protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker Class Reference

#include <RNA_VDW_BinChecker.hh>

Public Member Functions
	RNA_VDW_BinChecker ()
virtual	~RNA_VDW_BinChecker ()
void	FARFAR_setup_using_user_input_VDW_pose (utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose)
void	setup_using_user_input_VDW_pose (utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
void	setup_using_working_pose (core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
void	update_VDW_screen_bin (core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const is_prepend, std::ofstream &outfile_act)
void	create_VDW_screen_bin (core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose=false)
void	create_VDW_screen_bin (utility::vector1< VDW_RepScreeninfo > const &VDW_rep_screen_info_list, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose)
void	create_VDW_screen_bin (utility::vector1< core::pose::Pose > const &pose_list, utility::vector1< utility::vector1< core::Size > > const &list_of_ignore_res_list, utility::vector1< bool > const list_of_is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose)
bool	VDW_rep_screen (core::pose::Pose const &screening_pose, core::Size const &moving_res, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
bool	VDW_rep_screen (core::pose::Pose const &screening_pose, core::Size const &moving_res)
bool	VDW_rep_screen_with_act_pose (core::pose::Pose const &screening_pose, utility::vector1< core::Size > const &moving_res_list, bool const local_verbose=true)
	Warning, this version is very SLOW! More...
bool	user_inputted_VDW_screen_pose () const
void	reference_xyz_consistency_check (numeric::xyzVector< core::Real > const &inputted_reference_xyz) const
void	set_VDW_rep_alignment_RMSD_CUTOFF (core::Real const &setting)
void	set_VDW_rep_delete_matching_res (utility::vector1< std::string > const &setting)
void	set_physical_pose_clash_dist_cutoff (core::Real const &setting)
void	set_output_pdb (bool const setting)

Private Member Functions
void	check_VDW_screen_bin_is_setup () const
bool	is_atom_bin_in_range (Atom_Bin const &atom_pos_bin) const
bool	check_atom_bin_in_range (Atom_Bin const &atom_pos_bin)
core::Vector	get_reference_xyz (core::pose::Pose const &pose, core::Size const reference_res, bool const verbose=false)
void	set_reference_xyz (numeric::xyzVector< core::Real > const &reference_xyz)
Atom_Bin	get_atom_bin (numeric::xyzVector< core::Real > const &atom_pos) const
numeric::xyzVector< core::Real >	get_atom_pos (Atom_Bin const &atom_bin) const
void	output_atom_bin (std::string const filename) const
utility::vector1< core::Size >	get_matching_res_in_VDW_rep_screen_pose (core::pose::Pose const &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, std::map< core::Size, core::Size > &full_to_sub) const
void	align_VDW_rep_screen_pose (core::pose::Pose &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, bool const verbose) const
void	create_VDW_rep_screen_pose (VDW_RepScreeninfo &VDW_rep_screen_info, core::pose::Pose const &working_pose, std::map< core::Size, core::Size > &full_to_sub, bool const verbose) const

Private Attributes
core::Real	max_distance_
core::Real	atom_bin_size_
int const	bin_min_
int const	bin_max_
int const	bin_offset_
core::Size const	num_clash_atom_cutoff_
bool const	write_to_file_
bool	is_reference_xyz_setup_
bool	is_VDW_screen_bin_setup_
bool	user_inputted_VDW_screen_pose_
utility::vector1 < utility::vector1 < utility::vector1< bool > > >	VDW_screen_bin_
numeric::xyzVector< core::Real >	reference_xyz_
core::Real	VDW_rep_alignment_RMSD_CUTOFF_
bool	tolerate_off_range_atom_bin_
int	num_atom_pos_bin_out_of_range_message_outputted_
bool	VDW_rep_screen_with_physical_pose_verbose_
core::Real	physical_pose_clash_dist_cutoff_
utility::vector1< std::string >	VDW_rep_ignore_matching_res_
bool	use_VDW_rep_pose_for_screening_
utility::vector1 < VDW_RepScreeninfo >	VDW_rep_screen_info_list_
bool	output_pdb_

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker

(

)

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::~RNA_VDW_BinChecker ( )

virtual

Member Function Documentation

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose ( core::pose::Pose &  VDW_rep_screen_pose, core::pose::Pose const &  working_pose, utility::vector1< core::Size > const &  VDW_rep_screen_align_res, utility::vector1< core::Size > const &  working_align_res, bool const  verbose  ) const

private

References protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::stepwise::modeler::align::create_alignment_id_map(), core::pose::Pose::dump_pdb(), output_pdb_, protocols::stepwise::modeler::rna::output_title_text(), rmsd, core::scoring::superimpose_pose(), core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, and VDW_rep_alignment_RMSD_CUTOFF_.

