#include <StepWiseRNA_FloatingBaseSampler.hh>

Public Member Functions
	StepWiseRNA_FloatingBaseSampler (StepWiseRNA_JobParametersCOP &job_parameters_)

	~StepWiseRNA_FloatingBaseSampler ()

virtual void	apply (core::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 (core::scoring::ScoreFunctionOP const &scorefxn)

utility::vector1 < core::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 (core::pose::Pose &pose)

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

void	initialize_euler_angle_grid_parameters ()

void	initialize_xyz_grid_parameters ()

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

bool	break_early_for_integration_tests ()

core::Size	screen_anchor_sugar_conformation (core::pose::Pose &pose, std::string &tag)

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

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

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

void	update_base_bin_map (utility::vector1< core::Real > const &rigid_body_values)

void	output_count_data ()

void	instantiate_moving_sugar_and_o2prime (core::pose::Pose &pose)

void	virtualize_moving_sugar_and_o2prime (core::pose::Pose &pose)

bool	check_moving_sugar (core::pose::Pose &pose)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

core::Size const	moving_res_

core::Size const	moving_suite_

bool const	is_prepend_

bool const	is_internal_

core::Size const	gap_size_

core::Size const	gap_size_to_anchor_

core::Size const	five_prime_chain_break_res_

core::Size const	chain_break_reference_res_

core::Size const	reference_res_

core::Size const	floating_base_five_prime_chain_break_

core::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 < core::pose::PoseOP >	pose_list_

core::scoring::ScoreFunctionOP	scorefxn_

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerOP	sampler_

StepWiseRNA_CountStruct	count_data_

std::string	silent_file_

bool	native_rmsd_screen_

core::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_

core::pose::PoseOP	screening_pose_

core::pose::PoseOP	sugar_screening_pose_

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

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

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

StepWiseRNA_PoseSelectionOP	pose_selection_

o2prime::O2PrimePackerOP	o2prime_packer_

phosphate::MultiPhosphateSamplerOP	phosphate_sampler_

core::kinematics::Stub	reference_stub_

utility::vector1 < core::kinematics::Stub >	other_residues_base_list_

std::map < protocols::stepwise::sampling::rna::rigid_body::BaseBin, int, protocols::stepwise::sampling::rna::rigid_body::compare_base_bin >	base_bin_map_

core::Size	max_ntries_

int	euler_angle_bin_min_

int	euler_angle_bin_max_

core::Real	euler_angle_bin_size_

int	euler_z_bin_min_

int	euler_z_bin_max_

core::Real	euler_z_bin_size_

int	centroid_bin_min_

int	centroid_bin_max_

core::Real	centroid_bin_size_

core::Distance	max_distance_

core::Real	max_distance_squared_

bool	try_sugar_instantiation_

core::Distance	o2prime_instantiation_distance_cutoff_

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_FloatingBaseSampler::StepWiseRNA_FloatingBaseSampler ( 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_FloatingBaseSampler::~StepWiseRNA_FloatingBaseSampler ( )

Member Function Documentation

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

virtual

Implements protocols::moves::MoverForPoseList.

bool protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::break_early_for_integration_tests ( )

private

References protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::both_count, count_data_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::full_score_count, native_rmsd_screen_, options_, and protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::rmsd_count.

Referenced by apply().

bool protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::check_moving_sugar ( core::pose::Pose & pose )

private

References core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::is_virtual_residue(), j, length, moving_res_, core::conformation::Residue::nheavyatoms(), o2prime_instantiation_distance_cutoff_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), try_sugar_instantiation_, and core::conformation::Residue::xyz().

Referenced by apply().

std::string protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::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_FloatingBaseSampler::get_pose_list ( )

References pose_list_.

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

private

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

private

Referenced by apply().

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

private

References centroid_bin_size_, euler_angle_bin_size_, euler_z_bin_size_, protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::init(), max_distance_, moving_res_, moving_rsd_at_origin_list_, options_, reference_stub_, sampler_, protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange::set_centroid_bin_size(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange::set_euler_angle_bin_size(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange::set_euler_z_bin_size(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRange::set_max_distance(), protocols::rotamer_sampler::RotamerSizedComb::set_random(), and protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::value_range().

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::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_, and moving_rsd_at_origin_list_.

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::instantiate_moving_sugar_and_o2prime ( core::pose::Pose & pose )

private

References core::conformation::Residue::has_variant_type(), moving_res_, and core::pose::Pose::residue().

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::output_count_data ( )

private

Referenced by apply().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::reinstantiate_backbone_and_add_constraint_at_moving_res	(	core::pose::Pose &	pose,
		core::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().

Size protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::screen_anchor_sugar_conformation	(	core::pose::Pose &	pose,
		std::string &	tag
	)

private

References anchor_sugar_modeling_, atr_rep_checker_with_instantiated_sugar_, atr_rep_checkers_for_anchor_sugar_models_, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::chain_closable_geometry_count3, chain_closable_geometry_to_anchor_checker_, protocols::stepwise::sampling::rna::sugar::copy_bulge_res_and_sugar_torsion(), count_data_, is_prepend_, o2prime_packer_, options_, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, protocols::stepwise::sampling::rna::sugar::SugarModeling::sample_sugar, sugar_screening_pose_, and tag_from_pose().

Referenced by apply().

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

References anchor_sugar_modeling_.

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

References base_centroid_checker_.

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

References options_.

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

References scorefxn_.

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

inline

References silent_file_.

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

References user_input_VDW_bin_checker_.

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

private

References base_bin_map_.

