#include <StepWiseRNA_ResidueSampler.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_ResidueSampler:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_ResidueSampler:

Public Member Functions
	StepWiseRNA_ResidueSampler (StepWiseRNA_JobParametersCOP &job_parameters_)

	~StepWiseRNA_ResidueSampler ()

virtual void	apply (core::pose::Pose &pose_to_visualize)
	Apply the minimizer to one pose. More...

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

void	set_centroid_screen (bool const setting)

void	set_allow_base_pair_only_centroid_screen (bool const setting)

void	set_VDW_atr_rep_screen (bool const setting)

void	set_silent_file (std::string const &setting)

void	set_output_filename (std::string const &output_filename)

void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

void	set_fast (bool const &setting)

void	set_medium_fast (bool const &setting)

void	set_native_rmsd_screen (bool const &setting)

void	set_native_screen_rmsd_cutoff (core::Real const &setting)

void	set_integration_test_mode (bool const &setting)

void	set_verbose (bool const &setting)

void	set_perform_o2star_pack (bool const &setting)

void	set_cluster_rmsd (core::Real const &setting)

void	set_allow_bulge_at_chainbreak (bool const &setting)

utility::vector1 < pose_data_struct2 > &	get_pose_data_list ()

core::io::silent::SilentFileDataOP &	silent_file_data ()

void	output_pose_data_list (std::string const final_sampler_output_silent_file) const

void	set_num_pose_kept (core::Size const &num_pose_kept)

void	set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener)

void	set_parin_favorite_output (bool const &setting)

void	set_floating_base (bool const &setting)

void	set_include_syn_chi (bool const &setting)

void	set_allow_syn_pyrimidine (bool const &setting)

void	set_distinguish_pucker (bool const &setting)

void	set_finer_sampling_at_chain_closure (bool const &setting)

void	set_PBP_clustering_at_chain_closure (bool const &setting)

void	set_reinitialize_CCD_torsions (bool const &setting)

void	set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)

void	set_extra_epsilon_rotamer (bool const &setting)

void	set_extra_beta_rotamer (bool const &setting)

void	set_extra_anti_chi_rotamer (bool const &setting)

void	set_extra_syn_chi_rotamer (bool const &setting)

void	set_sample_both_sugar_base_rotamer (bool const &setting)

void	set_include_torsion_value_in_tag (bool const &setting)

void	set_rebuild_bulge_mode (bool const &setting)

void	set_debug_eplison_south_sugar_mode (bool const &setting)

void	set_exclude_alpha_beta_gamma_sampling (bool const &setting)

void	set_combine_long_loop_mode (bool const &setting)

void	set_do_not_sample_multiple_virtual_sugar (bool const &setting)

void	set_sample_ONLY_multiple_virtual_sugar (bool const &setting)

void	set_assert_no_virt_ribose_sampling (bool const &setting)

void	set_output_pdb (bool const setting)

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 MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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
void	initialize_scorefunctions ()

void	Copy_CCD_torsions (core::pose::Pose &pose, core::pose::Pose const &template_pose) const

void	Copy_CCD_torsions_general (core::pose::Pose &pose, core::pose::Pose const &template_pose, core::Size const five_prime_res, core::Size const three_prime_res) const

bool	Chain_break_screening (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &constraint_scorefxn)

bool	Chain_break_screening_general (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::Size const five_prime_res)

void	standard_sampling_WRAPPER (core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &curr_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &five_prime_CB_sugar_FB_JP, FloatingBaseChainClosureJobParameter const &three_prime_CB_sugar_FB_JP)

void	standard_sampling (core::pose::Pose &pose, utility::vector1< pose_data_struct2 > &pose_data_list, std::string const sugar_tag)

void	floating_base_sampling (core::pose::Pose &pose, FloatingBaseChainClosureJobParameter const &prev_sugar_FB_JP)