Referenced by create_VDW_rep_screen_pose(), and VDW_rep_screen_with_act_pose().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin )

private

References bin_max_, is_atom_bin_in_range(), num_atom_pos_bin_out_of_range_message_outputted_, tolerate_off_range_atom_bin_, protocols::TR, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by VDW_rep_screen().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_VDW_screen_bin_is_setup ( ) const

private

References is_VDW_screen_bin_setup_, utility_exit_with_message, and VDW_screen_bin_.

Referenced by output_atom_bin(), and VDW_rep_screen().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose ( VDW_RepScreeninfo &  VDW_rep_screen_info, core::pose::Pose const &  working_pose, std::map< core::Size, core::Size > &  full_to_sub, bool const  verbose  ) const

private

References protocols::stepwise::modeler::rna::add_virtual_O2Prime_hydrogen(), align_VDW_rep_screen_pose(), FA_RNA, core::chemical::ChemicalManager::get_instance(), get_matching_res_in_VDW_rep_screen_pose(), protocols::farna::make_phosphate_nomenclature_matches_mini(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::pose_name, core::chemical::ChemicalManager::residue_type_set(), protocols::TR, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_align_res, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_ignore_res, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_pose, and protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::working_align_res.

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and setup_using_user_input_VDW_pose().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ignore_res_list,
		bool const	is_prepend,
		numeric::xyzVector< core::Real > const &	reference_xyz,
		bool const	verbose = false
	)

Referenced by create_VDW_screen_bin(), setup_using_user_input_VDW_pose(), setup_using_working_pose(), and protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin	(	utility::vector1< VDW_RepScreeninfo > const &	VDW_rep_screen_info_list,
		numeric::xyzVector< core::Real > const &	reference_xyz,
		bool const	verbose
	)

References create_VDW_screen_bin().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin	(	utility::vector1< core::pose::Pose > const &	pose_list,
		utility::vector1< utility::vector1< core::Size > > const &	list_of_ignore_res_list,
		utility::vector1< bool > const	list_of_is_prepend,
		numeric::xyzVector< core::Real > const &	reference_xyz,
		bool const	verbose
	)

References atom_bin_size_, bin_max_, bin_min_, bin_offset_, is_VDW_screen_bin_setup_, max_distance_, num_clash_atom_cutoff_, output_atom_bin(), protocols::stepwise::modeler::output_boolean(), set_reference_xyz(), tolerate_off_range_atom_bin_, protocols::TR, update_VDW_screen_bin(), user_inputted_VDW_screen_pose_, utility_exit_with_message, VDW_screen_bin_, and write_to_file_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose	(	utility::vector1< std::string > const &	VDW_rep_screen_pose_info,
		core::pose::Pose const &	const_working_pose
	)

References protocols::stepwise::modeler::rna::add_virtual_O2Prime_hydrogen(), create_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::full_align_res, full_to_sub(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::import_ID, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::input_string, protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::pose_name, protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), core::pose::Pose::total_residue(), protocols::TR, use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_align_res, VDW_rep_screen_info, VDW_rep_screen_info_list_, verbose, and protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::working_align_res.

Atom_Bin protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_atom_bin ( numeric::xyzVector< core::Real > const &  atom_pos ) const

private

References atom_bin_size_, bin_offset_, is_reference_xyz_setup_, reference_xyz_, runtime_assert, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by update_VDW_screen_bin(), and VDW_rep_screen().

numeric::xyzVector< core::Real > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_atom_pos ( Atom_Bin const &  atom_bin ) const

private

References atom_bin_size_, bin_offset_, is_reference_xyz_setup_, reference_xyz_, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by output_atom_bin(), and update_VDW_screen_bin().

