#include <StepWiseRNA_RigidBodySampler.hh>

Public Member Functions
	StepWiseRNA_RigidBodySampler (StepWiseRNA_JobParametersCOP &job_parameters_)

	~StepWiseRNA_RigidBodySampler ()

virtual void	apply (pose::Pose &pose_to_visualize)

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

void	set_silent_file (std::string const &setting)

void	set_scorefxn (scoring::ScoreFunctionOP const &scorefxn)

utility::vector1< pose::PoseOP > &	get_pose_list ()

void	set_base_centroid_checker (checker::RNA_BaseCentroidCheckerOP &checker)

void	set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)

void	set_anchor_sugar_modeling (sugar::SugarModeling const &anchor_sugar_modeling)

void	set_options (StepWiseRNA_ModelerOptionsCOP options)

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

	~MoverForPoseList ()

virtual void	apply (utility::vector1< core::pose::PoseOP > &pose_list)

virtual void	apply (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

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
	Return a clone of the Mover object. More...

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...

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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	initialize_poses_and_stubs_and_checkers (pose::Pose &pose)

void	reinstantiate_backbone_and_add_constraint_at_moving_res (pose::Pose &pose, Size const &five_prime_chain_break_res)

void	initialize_euler_angle_grid_parameters ()

void	initialize_xyz_grid_parameters ()

void	initialize_rigid_body_sampler (pose::Pose const &pose)

rotamer_sampler::rigid_body::RigidBodyRotamerOP	define_rigid_body_rotamer (pose::Pose const &pose)

void	initialize_screeners (pose::Pose &pose)

void	initialize_residue_level_screeners (pose::Pose &pose)

void	initialize_pose_level_screeners (pose::Pose &pose)

kinematics::Stub	get_reference_stub (pose::Pose const &pose) const

void	update_base_bin_map (rna::rigid_body::BaseBin const &base_bin)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

Size const	moving_res_

Size const	moving_suite_

bool const	is_prepend_

bool const	is_internal_

Size const	gap_size_

Size const	gap_size_to_anchor_

Size const	five_prime_chain_break_res_

Size const	chain_break_reference_res_

Size const	reference_res_

Size const	floating_base_five_prime_chain_break_

Size const	floating_base_three_prime_chain_break_

bool const	is_dinucleotide_

bool const	close_chain_to_distal_

bool const	close_chain_to_anchor_

utility::vector1< pose::PoseOP >	pose_list_

scoring::ScoreFunctionOP	scorefxn_

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternativesOP	sampler_

utility::vector1 < screener::StepWiseScreenerOP >	screeners_

screener::TagDefinitionOP	tag_definition_

StepWiseRNA_CountStruct	count_data_

std::string	silent_file_

bool	native_rmsd_screen_

Size	num_pose_kept_to_use_

StepWiseRNA_ModelerOptionsCOP	options_

sugar::SugarModeling	anchor_sugar_modeling_

checker::AtrRepCheckerOP	atr_rep_checker_

checker::AtrRepCheckerOP	atr_rep_checker_with_instantiated_sugar_

utility::vector1 < checker::AtrRepCheckerOP >	atr_rep_checkers_for_anchor_sugar_models_

checker::RNA_VDW_BinCheckerOP	VDW_bin_checker_

checker::RNA_VDW_BinCheckerOP	user_input_VDW_bin_checker_

checker::ChainClosableGeometryCheckerOP	chain_closable_geometry_to_distal_checker_

checker::ChainClosableGeometryCheckerOP	chain_closable_geometry_to_anchor_checker_

checker::ChainClosureCheckerOP	chain_break_to_distal_checker_

checker::ChainClosureCheckerOP	chain_break_to_anchor_checker_

checker::RNA_BaseCentroidCheckerOP	base_centroid_checker_

pose::PoseOP	screening_pose_

pose::PoseOP	sugar_screening_pose_

utility::vector1< pose::PoseOP >	pose_at_origin_list_

utility::vector1 < conformation::ResidueOP >	moving_rsd_at_origin_list_

utility::vector1 < conformation::ResidueOP >	screening_moving_rsd_at_origin_list_

utility::vector1 < conformation::ResidueOP >	sugar_screening_moving_rsd_at_origin_list_