void	get_base_atr_rep_score (core::pose::Pose const &pose, core::Real &base_atr_score, core::Real &base_rep_score)

bool	Full_atom_van_der_Waals_screening_REPLICATE (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)

bool	Full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)

void	initialize_o2star_packer_task (core::pose::Pose const &pose)

void	initialize_o2star_green_packer (core::pose::Pose &pose)

void	sample_o2star_hydrogen (core::pose::Pose &pose, core::pose::Pose &pose_with_original_HO2star_torsion)

core::Real	Pose_selection_by_full_score (utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose &current_pose, std::string const &tag)

bool	apply_bulge_variant (core::pose::Pose &pose, core::Real const &delta_atr_score)

void	Update_pose_data_list (std::string const &tag, utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose const &current_pose, core::Real const &current_score) const

void	cluster_pose_data_list (utility::vector1< pose_data_struct2 > &pose_data_list)

std::string	create_tag (std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const &rotamer_generator) const

core::kinematics::Stub	get_reference_stub (core::Size const reference_res, core::pose::Pose const &pose) const

std::string	create_torsion_value_string (core::Real const &torsion_value) const

std::string	create_rotamer_string (core::pose::Pose const &pose) const

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

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

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

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

utility::vector1 < pose_data_struct2 >	previous_floating_base_chain_closure (core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

core::io::silent::SilentFileDataOP	sfd_

utility::vector1 < pose_data_struct2 >	pose_data_list_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	atr_rep_screening_scorefxn_

core::scoring::ScoreFunctionOP	chainbreak_scorefxn_

core::scoring::ScoreFunctionOP	sampling_scorefxn_

core::scoring::ScoreFunctionOP	o2star_pack_scorefxn_

utility::vector1< core::Size >	working_rmsd_res_

SillyCountStruct	count_data_

std::string	silent_file_

std::string	output_filename_

core::Real const	bin_size_

core::Real const	rep_cutoff_

core::Size	num_pose_kept_

core::Size const	multiplier_

core::Real	cluster_rmsd_

bool	verbose_

bool	native_rmsd_screen_

core::Real	native_screen_rmsd_cutoff_

bool	perform_o2star_pack_

core::pack::task::PackerTaskOP	o2star_pack_task_

protocols::simple_moves::GreenPackerOP	o2star_green_packer_

bool const	use_green_packer_

bool	allow_bulge_at_chainbreak_

bool	fast_

bool	medium_fast_

bool	integration_test_mode_

bool	floating_base_

StepWiseRNA_BaseCentroidScreenerOP	base_centroid_screener_

bool	parin_favorite_output_

bool	centroid_screen_

bool	allow_base_pair_only_centroid_screen_

bool	VDW_atr_rep_screen_

bool	include_syn_chi_

bool	allow_syn_pyrimidine_

bool	distinguish_pucker_

bool	build_pose_from_scratch_

core::Real	current_score_cutoff_

bool	finer_sampling_at_chain_closure_

bool	PBP_clustering_at_chain_closure_

bool	reinitialize_CCD_torsions_

bool	extra_epsilon_rotamer_

bool	extra_beta_rotamer_

bool	extra_anti_chi_rotamer_

bool	extra_syn_chi_rotamer_

bool	sample_both_sugar_base_rotamer_

bool	include_torsion_value_in_tag_

bool	rebuild_bulge_mode_

bool	debug_eplison_south_sugar_mode_

bool	exclude_alpha_beta_gamma_sampling_

bool	combine_long_loop_mode_

bool	do_not_sample_multiple_virtual_sugar_

bool	sample_ONLY_multiple_virtual_sugar_

bool	assert_no_virt_ribose_sampling_

bool	output_pdb_

StepWiseRNA_VDW_Bin_ScreenerOP	user_input_VDW_bin_screener_

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

Definition at line 52 of file StepWiseRNA_ResidueSampler.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_ResidueSampler::StepWiseRNA_ResidueSampler ( StepWiseRNA_JobParametersCOP & job_parameters_)

Definition at line 112 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::apply_full_to_sub_mapping(), job_parameters_, protocols::swa::rna::Output_is_prepend_map(), protocols::swa::rna::Output_seq_num_list(), protocols::moves::Mover::set_native_pose(), and working_rmsd_res_.

protocols::swa::rna::StepWiseRNA_ResidueSampler::~StepWiseRNA_ResidueSampler ( )

Definition at line 178 of file StepWiseRNA_ResidueSampler.cc.

