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

#include <CoarseRNA_LoopCloser.hh>

Inheritance diagram for protocols::coarse_rna::CoarseRNA_LoopCloser:

Collaboration diagram for protocols::coarse_rna::CoarseRNA_LoopCloser:

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

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

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

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

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

virtual std::string	get_name () const
	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_allow_insert (protocols::toolbox::AllowInsertOP allow_insert)

protocols::toolbox::AllowInsertOP	allow_insert ()

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	~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_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, Size const &res)

void	backtrack (core::kinematics::tree::AtomCOP 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, 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::vector1< core::Real > > &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_

protocols::toolbox::AllowInsertOP	allow_insert_

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_

bool	choose_random_solution_

bool	save_all_solutions_

ObjexxFCL::FArray1D< bool >	partition_definition_

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 40 of file CoarseRNA_LoopCloser.hh.

Constructor & Destructor Documentation

protocols::coarse_rna::CoarseRNA_LoopCloser::CoarseRNA_LoopCloser ( )

Construct the protocol object.

Definition at line 68 of file CoarseRNA_LoopCloser.cc.

Referenced by clone().

Member Function Documentation

protocols::toolbox::AllowInsertOP protocols::coarse_rna::CoarseRNA_LoopCloser::allow_insert ( )

Definition at line 982 of file CoarseRNA_LoopCloser.cc.

References allow_insert_.

Referenced by set_allow_insert().

void protocols::coarse_rna::CoarseRNA_LoopCloser::apply ( core::pose::Pose & pose)

virtual

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

Implements protocols::moves::Mover.

Definition at line 86 of file CoarseRNA_LoopCloser.cc.

bool protocols::coarse_rna::CoarseRNA_LoopCloser::apply	(	core::pose::Pose &	pose,
		Size const &	seqpos_moved
	)

Apply the loop-rebuild protocol to the input pose.

Definition at line 93 of file CoarseRNA_LoopCloser.cc.

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::total_residue(), protocols::coarse_rna::TR(), and verbose_.

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

Definition at line 114 of file CoarseRNA_LoopCloser.cc.

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::total_residue(), protocols::coarse_rna::TR(), and verbose_.

void protocols::coarse_rna::CoarseRNA_LoopCloser::apply_solutions ( core::pose::Pose & pose)

private

Definition at line 728 of file CoarseRNA_LoopCloser.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::coarse_rna::RG(), scorefxn_, t_ang_, core::pose::Pose::total_residue(), verbose_, and core::pose::Pose::xyz().

Referenced by close_the_loop().

void protocols::coarse_rna::CoarseRNA_LoopCloser::backtrack	(	core::kinematics::tree::AtomCOP	current_atom,
		utility::vector1< core::Size > &	upstream_res,
		utility::vector1< bool > &	is_upstream_res,
		core::pose::Pose const &	pose
	)

private

Definition at line 248 of file CoarseRNA_LoopCloser.cc.

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

Referenced by figure_out_forward_backward_res_by_backtracking().

void protocols::coarse_rna::CoarseRNA_LoopCloser::choose_best_solution_based_on_score_function ( core::scoring::ScoreFunctionOP scorefxn)

Definition at line 878 of file CoarseRNA_LoopCloser.cc.

References choose_best_solution_, choose_least_perturb_solution_, and scorefxn_.

void protocols::coarse_rna::CoarseRNA_LoopCloser::choose_least_perturb_solution ( )

Definition at line 886 of file CoarseRNA_LoopCloser.cc.

References choose_best_solution_, and choose_least_perturb_solution_.

virtual protocols::moves::MoverOP protocols::coarse_rna::CoarseRNA_LoopCloser::clone ( ) const

inlinevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

Definition at line 46 of file CoarseRNA_LoopCloser.hh.

References CoarseRNA_LoopCloser().

bool protocols::coarse_rna::CoarseRNA_LoopCloser::close_at_all_cutpoints ( core::pose::Pose & pose)

private

Definition at line 139 of file CoarseRNA_LoopCloser.cc.

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

Referenced by apply(), and apply_after_jump_change().

void protocols::coarse_rna::CoarseRNA_LoopCloser::close_the_loop ( core::pose::Pose & pose)

private

Definition at line 469 of file CoarseRNA_LoopCloser.cc.

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::coarse_rna::TR(), verbose_, which_scratch_res_is_cut_, and core::pose::Pose::xyz().

Referenced by close_at_all_cutpoints().

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

inline

Definition at line 83 of file CoarseRNA_LoopCloser.hh.

References cutpos_list_.

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

private

Definition at line 627 of file CoarseRNA_LoopCloser.cc.

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::ResidueType::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().

void protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking ( core::pose::Pose const & pose)

private

Definition at line 266 of file CoarseRNA_LoopCloser.cc.

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::total_residue(), and verbose_.

Referenced by figure_out_pivots().

void protocols::coarse_rna::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

Definition at line 698 of file CoarseRNA_LoopCloser.cc.