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose ( core::pose::Pose const &  VDW_rep_screen_pose, core::pose::Pose const &  working_pose, utility::vector1< core::Size > const &  VDW_rep_screen_align_res, utility::vector1< core::Size > const &  working_align_res, std::map< core::Size, core::Size > &  full_to_sub  ) const

private

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), dist_cutoff, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), utility::vector1< T, class >::has_value(), core::conformation::Residue::is_virtual(), length, core::conformation::Residue::natoms(), protocols::stepwise::modeler::output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), core::pose::Pose::total_residue(), protocols::TR, core::conformation::Residue::type(), utility_exit_with_message, VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_ignore_matching_res_, and core::conformation::Residue::xyz().

Referenced by create_VDW_rep_screen_pose().

core::Vector protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz ( core::pose::Pose const &  pose, core::Size const  reference_res, bool const  verbose = false  )

private

References core::chemical::rna::get_rna_base_centroid(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by setup_using_user_input_VDW_pose(), and setup_using_working_pose().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin ) const

private

References bin_max_, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by check_atom_bin_in_range(), and update_VDW_screen_bin().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_atom_bin ( std::string const  filename ) const

private

References bin_max_, check_VDW_screen_bin_is_setup(), get_atom_pos(), is_reference_xyz_setup_, utility_exit_with_message, VDW_screen_bin_, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_consistency_check

(

numeric::xyzVector< core::Real > const &

inputted_reference_xyz

)

const

References is_reference_xyz_setup_, reference_xyz_, protocols::TR, and utility_exit_with_message.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_output_pdb ( bool const  setting )

inline

References output_pdb_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_physical_pose_clash_dist_cutoff ( core::Real const &  setting )

inline

References physical_pose_clash_dist_cutoff_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_reference_xyz ( numeric::xyzVector< core::Real > const &  reference_xyz )

private

References is_reference_xyz_setup_, reference_xyz_, and utility_exit_with_message.

Referenced by create_VDW_screen_bin().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting )

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting )

inline

References VDW_rep_ignore_matching_res_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose	(	utility::vector1< std::string > const &	VDW_rep_screen_pose_info,
		core::pose::Pose const &	const_working_pose,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters
	)

References protocols::stepwise::modeler::rna::add_virtual_O2Prime_hydrogen(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), create_VDW_rep_screen_pose(), create_VDW_screen_bin(), core::pose::Pose::fold_tree(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::full_align_res, full_to_sub(), get_reference_xyz(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::import_ID, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::input_string, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::pose_name, core::kinematics::FoldTree::root(), protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR, use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_align_res, VDW_rep_screen_info, VDW_rep_screen_info_list_, verbose, and protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::working_align_res.

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose	(	core::pose::Pose const &	const_working_pose,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters
	)

References create_VDW_screen_bin(), get_reference_xyz(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, and protocols::stepwise::modeler::virtualize_side_chains().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ignore_res_list,
		bool const	is_prepend,
		std::ofstream &	outfile_act
	)

References at(), atom_bin_size_, core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), get_atom_bin(), get_atom_pos(), utility::vector1< T, class >::has_value(), is_atom_bin_in_range(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), protocols::stepwise::modeler::rna::output_seq_num_list(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR, core::conformation::Residue::type(), VDW_screen_bin_, write_to_file_, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, core::conformation::Residue::xyz(), protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose

(

)

const

References user_inputted_VDW_screen_pose_.

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), and protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen	(	core::pose::Pose const &	screening_pose,
		core::Size const &	moving_res,
		core::conformation::Residue const &	rsd_at_origin,
		core::kinematics::Stub const &	moving_res_base_stub
	)

References at(), check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), get_atom_bin(), protocols::stepwise::sampler::rigid_body::get_atom_coordinates(), core::conformation::Residue::is_virtual(), num_clash_atom_cutoff_, core::pose::Pose::residue(), protocols::TR, utility_exit_with_message, VDW_screen_bin_, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

Referenced by protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), and protocols::stepwise::screener::VDW_BinScreener::check_screen().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen	(	core::pose::Pose const &	screening_pose,
		core::Size const &	moving_res
	)

References at(), check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), get_atom_bin(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), num_clash_atom_cutoff_, core::pose::Pose::residue(), VDW_screen_bin_, protocols::stepwise::modeler::rna::checker::Atom_Bin::x, core::conformation::Residue::xyz(), protocols::stepwise::modeler::rna::checker::Atom_Bin::y, and protocols::stepwise::modeler::rna::checker::Atom_Bin::z.