StepWiseRNA_PoseSelectionOP	pose_selection_

o2prime::O2PrimePackerOP	o2prime_packer_

phosphate::MultiPhosphateSamplerOP	phosphate_sampler_

kinematics::Stub	reference_stub_

kinematics::Stub	moving_res_base_stub_

core::conformation::ResidueOP	moving_rsd_at_origin_

utility::vector1 < core::conformation::ResidueOP >	moving_rsd_at_origin_from_sampler_

rna::rigid_body::BaseBinMap	base_bin_map_

Size	max_ntries_

int	euler_angle_bin_min_

int	euler_angle_bin_max_

Real	euler_angle_bin_size_

int	euler_z_bin_min_

int	euler_z_bin_max_

Real	euler_z_bin_size_

int	centroid_bin_min_

int	centroid_bin_max_

Real	centroid_bin_size_

Distance	max_distance_

Real	max_distance_squared_

bool	try_sugar_instantiation_

Distance	o2prime_instantiation_distance_cutoff_

std::string const	extra_tag_

bool const	rigid_body_sampling_

bool const	anchor_sugar_screener_legacy_

bool const	legacy_mode_

bool const	residue_level_screening_

bool const	full_pose_level_screening_

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...

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::StepWiseRNA_RigidBodySampler ( StepWiseRNA_JobParametersCOP & job_parameters_ )

References five_prime_chain_break_res_, gap_size_, gap_size_to_anchor_, is_dinucleotide_, is_internal_, job_parameters_, moving_res_, reference_res_, runtime_assert, scoring, protocols::moves::Mover::set_native_pose(), and protocols::TR.

protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::~StepWiseRNA_RigidBodySampler ( )

Member Function Documentation

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply ( pose::Pose & pose_to_visualize )

virtual

Implements protocols::moves::MoverForPoseList.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

rotamer_sampler::rigid_body::RigidBodyRotamerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::define_rigid_body_rotamer ( pose::Pose const & pose )

private

References centroid_bin_size_, euler_angle_bin_size_, euler_z_bin_size_, max_distance_, moving_res_, moving_rsd_at_origin_list_, options_, and runtime_assert.

Referenced by initialize_rigid_body_sampler().

std::string protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

utility::vector1< PoseOP > & protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::get_pose_list ( )

References pose_list_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

core::kinematics::Stub protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::get_reference_stub ( pose::Pose const & pose ) const

private

References core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::stepwise::sampling::rna::rigid_body::get_sugar_stub(), is_prepend_, core::kinematics::Stub::M, options_, reference_res_, core::pose::Pose::residue(), protocols::TR, and core::kinematics::Stub::v.

Referenced by initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_euler_angle_grid_parameters ( )

private

References centroid_bin_size_, euler_angle_bin_max_, euler_angle_bin_min_, euler_angle_bin_size_, euler_z_bin_max_, euler_z_bin_min_, euler_z_bin_size_, options_, STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, and STANDARD_EULER_Z_BIN_SIZE.

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_pose_level_screeners ( pose::Pose & pose )

private

References anchor_sugar_modeling_, anchor_sugar_screener_legacy_, atr_rep_checker_, atr_rep_checker_with_instantiated_sugar_, atr_rep_checkers_for_anchor_sugar_models_, base_bin_map_, base_centroid_checker_, chain_break_to_anchor_checker_, chain_break_to_distal_checker_, chain_closable_geometry_to_anchor_checker_, chain_closable_geometry_to_distal_checker_, close_chain_to_anchor_, close_chain_to_distal_, extra_tag_, full_pose_level_screening_, protocols::moves::Mover::get_native_pose(), is_internal_, is_prepend_, job_parameters_, utility::tools::make_vector1(), max_distance_squared_, moving_res_, native_rmsd_screen_, o2prime_instantiation_distance_cutoff_, o2prime_packer_, options_, phosphate_sampler_, pose_selection_, reference_stub_, rigid_body_sampling_, screeners_, screening_pose_, silent_file_, sugar_screening_pose_, tag_definition_, try_sugar_instantiation_, user_input_VDW_bin_checker_, protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose(), core::kinematics::Stub::v, and VDW_bin_checker_.

Referenced by initialize_screeners().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers ( pose::Pose & pose )

private

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_residue_level_screeners ( pose::Pose & pose )

private

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_rigid_body_sampler ( pose::Pose const & pose )

private

References anchor_sugar_modeling_, anchor_sugar_screener_legacy_, define_rigid_body_rotamer(), protocols::stepwise::get_res_map(), protocols::rotamer_sampler::RotamerComb::init(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, moving_res_, options_, pose_at_origin_list_, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, protocols::stepwise::sampling::rna::sugar::SugarModeling::sample_sugar, sampler_, and protocols::rotamer_sampler::RotamerComb::set_random().

