offset(), moving_suite_, offset_save_, core::pose::Pose::residue(), and core::kinematics::AtomTree::torsion_angle_dof_id().

Referenced by close_at_cutpoint().

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

private

Definition at line 259 of file RNA_AnalyticLoopCloser.cc.

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

Referenced by figure_out_dof_ids_and_offsets().

void protocols::swa::rna::RNA_AnalyticLoopCloser::fill_chainTORS	(	pose::Pose const &	pose,
		utility::vector1< id::NamedAtomID > const &	atom_ids,
		utility::vector1< utility::vector1< Real > > &	atoms,
		utility::vector1< Real > &	dt_ang,
		utility::vector1< Real > &	db_ang,
		utility::vector1< Real > &	db_len
	)		const

private

Definition at line 476 of file RNA_AnalyticLoopCloser.cc.

References core::pose::Pose::xyz().

Referenced by apply_solutions(), and close_at_cutpoint().

void protocols::swa::rna::RNA_AnalyticLoopCloser::fill_solution	(	pose::Pose &	pose,
		Size const	n
	)		const

Definition at line 399 of file RNA_AnalyticLoopCloser.cc.

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

Referenced by protocols::swa::rna::RNA_LoopCloseSampler::apply(), apply_solutions(), and get_all_solutions().

void protocols::swa::rna::RNA_AnalyticLoopCloser::get_all_solutions	(	pose::Pose &	pose,
		utility::vector1< pose::PoseOP > &	pose_list
	)

Definition at line 380 of file RNA_AnalyticLoopCloser.cc.

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

virtual std::string protocols::swa::rna::RNA_AnalyticLoopCloser::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

Definition at line 51 of file RNA_AnalyticLoopCloser.hh.

utility::vector1< Real > protocols::swa::rna::RNA_AnalyticLoopCloser::get_torsions ( Size const n)

Definition at line 414 of file RNA_AnalyticLoopCloser.cc.

References offset_save_, and t_ang_.

Referenced by get_torsions_for_all_solutions().

utility::vector1< utility::vector1< Real > > protocols::swa::rna::RNA_AnalyticLoopCloser::get_torsions_for_all_solutions ( )

Definition at line 431 of file RNA_AnalyticLoopCloser.cc.

References get_torsions(), and t_ang_.

Size protocols::swa::rna::RNA_AnalyticLoopCloser::nsol ( )

inline

Definition at line 71 of file RNA_AnalyticLoopCloser.hh.

Referenced by protocols::swa::rna::RNA_LoopCloseSampler::apply().

void protocols::swa::rna::RNA_AnalyticLoopCloser::output_chainTORS	(	utility::vector1< Real > const &	dt_ang,
		utility::vector1< Real > const &	db_ang,
		utility::vector1< Real > const &	db_len
	)		const