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_ResidueSampler::apply ( core::pose::Pose & pose_to_visualize)

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 197 of file StepWiseRNA_ResidueSampler.cc.

References allow_base_pair_only_centroid_screen_, assert_no_virt_ribose_sampling_, centroid_screen_, distinguish_pucker_, do_not_sample_multiple_virtual_sugar_, fast_, floating_base_, floating_base_sampling(), initialize_scorefunctions(), integration_test_mode_, Is_current_sugar_virtual(), Is_five_prime_chain_break_sugar_virtual(), Is_previous_sugar_virtual(), Is_three_prime_chain_break_sugar_virtual(), job_parameters_, medium_fast_, native_rmsd_screen_, native_screen_rmsd_cutoff_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), perform_o2star_pack_, pose_data_list_, previous_floating_base_chain_closure(), rebuild_bulge_mode_, protocols::swa::rna::remove_virtual_rna_residue_variant_type(), sample_both_sugar_base_rotamer_, sample_ONLY_multiple_virtual_sugar_, protocols::swa::rna::sort_criteria(), standard_sampling_WRAPPER(), and VDW_atr_rep_screen_.

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::apply_bulge_variant	(	core::pose::Pose &	pose,
		core::Real const &	delta_atr_score
	)

private

Definition at line 1890 of file StepWiseRNA_ResidueSampler.cc.

References allow_bulge_at_chainbreak_, protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::swa::rna::SillyCountStruct::both_count, protocols::swa::rna::SillyCountStruct::bulge_at_chain_closure_count, count_data_, protocols::swa::rna::Is_virtual_base(), job_parameters_, rebuild_bulge_mode_, core::pose::Pose::residue(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, and verbose_.

Referenced by standard_sampling().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening	(	core::pose::Pose &	chain_break_screening_pose,
		core::scoring::ScoreFunctionOP const &	constraint_scorefxn
	)

private

Definition at line 1879 of file StepWiseRNA_ResidueSampler.cc.

References Chain_break_screening_general(), and job_parameters_.

Referenced by floating_base_sampling(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general	(	core::pose::Pose &	chain_break_screening_pose,
		core::scoring::ScoreFunctionOP const &	chainbreak_scorefxn,
		core::Size const	five_prime_res
	)

private

Definition at line 1833 of file StepWiseRNA_ResidueSampler.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::swa::rna::SillyCountStruct::chain_break_screening_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, count_data_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::energies(), protocols::swa::rna::SillyCountStruct::good_angle_count, protocols::swa::rna::SillyCountStruct::good_distance_count, core::conformation::Residue::has_variant_type(), reinitialize_CCD_torsions_, core::pose::Pose::residue(), protocols::swa::rna::set_CCD_torsions_to_zero(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), and verbose_.

Referenced by Chain_break_screening(), and floating_base_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list ( utility::vector1< pose_data_struct2 > & pose_data_list)

private

Definition at line 2009 of file StepWiseRNA_ResidueSampler.cc.

References build_pose_from_scratch_, cluster_rmsd_, current_score_cutoff_, distinguish_pucker_, protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::Is_same_ribose_pucker(), job_parameters_, num_pose_kept_, protocols::swa::rna::Output_boolean(), PBP_clustering_at_chain_closure_, protocols::swa::rna::phosphate_base_phosphate_rmsd(), protocols::swa::rna::print_ribose_pucker_state(), protocols::swa::rna::suite_rmsd(), and verbose_.