Referenced by apply(), and update_base_bin_map().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::update_base_bin_map ( utility::vector1< core::Real > const & rigid_body_values )

private

References protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_x, protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_y, protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_z, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_alpha, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_gamma, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_z, and update_base_bin_map().

void protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::virtualize_moving_sugar_and_o2prime ( core::pose::Pose & pose )

private

References core::conformation::Residue::has_variant_type(), moving_res_, and core::pose::Pose::residue().

Referenced by apply().

Member Data Documentation

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

private

Referenced by apply(), initialize_poses_and_stubs_and_checkers(), screen_anchor_sugar_conformation(), and set_anchor_sugar_modeling().

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

private

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

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

private

Referenced by initialize_poses_and_stubs_and_checkers(), and screen_anchor_sugar_conformation().

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

private

Referenced by initialize_poses_and_stubs_and_checkers(), and screen_anchor_sugar_conformation().

std::map< protocols::stepwise::sampling::rna::rigid_body::BaseBin, int, protocols::stepwise::sampling::rna::rigid_body::compare_base_bin > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::base_bin_map_

private

Referenced by apply(), initialize_xyz_grid_parameters(), output_count_data(), and update_base_bin_map().

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

private

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

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

private

Referenced by initialize_xyz_grid_parameters().

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

private

Referenced by initialize_xyz_grid_parameters().

core::Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::centroid_bin_size_

private

Referenced by initialize_euler_angle_grid_parameters(), and initialize_rigid_body_sampler().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::chain_break_reference_res_

private

Referenced by apply().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

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

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

Referenced by apply(), break_early_for_integration_tests(), initialize_poses_and_stubs_and_checkers(), output_count_data(), and screen_anchor_sugar_conformation().

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

private

Referenced by initialize_euler_angle_grid_parameters(), and output_count_data().

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

private

Referenced by initialize_euler_angle_grid_parameters(), and output_count_data().

core::Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::euler_angle_bin_size_

private

Referenced by initialize_euler_angle_grid_parameters(), and initialize_rigid_body_sampler().

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

private

Referenced by initialize_euler_angle_grid_parameters().

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

private

Referenced by initialize_euler_angle_grid_parameters().

core::Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::euler_z_bin_size_

private

Referenced by initialize_euler_angle_grid_parameters(), and initialize_rigid_body_sampler().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::five_prime_chain_break_res_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_FloatingBaseSampler().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::floating_base_five_prime_chain_break_

private

Referenced by initialize_poses_and_stubs_and_checkers().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::floating_base_three_prime_chain_break_

private

Referenced by initialize_poses_and_stubs_and_checkers().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::gap_size_

private

Referenced by initialize_poses_and_stubs_and_checkers(), output_count_data(), and StepWiseRNA_FloatingBaseSampler().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::gap_size_to_anchor_

private

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

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

private

Referenced by initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_FloatingBaseSampler().

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

private

Referenced by apply(), and StepWiseRNA_FloatingBaseSampler().

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

private

Referenced by apply(), get_reference_stub(), and screen_anchor_sugar_conformation().

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

private

Referenced by apply(), initialize_other_residues_base_list(), initialize_poses_and_stubs_and_checkers(), output_count_data(), and StepWiseRNA_FloatingBaseSampler().

core::Distance protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::max_distance_

private

Referenced by initialize_other_residues_base_list(), initialize_rigid_body_sampler(), and initialize_xyz_grid_parameters().

core::Real protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::max_distance_squared_

private

Referenced by apply(), and initialize_xyz_grid_parameters().

core::Size protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::max_ntries_

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::moving_res_

private

Referenced by apply(), check_moving_sugar(), initialize_poses_and_stubs_and_checkers(), initialize_rigid_body_sampler(), instantiate_moving_sugar_and_o2prime(), reinstantiate_backbone_and_add_constraint_at_moving_res(), StepWiseRNA_FloatingBaseSampler(), and virtualize_moving_sugar_and_o2prime().

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

private

Referenced by apply(), initialize_poses_and_stubs_and_checkers(), initialize_rigid_body_sampler(), and initialize_xyz_grid_parameters().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::moving_suite_

private

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

private

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

core::Size protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::num_pose_kept_to_use_

private

Referenced by initialize_poses_and_stubs_and_checkers().

core::Distance protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::o2prime_instantiation_distance_cutoff_

private

Referenced by check_moving_sugar().

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

private

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

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

private

Referenced by apply(), break_early_for_integration_tests(), get_reference_stub(), initialize_euler_angle_grid_parameters(), initialize_other_residues_base_list(), initialize_poses_and_stubs_and_checkers(), initialize_rigid_body_sampler(), screen_anchor_sugar_conformation(), and set_options().

utility::vector1< core::kinematics::Stub > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::other_residues_base_list_

private

Referenced by initialize_other_residues_base_list().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::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_FloatingBaseSampler::pose_selection_

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

core::Size const protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::reference_res_

private

Referenced by apply(), get_reference_stub(), initialize_other_residues_base_list(), initialize_poses_and_stubs_and_checkers(), and StepWiseRNA_FloatingBaseSampler().

core::kinematics::Stub protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::reference_stub_

private

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

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::sampler_

private

Referenced by apply(), and initialize_rigid_body_sampler().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::scorefxn_

private

Referenced by initialize_poses_and_stubs_and_checkers(), and set_scorefxn().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

core::pose::PoseOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::screening_pose_

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

private

Referenced by apply(), and set_silent_file().

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

core::pose::PoseOP protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::sugar_screening_pose_

private

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

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

private

Referenced by apply(), and check_moving_sugar().

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

private

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

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

private

Referenced by apply(), and initialize_poses_and_stubs_and_checkers().

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

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

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