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose	(	core::pose::Pose const &	screening_pose,
		utility::vector1< core::Size > const &	moving_res_list,
		bool const	local_verbose = true
	)

Warning, this version is very SLOW!

References align_VDW_rep_screen_pose(), utility::vector1< T, class >::has_value(), protocols::stepwise::modeler::rna::is_residues_in_contact(), num_clash_atom_cutoff_, protocols::stepwise::modeler::rna::output_seq_num_list(), physical_pose_clash_dist_cutoff_, core::pose::Pose::total_residue(), protocols::TR, use_VDW_rep_pose_for_screening_, utility_exit_with_message, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_align_res, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_ignore_res, protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::VDW_pose, VDW_rep_screen_info, VDW_rep_screen_info_list_, VDW_rep_screen_with_physical_pose_verbose_, and protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo::working_align_res.

Member Data Documentation

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::atom_bin_size_

private

Referenced by create_VDW_screen_bin(), get_atom_bin(), get_atom_pos(), and update_VDW_screen_bin().

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_max_

private

Referenced by check_atom_bin_in_range(), create_VDW_screen_bin(), is_atom_bin_in_range(), and output_atom_bin().

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_min_

private

Referenced by create_VDW_screen_bin().

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_offset_

private

Referenced by create_VDW_screen_bin(), get_atom_bin(), and get_atom_pos().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_reference_xyz_setup_

private

Referenced by get_atom_bin(), get_atom_pos(), output_atom_bin(), reference_xyz_consistency_check(), and set_reference_xyz().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_VDW_screen_bin_setup_

private

Referenced by check_VDW_screen_bin_is_setup(), and create_VDW_screen_bin().

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::max_distance_

private

Referenced by create_VDW_screen_bin().

int protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::num_atom_pos_bin_out_of_range_message_outputted_

private

Referenced by check_atom_bin_in_range().

core::Size const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::num_clash_atom_cutoff_

private

Referenced by create_VDW_screen_bin(), VDW_rep_screen(), and VDW_rep_screen_with_act_pose().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_pdb_

private

Referenced by align_VDW_rep_screen_pose(), and set_output_pdb().

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::physical_pose_clash_dist_cutoff_

private

Referenced by set_physical_pose_clash_dist_cutoff(), and VDW_rep_screen_with_act_pose().

numeric::xyzVector< core::Real > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_

private

Referenced by get_atom_bin(), get_atom_pos(), reference_xyz_consistency_check(), and set_reference_xyz().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::tolerate_off_range_atom_bin_

private

Referenced by check_atom_bin_in_range(), and create_VDW_screen_bin().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::use_VDW_rep_pose_for_screening_

private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and VDW_rep_screen_with_act_pose().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose_

private

Referenced by create_VDW_screen_bin(), FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and user_inputted_VDW_screen_pose().

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_alignment_RMSD_CUTOFF_

private

Referenced by align_VDW_rep_screen_pose(), get_matching_res_in_VDW_rep_screen_pose(), and set_VDW_rep_alignment_RMSD_CUTOFF().

utility::vector1< std::string > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_ignore_matching_res_

private

Referenced by get_matching_res_in_VDW_rep_screen_pose(), and set_VDW_rep_delete_matching_res().

utility::vector1< VDW_RepScreeninfo > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_info_list_

private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and VDW_rep_screen_with_act_pose().

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_physical_pose_verbose_

private

Referenced by VDW_rep_screen_with_act_pose().

utility::vector1< utility::vector1< utility::vector1< bool > > > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_screen_bin_

private

Referenced by check_VDW_screen_bin_is_setup(), create_VDW_screen_bin(), output_atom_bin(), update_VDW_screen_bin(), and VDW_rep_screen().

bool const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::write_to_file_

private

Referenced by create_VDW_screen_bin(), and update_VDW_screen_bin().

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

• src/protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh
• src/protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.cc