Referenced by floating_base_sampling(), Pose_selection_by_full_score(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::Copy_CCD_torsions	(	core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose
	)		const

private

Definition at line 1793 of file StepWiseRNA_ResidueSampler.cc.

References Copy_CCD_torsions_general(), and job_parameters_.

Referenced by floating_base_sampling(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::Copy_CCD_torsions_general	(	core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose,
		core::Size const	five_prime_res,
		core::Size const	three_prime_res
	)		const

private

Definition at line 1811 of file StepWiseRNA_ResidueSampler.cc.

References core::id::BB, core::pose::Pose::residue(), and core::pose::Pose::set_torsion().

Referenced by Copy_CCD_torsions(), and floating_base_sampling().

std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_rotamer_string ( core::pose::Pose const & pose) const

private

Definition at line 2345 of file StepWiseRNA_ResidueSampler.cc.

References core::conformation::Residue::chi(), create_torsion_value_string(), job_parameters_, core::conformation::Residue::mainchain_torsion(), and core::pose::Pose::residue().

Referenced by standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_tag	(	std::string const	prestring,
		StepWiseRNA_RotamerGenerator_WrapperOP const &	rotamer_generator
	)		const

private

Definition at line 2378 of file StepWiseRNA_ResidueSampler.cc.

Referenced by standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::create_torsion_value_string ( core::Real const & torsion_value) const

private

Definition at line 2323 of file StepWiseRNA_ResidueSampler.cc.

Referenced by create_rotamer_string().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling	(	core::pose::Pose &	pose,
		FloatingBaseChainClosureJobParameter const &	prev_sugar_FB_JP
	)

private

Definition at line 420 of file StepWiseRNA_ResidueSampler.cc.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Full_atom_van_der_Waals_screening	(	core::pose::Pose &	current_pose_screen,
		core::Real const &	base_rep_score,
		core::Real const &	base_atr_score,
		core::Real &	delta_rep_score,
		core::Real &	delta_atr_score,
		core::Size const &	gap_size,
		bool const &	Is_internal
	)

private

Definition at line 2147 of file StepWiseRNA_ResidueSampler.cc.

Referenced by floating_base_sampling(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Full_atom_van_der_Waals_screening_REPLICATE	(	core::pose::Pose &	current_pose_screen,
		core::Real const &	base_rep_score,
		core::Real const &	base_atr_score,
		core::Real &	delta_rep_score,
		core::Real &	delta_atr_score,
		core::Size const &	gap_size,
		bool const &	Is_internal
	)

private

Definition at line 2079 of file StepWiseRNA_ResidueSampler.cc.

Referenced by floating_base_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::get_base_atr_rep_score	(	core::pose::Pose const &	pose,
		core::Real &	base_atr_score,
		core::Real &	base_rep_score
	)

private

Definition at line 1690 of file StepWiseRNA_ResidueSampler.cc.

References core::pose::add_variant_type_to_pose_residue(), atr_rep_screening_scorefxn_, core::pose::Pose::dump_pdb(), core::scoring::fa_atr, core::scoring::fa_rep, job_parameters_, protocols::swa::rna::make_cut_at_moving_suite(), output_pdb_, sample_both_sugar_base_rotamer_, core::kinematics::Jump::set_translation(), and verbose_.

Referenced by floating_base_sampling(), and standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_ResidueSampler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 183 of file StepWiseRNA_ResidueSampler.cc.

utility::vector1< pose_data_struct2 > & protocols::swa::rna::StepWiseRNA_ResidueSampler::get_pose_data_list ( )

Definition at line 1785 of file StepWiseRNA_ResidueSampler.cc.

References pose_data_list_.

core::kinematics::Stub protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub	(	core::Size const	reference_res,
		core::pose::Pose const &	pose
	)		const

private

Definition at line 1557 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::Get_ribose_stub(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), job_parameters_, core::kinematics::Stub::M, core::pose::Pose::residue(), and core::kinematics::Stub::v.