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

Referenced by figure_out_dof_ids_and_offsets().

void protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_pivot_res_and_scratch_res ( )

private

Definition at line 332 of file CoarseRNA_LoopCloser.cc.

References a_little_verbose_, backward_res_, cutpos_, forward_res_, is_backward_res_, is_pivot_res_, is_scratch_res_, pivot_res_, pivot_to_scratch_res_, protocols::coarse_rna::RG(), scratch_res_, protocols::coarse_rna::TR(), verbose_, and which_scratch_res_is_cut_.

Referenced by figure_out_pivots().

bool protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_pivots ( core::pose::Pose const & pose)

private

Definition at line 206 of file CoarseRNA_LoopCloser.cc.

References allow_insert_, 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().

void protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected ( core::pose::Pose const & pose)

private

Definition at line 170 of file CoarseRNA_LoopCloser.cc.

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

Referenced by apply(), and apply_after_jump_change().

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

private

Definition at line 916 of file CoarseRNA_LoopCloser.cc.

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

Referenced by apply_solutions(), and close_the_loop().

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

private

Definition at line 858 of file CoarseRNA_LoopCloser.cc.

References core::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().

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

private

Definition at line 304 of file CoarseRNA_LoopCloser.cc.

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

Referenced by figure_out_forward_backward_res_by_backtracking().

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

Definition at line 835 of file CoarseRNA_LoopCloser.cc.

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

std::string protocols::coarse_rna::CoarseRNA_LoopCloser::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 132 of file CoarseRNA_LoopCloser.cc.

Size protocols::coarse_rna::CoarseRNA_LoopCloser::nsol ( )

inline

Definition at line 81 of file CoarseRNA_LoopCloser.hh.

References nsol_.

void protocols::coarse_rna::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

Definition at line 893 of file CoarseRNA_LoopCloser.cc.

Referenced by apply_solutions(), and close_the_loop().

void protocols::coarse_rna::CoarseRNA_LoopCloser::output_forward_backward_res ( )

private

Definition at line 194 of file CoarseRNA_LoopCloser.cc.

References backward_res_, and forward_res_.

Referenced by figure_out_forward_backward_res_by_backtracking(), and figure_out_pivots().

ObjexxFCL::FArray1D< bool > const& protocols::coarse_rna::CoarseRNA_LoopCloser::partition_definition ( )

inline

Definition at line 85 of file CoarseRNA_LoopCloser.hh.

References partition_definition_.

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

private

Definition at line 231 of file CoarseRNA_LoopCloser.cc.

Referenced by figure_out_pivots().

void protocols::coarse_rna::CoarseRNA_LoopCloser::set_allow_insert ( protocols::toolbox::AllowInsertOP allow_insert)

Definition at line 976 of file CoarseRNA_LoopCloser.cc.

References allow_insert(), and allow_insert_.

Member Data Documentation

bool const protocols::coarse_rna::CoarseRNA_LoopCloser::a_little_verbose_

private

Definition at line 164 of file CoarseRNA_LoopCloser.hh.

Referenced by apply(), apply_after_jump_change(), close_at_all_cutpoints(), close_the_loop(), and figure_out_pivot_res_and_scratch_res().

protocols::toolbox::AllowInsertOP protocols::coarse_rna::CoarseRNA_LoopCloser::allow_insert_

private

Definition at line 171 of file CoarseRNA_LoopCloser.hh.

Referenced by allow_insert(), figure_out_pivots(), filter_path(), and set_allow_insert().

utility::vector1< core::id::NamedAtomID > protocols::coarse_rna::CoarseRNA_LoopCloser::atom_ids_

private

Definition at line 178 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), and close_the_loop().

utility::vector1<utility::vector1<core::Real> > protocols::coarse_rna::CoarseRNA_LoopCloser::b_ang_

private

Definition at line 182 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), and close_the_loop().

utility::vector1<utility::vector1<core::Real> > protocols::coarse_rna::CoarseRNA_LoopCloser::b_len_

private

Definition at line 182 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), and close_the_loop().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::backward_res_

private

Definition at line 172 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_forward_backward_res_by_backtracking(), figure_out_pivot_res_and_scratch_res(), figure_out_pivots(), and output_forward_backward_res().

bool protocols::coarse_rna::CoarseRNA_LoopCloser::choose_best_solution_

private

Definition at line 185 of file CoarseRNA_LoopCloser.hh.

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

bool protocols::coarse_rna::CoarseRNA_LoopCloser::choose_least_perturb_solution_

private

Definition at line 184 of file CoarseRNA_LoopCloser.hh.

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

bool protocols::coarse_rna::CoarseRNA_LoopCloser::choose_random_solution_

private

Definition at line 186 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions().

core::Size protocols::coarse_rna::CoarseRNA_LoopCloser::cutpos_

private

Definition at line 167 of file CoarseRNA_LoopCloser.hh.

Referenced by close_at_all_cutpoints(), close_the_loop(), figure_out_forward_backward_res_by_backtracking(), figure_out_pivot_res_and_scratch_res(), and figure_out_which_cutpoints_were_affected().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::cutpos_list_

private

Definition at line 168 of file CoarseRNA_LoopCloser.hh.