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_screeners ( pose::Pose & pose )

private

References initialize_pose_level_screeners(), initialize_residue_level_screeners(), residue_level_screening_, and screeners_.

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_xyz_grid_parameters ( )

private

References base_bin_map_, centroid_bin_max_, centroid_bin_min_, gap_size_to_anchor_, protocols::stepwise::sampling::rna::rigid_body::initialize_xyz_parameters(), max_distance_, max_distance_squared_, moving_rsd_at_origin_list_, and options_.

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::reinstantiate_backbone_and_add_constraint_at_moving_res	(	pose::Pose &	pose,
		Size const &	five_prime_chain_break_res
	)

private

References protocols::stepwise::sampling::rna::add_harmonic_chain_break_constraint(), core::conformation::Residue::has_variant_type(), moving_res_, core::pose::Pose::residue(), and runtime_assert.

Referenced by initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_anchor_sugar_modeling ( sugar::SugarModeling const & anchor_sugar_modeling )

References anchor_sugar_modeling_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_base_centroid_checker ( checker::RNA_BaseCentroidCheckerOP & checker )

References base_centroid_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_options ( StepWiseRNA_ModelerOptionsCOP options )

References options_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_scorefxn ( scoring::ScoreFunctionOP const & scorefxn )

References scorefxn_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_silent_file ( std::string const & setting )

inline

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const & user_input_VDW_bin_checker )

References user_input_VDW_bin_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::update_base_bin_map ( rna::rigid_body::BaseBin const & base_bin )

private

Member Data Documentation

sugar::SugarModeling protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::anchor_sugar_modeling_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), initialize_residue_level_screeners(), initialize_rigid_body_sampler(), and set_anchor_sugar_modeling().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::anchor_sugar_screener_legacy_

private

Referenced by initialize_pose_level_screeners(), and initialize_rigid_body_sampler().

checker::AtrRepCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::atr_rep_checker_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

checker::AtrRepCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::atr_rep_checker_with_instantiated_sugar_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

utility::vector1< checker::AtrRepCheckerOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::atr_rep_checkers_for_anchor_sugar_models_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

rna::rigid_body::BaseBinMap protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::base_bin_map_

private

Referenced by apply(), initialize_pose_level_screeners(), and initialize_xyz_grid_parameters().

checker::RNA_BaseCentroidCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::base_centroid_checker_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), initialize_residue_level_screeners(), and set_base_centroid_checker().

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::centroid_bin_max_

private

Referenced by initialize_xyz_grid_parameters().

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::centroid_bin_min_

private

Referenced by initialize_xyz_grid_parameters().

Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::centroid_bin_size_

private

Referenced by define_rigid_body_rotamer(), and initialize_euler_angle_grid_parameters().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::chain_break_reference_res_

private

checker::ChainClosureCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::chain_break_to_anchor_checker_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

checker::ChainClosureCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::chain_break_to_distal_checker_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

checker::ChainClosableGeometryCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::chain_closable_geometry_to_anchor_checker_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

checker::ChainClosableGeometryCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::chain_closable_geometry_to_distal_checker_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::close_chain_to_anchor_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::close_chain_to_distal_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

StepWiseRNA_CountStruct protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::count_data_

private

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_angle_bin_max_

private

Referenced by initialize_euler_angle_grid_parameters().

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_angle_bin_min_

private

Referenced by initialize_euler_angle_grid_parameters().

Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_angle_bin_size_

private

Referenced by define_rigid_body_rotamer(), and initialize_euler_angle_grid_parameters().

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_z_bin_max_

private

Referenced by initialize_euler_angle_grid_parameters().

int protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_z_bin_min_

private

Referenced by initialize_euler_angle_grid_parameters().

Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::euler_z_bin_size_

private

Referenced by define_rigid_body_rotamer(), and initialize_euler_angle_grid_parameters().

std::string const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::extra_tag_

private

Referenced by initialize_pose_level_screeners().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::five_prime_chain_break_res_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_RigidBodySampler().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::floating_base_five_prime_chain_break_

private

Referenced by initialize_poses_and_stubs_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::floating_base_three_prime_chain_break_

private

Referenced by initialize_poses_and_stubs_and_checkers().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::full_pose_level_screening_

private

Referenced by initialize_pose_level_screeners().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::gap_size_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_RigidBodySampler().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::gap_size_to_anchor_

private

Referenced by initialize_poses_and_stubs_and_checkers(), initialize_xyz_grid_parameters(), and StepWiseRNA_RigidBodySampler().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::is_dinucleotide_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_RigidBodySampler().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::is_internal_

private

Referenced by initialize_pose_level_screeners(), initialize_residue_level_screeners(), and StepWiseRNA_RigidBodySampler().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::is_prepend_

private

Referenced by get_reference_stub(), and initialize_pose_level_screeners().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::job_parameters_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_RigidBodySampler().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::legacy_mode_

private

Distance protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::max_distance_

private

Referenced by define_rigid_body_rotamer(), and initialize_xyz_grid_parameters().

Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::max_distance_squared_

private

Referenced by initialize_pose_level_screeners(), initialize_residue_level_screeners(), and initialize_xyz_grid_parameters().

Size protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::max_ntries_

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_res_

private

Referenced by define_rigid_body_rotamer(), initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), initialize_residue_level_screeners(), initialize_rigid_body_sampler(), reinstantiate_backbone_and_add_constraint_at_moving_res(), and StepWiseRNA_RigidBodySampler().

kinematics::Stub protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_res_base_stub_

private

Referenced by initialize_residue_level_screeners().

core::conformation::ResidueOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_rsd_at_origin_

private

utility::vector1< core::conformation::ResidueOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_rsd_at_origin_from_sampler_

private

utility::vector1< conformation::ResidueOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_rsd_at_origin_list_

private

Referenced by define_rigid_body_rotamer(), initialize_poses_and_stubs_and_checkers(), initialize_residue_level_screeners(), and initialize_xyz_grid_parameters().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::moving_suite_

private

bool protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::native_rmsd_screen_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

Size protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::num_pose_kept_to_use_

private

Referenced by initialize_poses_and_stubs_and_checkers().

Distance protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::o2prime_instantiation_distance_cutoff_

private

Referenced by initialize_pose_level_screeners().

o2prime::O2PrimePackerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::o2prime_packer_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::options_

private

Referenced by apply(), define_rigid_body_rotamer(), get_reference_stub(), initialize_euler_angle_grid_parameters(), initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), initialize_rigid_body_sampler(), initialize_xyz_grid_parameters(), and set_options().

phosphate::MultiPhosphateSamplerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::phosphate_sampler_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

utility::vector1< pose::PoseOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::pose_at_origin_list_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and initialize_rigid_body_sampler().

utility::vector1< pose::PoseOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::pose_list_

private

Referenced by apply(), get_pose_list(), and initialize_poses_and_stubs_and_checkers().

StepWiseRNA_PoseSelectionOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::pose_selection_

private

Referenced by apply(), initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::reference_res_

private

Referenced by get_reference_stub(), initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_RigidBodySampler().

kinematics::Stub protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::reference_stub_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::residue_level_screening_

private

Referenced by initialize_screeners().

bool const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::rigid_body_sampling_

private

Referenced by initialize_pose_level_screeners().

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternativesOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::sampler_

private

Referenced by apply(), and initialize_rigid_body_sampler().

scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::scorefxn_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and set_scorefxn().

utility::vector1< screener::StepWiseScreenerOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::screeners_

private

Referenced by apply(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), and initialize_screeners().

utility::vector1< conformation::ResidueOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::screening_moving_rsd_at_origin_list_

private

Referenced by initialize_poses_and_stubs_and_checkers().

pose::PoseOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::screening_pose_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

std::string protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::silent_file_

private

Referenced by initialize_pose_level_screeners().

utility::vector1< conformation::ResidueOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::sugar_screening_moving_rsd_at_origin_list_

private

pose::PoseOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::sugar_screening_pose_

private

Referenced by initialize_pose_level_screeners(), and initialize_poses_and_stubs_and_checkers().

screener::TagDefinitionOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::tag_definition_

private

Referenced by initialize_pose_level_screeners(), and initialize_residue_level_screeners().

bool protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::try_sugar_instantiation_

private

Referenced by initialize_pose_level_screeners().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::user_input_VDW_bin_checker_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), initialize_residue_level_screeners(), and set_user_input_VDW_bin_checker().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::VDW_bin_checker_

private

Referenced by initialize_pose_level_screeners(), initialize_poses_and_stubs_and_checkers(), and initialize_residue_level_screeners().

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

symlinks/rosetta/src/protocols/stepwise/sampling/rna/legacy/rigid_body/StepWiseRNA_RigidBodySampler.hh
symlinks/rosetta/src/protocols/stepwise/sampling/rna/legacy/rigid_body/StepWiseRNA_RigidBodySampler.cc

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