Referenced by floating_base_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_green_packer ( core::pose::Pose & pose)

private

Definition at line 2243 of file StepWiseRNA_ResidueSampler.cc.

References core::pose::Pose::fold_tree(), core::conformation::Residue::is_RNA(), job_parameters_, o2star_green_packer_, o2star_pack_scorefxn_, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().

Referenced by standard_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_packer_task ( core::pose::Pose const & pose)

private

Definition at line 2231 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::create_standard_o2star_pack_task(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), job_parameters_, and o2star_pack_task_.

Referenced by sample_o2star_hydrogen(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_scorefunctions ( )

private

Definition at line 1777 of file StepWiseRNA_ResidueSampler.cc.

References atr_rep_screening_scorefxn_, chainbreak_scorefxn_, protocols::swa::rna::initialize_common_scorefxns(), o2star_pack_scorefxn_, sampling_scorefxn_, and scorefxn_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_current_sugar_virtual ( core::pose::Pose const & pose) const

private

Definition at line 1594 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::Is_ribose_virtual(), and job_parameters_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_five_prime_chain_break_sugar_virtual ( core::pose::Pose const & pose) const

private

Definition at line 1608 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::Is_ribose_virtual(), and job_parameters_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_previous_sugar_virtual ( core::pose::Pose const & pose) const

private

Definition at line 1579 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::Is_ribose_virtual(), and job_parameters_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_three_prime_chain_break_sugar_virtual ( core::pose::Pose const & pose) const

private

Definition at line 1648 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::Is_ribose_virtual(), and job_parameters_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::output_pose_data_list ( std::string const final_sampler_output_silent_file) const

Definition at line 2484 of file StepWiseRNA_ResidueSampler.cc.

References protocols::moves::Mover::get_native_pose(), job_parameters_, protocols::swa::rna::Output_data(), pose_data_list_, silent_file_data(), and verbose_.

Real protocols::swa::rna::StepWiseRNA_ResidueSampler::Pose_selection_by_full_score	(	utility::vector1< pose_data_struct2 > &	pose_data_list,
		core::pose::Pose &	current_pose,
		std::string const &	tag
	)

private

Definition at line 1982 of file StepWiseRNA_ResidueSampler.cc.

References cluster_pose_data_list(), multiplier_, num_pose_kept_, protocols::swa::rna::sort_criteria(), and Update_pose_data_list().

Referenced by floating_base_sampling(), and standard_sampling().

utility::vector1< pose_data_struct2 > protocols::swa::rna::StepWiseRNA_ResidueSampler::previous_floating_base_chain_closure	(	core::pose::Pose &	viewer_pose,
		FloatingBaseChainClosureJobParameter const &	FB_job_params,
		std::string const	name
	)

private

Definition at line 1546 of file StepWiseRNA_ResidueSampler.cc.

References atr_rep_screening_scorefxn_, chainbreak_scorefxn_, job_parameters_, protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), sampling_scorefxn_, and scorefxn_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_o2star_hydrogen	(	core::pose::Pose &	pose,
		core::pose::Pose &	pose_with_original_HO2star_torsion
	)

private

Definition at line 2298 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::copy_all_o2star_torsions(), initialize_o2star_packer_task(), o2star_green_packer_, o2star_pack_scorefxn_, o2star_pack_task_, core::pack::rotamer_trials(), and use_green_packer_.

Referenced by floating_base_sampling(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_base_pair_only_centroid_screen ( bool const setting)

inline

Definition at line 70 of file StepWiseRNA_ResidueSampler.hh.

References allow_base_pair_only_centroid_screen_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_bulge_at_chainbreak ( bool const & setting)

Definition at line 2458 of file StepWiseRNA_ResidueSampler.cc.