Referenced by close_at_all_cutpoints(), cutpos_list(), and figure_out_which_cutpoints_were_affected().

utility::vector1< core::id::DOF_ID > protocols::coarse_rna::CoarseRNA_LoopCloser::dof_ids1_

private

Definition at line 180 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_dof_ids_and_offsets(), and fill_solution().

utility::vector1< core::id::DOF_ID > protocols::coarse_rna::CoarseRNA_LoopCloser::dof_ids2_

private

Definition at line 180 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_dof_ids_and_offsets(), and fill_solution().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::forward_res_

private

Definition at line 172 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_forward_backward_res_by_backtracking(), figure_out_pivot_res_and_scratch_res(), figure_out_pivots(), and output_forward_backward_res().

utility::vector1< bool > protocols::coarse_rna::CoarseRNA_LoopCloser::is_backward_res_

private

Definition at line 173 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_forward_backward_res_by_backtracking(), and figure_out_pivot_res_and_scratch_res().

utility::vector1< bool > protocols::coarse_rna::CoarseRNA_LoopCloser::is_forward_res_

private

Definition at line 173 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_forward_backward_res_by_backtracking().

utility::vector1< bool > protocols::coarse_rna::CoarseRNA_LoopCloser::is_pivot_res_

private

Definition at line 173 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_pivot_res_and_scratch_res().

utility::vector1< bool > protocols::coarse_rna::CoarseRNA_LoopCloser::is_scratch_res_

private

Definition at line 173 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_pivot_res_and_scratch_res().

int protocols::coarse_rna::CoarseRNA_LoopCloser::nsol_

private

Definition at line 169 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), close_at_all_cutpoints(), close_the_loop(), get_all_solutions(), and nsol().

utility::vector1< core::Real > protocols::coarse_rna::CoarseRNA_LoopCloser::offset_save1_

private

Definition at line 179 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_dof_ids_and_offsets(), and fill_solution().

utility::vector1< core::Real > protocols::coarse_rna::CoarseRNA_LoopCloser::offset_save2_

private

Definition at line 179 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_dof_ids_and_offsets(), and fill_solution().

ObjexxFCL::FArray1D< bool > protocols::coarse_rna::CoarseRNA_LoopCloser::partition_definition_

private

Definition at line 189 of file CoarseRNA_LoopCloser.hh.

Referenced by apply(), apply_after_jump_change(), figure_out_which_cutpoints_were_affected(), and partition_definition().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::pivot_res_

private

Definition at line 172 of file CoarseRNA_LoopCloser.hh.

Referenced by figure_out_dof_ids_and_offsets(), and figure_out_pivot_res_and_scratch_res().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::pivot_to_scratch_res_

private

Definition at line 172 of file CoarseRNA_LoopCloser.hh.

Referenced by close_the_loop(), figure_out_dof_ids_and_offsets(), figure_out_pivot_res_and_scratch_res(), and fill_solution().

bool protocols::coarse_rna::CoarseRNA_LoopCloser::save_all_solutions_

private

Definition at line 187 of file CoarseRNA_LoopCloser.hh.

core::scoring::ScoreFunctionOP protocols::coarse_rna::CoarseRNA_LoopCloser::scorefxn_

private

Definition at line 176 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), and choose_best_solution_based_on_score_function().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_LoopCloser::scratch_res_

private

Definition at line 172 of file CoarseRNA_LoopCloser.hh.

Referenced by close_the_loop(), and figure_out_pivot_res_and_scratch_res().

core::Size protocols::coarse_rna::CoarseRNA_LoopCloser::seqpos_moved_

private

Definition at line 166 of file CoarseRNA_LoopCloser.hh.

Referenced by apply(), apply_after_jump_change(), and figure_out_pivots().

utility::vector1<utility::vector1<core::Real> > protocols::coarse_rna::CoarseRNA_LoopCloser::t_ang_

private

Definition at line 182 of file CoarseRNA_LoopCloser.hh.

Referenced by apply_solutions(), close_the_loop(), and fill_solution().

bool const protocols::coarse_rna::CoarseRNA_LoopCloser::verbose_

private

Definition at line 165 of file CoarseRNA_LoopCloser.hh.

Referenced by apply(), apply_after_jump_change(), apply_solutions(), close_at_all_cutpoints(), close_the_loop(), figure_out_forward_backward_res_by_backtracking(), figure_out_offset(), figure_out_pivot_res_and_scratch_res(), figure_out_pivots(), figure_out_which_cutpoints_were_affected(), and get_all_solutions().

core::Size protocols::coarse_rna::CoarseRNA_LoopCloser::which_scratch_res_is_cut_

private

Definition at line 174 of file CoarseRNA_LoopCloser.hh.

Referenced by close_the_loop(), and figure_out_pivot_res_and_scratch_res().

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

src/protocols/coarse_rna/CoarseRNA_LoopCloser.hh
src/protocols/coarse_rna/CoarseRNA_LoopCloser.cc

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