References allow_bulge_at_chainbreak_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_allow_syn_pyrimidine ( bool const & setting)

inline

Definition at line 133 of file StepWiseRNA_ResidueSampler.hh.

References allow_syn_pyrimidine_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_assert_no_virt_ribose_sampling ( bool const & setting)

inline

Definition at line 187 of file StepWiseRNA_ResidueSampler.hh.

References assert_no_virt_ribose_sampling_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP & screener)

Definition at line 2501 of file StepWiseRNA_ResidueSampler.cc.

References base_centroid_screener_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_centroid_screen ( bool const setting)

inline

Definition at line 67 of file StepWiseRNA_ResidueSampler.hh.

References centroid_screen_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_cluster_rmsd ( core::Real const & setting)

Definition at line 2507 of file StepWiseRNA_ResidueSampler.cc.

References cluster_rmsd_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_combine_long_loop_mode ( bool const & setting)

inline

Definition at line 178 of file StepWiseRNA_ResidueSampler.hh.

References combine_long_loop_mode_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_debug_eplison_south_sugar_mode ( bool const & setting)

inline

Definition at line 172 of file StepWiseRNA_ResidueSampler.hh.

References debug_eplison_south_sugar_mode_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_distinguish_pucker ( bool const & setting)

inline

Definition at line 136 of file StepWiseRNA_ResidueSampler.hh.

References distinguish_pucker_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_do_not_sample_multiple_virtual_sugar ( bool const & setting)

inline

Definition at line 181 of file StepWiseRNA_ResidueSampler.hh.

References do_not_sample_multiple_virtual_sugar_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_exclude_alpha_beta_gamma_sampling ( bool const & setting)

inline

Definition at line 175 of file StepWiseRNA_ResidueSampler.hh.

References exclude_alpha_beta_gamma_sampling_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_anti_chi_rotamer ( bool const & setting)

inline

Definition at line 157 of file StepWiseRNA_ResidueSampler.hh.

References extra_anti_chi_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_beta_rotamer ( bool const & setting)

inline

Definition at line 154 of file StepWiseRNA_ResidueSampler.hh.

References extra_beta_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_epsilon_rotamer ( bool const & setting)

inline

Definition at line 151 of file StepWiseRNA_ResidueSampler.hh.

References extra_epsilon_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_extra_syn_chi_rotamer ( bool const & setting)

inline

Definition at line 160 of file StepWiseRNA_ResidueSampler.hh.

References extra_syn_chi_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_fast ( bool const & setting)

Definition at line 2409 of file StepWiseRNA_ResidueSampler.cc.

References fast_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_finer_sampling_at_chain_closure ( bool const & setting)

inline

Definition at line 139 of file StepWiseRNA_ResidueSampler.hh.

References finer_sampling_at_chain_closure_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_floating_base ( bool const & setting)

inline

Definition at line 127 of file StepWiseRNA_ResidueSampler.hh.

References floating_base_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_include_syn_chi ( bool const & setting)

inline

Definition at line 130 of file StepWiseRNA_ResidueSampler.hh.

References include_syn_chi_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_include_torsion_value_in_tag ( bool const & setting)

inline

Definition at line 166 of file StepWiseRNA_ResidueSampler.hh.

References include_torsion_value_in_tag_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_integration_test_mode ( bool const & setting)

Definition at line 2434 of file StepWiseRNA_ResidueSampler.cc.

References integration_test_mode_, native_rmsd_screen_, native_screen_rmsd_cutoff_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_medium_fast ( bool const & setting)

Definition at line 2416 of file StepWiseRNA_ResidueSampler.cc.

References medium_fast_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_native_rmsd_screen ( bool const & setting)

Definition at line 2423 of file StepWiseRNA_ResidueSampler.cc.

References native_rmsd_screen_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_native_screen_rmsd_cutoff ( core::Real const & setting)

Definition at line 2429 of file StepWiseRNA_ResidueSampler.cc.

References native_screen_rmsd_cutoff_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_num_pose_kept ( core::Size const & num_pose_kept)

Definition at line 2403 of file StepWiseRNA_ResidueSampler.cc.

References num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_output_filename ( std::string const & output_filename)

Definition at line 2465 of file StepWiseRNA_ResidueSampler.cc.

References output_filename_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_output_pdb ( bool const setting)

inline

Definition at line 190 of file StepWiseRNA_ResidueSampler.hh.

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_parin_favorite_output ( bool const & setting)

inline

Definition at line 124 of file StepWiseRNA_ResidueSampler.hh.

References parin_favorite_output_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_PBP_clustering_at_chain_closure ( bool const & setting)

inline

Definition at line 142 of file StepWiseRNA_ResidueSampler.hh.

References PBP_clustering_at_chain_closure_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_perform_o2star_pack ( bool const & setting)

Definition at line 2451 of file StepWiseRNA_ResidueSampler.cc.

References perform_o2star_pack_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_rebuild_bulge_mode ( bool const & setting)

inline

Definition at line 169 of file StepWiseRNA_ResidueSampler.hh.

References rebuild_bulge_mode_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_reinitialize_CCD_torsions ( bool const & setting)

inline

Definition at line 145 of file StepWiseRNA_ResidueSampler.hh.

References reinitialize_CCD_torsions_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_sample_both_sugar_base_rotamer ( bool const & setting)

inline

Definition at line 163 of file StepWiseRNA_ResidueSampler.hh.

References sample_both_sugar_base_rotamer_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_sample_ONLY_multiple_virtual_sugar ( bool const & setting)

inline

Definition at line 184 of file StepWiseRNA_ResidueSampler.hh.

References sample_ONLY_multiple_virtual_sugar_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn)

Definition at line 2471 of file StepWiseRNA_ResidueSampler.cc.

References scorefxn_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_silent_file ( std::string const & setting)

Definition at line 2397 of file StepWiseRNA_ResidueSampler.cc.

References silent_file_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_user_input_VDW_bin_screener ( StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener)

inline

Definition at line 148 of file StepWiseRNA_ResidueSampler.hh.

References user_input_VDW_bin_screener_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_VDW_atr_rep_screen ( bool const setting)

inline

Definition at line 73 of file StepWiseRNA_ResidueSampler.hh.

References VDW_atr_rep_screen_.

void protocols::swa::rna::StepWiseRNA_ResidueSampler::set_verbose ( bool const & setting)

Definition at line 2446 of file StepWiseRNA_ResidueSampler.cc.

References verbose_.

core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_ResidueSampler::silent_file_data ( )

Definition at line 2477 of file StepWiseRNA_ResidueSampler.cc.

References sfd_.

Referenced by floating_base_sampling(), output_pose_data_list(), standard_sampling(), and standard_sampling_WRAPPER().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling	(	core::pose::Pose &	pose,
		utility::vector1< pose_data_struct2 > &	pose_data_list,
		std::string const	sugar_tag
	)

private

Definition at line 1151 of file StepWiseRNA_ResidueSampler.cc.

Referenced by standard_sampling_WRAPPER().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER	(	core::pose::Pose &	pose,
		FloatingBaseChainClosureJobParameter const &	prev_sugar_FB_JP,
		FloatingBaseChainClosureJobParameter const &	curr_sugar_FB_JP,
		FloatingBaseChainClosureJobParameter const &	five_prime_CB_sugar_FB_JP,
		FloatingBaseChainClosureJobParameter const &	three_prime_CB_sugar_FB_JP
	)

private

Definition at line 1018 of file StepWiseRNA_ResidueSampler.cc.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_ResidueSampler::Update_pose_data_list	(	std::string const &	tag,
		utility::vector1< pose_data_struct2 > &	pose_data_list,
		core::pose::Pose const &	current_pose,
		core::Real const &	current_score
	)		const