protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener Class Reference

#include <StepWiseRNA_VDW_Bin_Screener.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener:

Public Member Functions
	StepWiseRNA_VDW_Bin_Screener ()
virtual	~StepWiseRNA_VDW_Bin_Screener ()
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, StepWiseRNA_JobParametersCOP const &job_parameters)
void	setup_using_working_pose (core::pose::Pose const &const_working_pose, StepWiseRNA_JobParametersCOP const &job_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)
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::swa::rna::StepWiseRNA_VDW_Bin_Screener::StepWiseRNA_VDW_Bin_Screener

(

)

protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::~StepWiseRNA_VDW_Bin_Screener ( )

virtual

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::base_atoms_square_deviation(), protocols::swa::create_alignment_id_map(), core::pose::Pose::dump_pdb(), output_pdb_, protocols::swa::rna::Output_title_text(), core::scoring::superimpose_pose(), core::pose::Pose::total_residue(), and VDW_rep_alignment_RMSD_CUTOFF_.

Referenced by create_VDW_rep_screen_pose(), and VDW_rep_screen_with_act_pose().

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by VDW_rep_screen().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::check_VDW_screen_bin_is_setup ( ) const

private

References Is_VDW_screen_bin_setup_, and VDW_screen_bin_.

Referenced by output_atom_bin(), and VDW_rep_screen().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::Add_virtual_O2Star_hydrogen(), align_VDW_rep_screen_pose(), core::chemical::ChemicalManager::get_instance(), get_matching_res_in_VDW_rep_screen_pose(), protocols::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::pose_from_pdb(), protocols::swa::rna::VDW_RepScreeninfo::pose_name, core::chemical::ChemicalManager::residue_type_set(), core::chemical::RNA, protocols::swa::rna::VDW_RepScreeninfo::VDW_align_res, protocols::swa::rna::VDW_RepScreeninfo::VDW_ignore_res, protocols::swa::rna::VDW_RepScreeninfo::VDW_pose, and protocols::swa::rna::VDW_RepScreeninfo::working_align_res.

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and setup_using_user_input_VDW_pose().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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(), and setup_using_working_pose().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::Output_boolean(), set_reference_xyz(), tolerate_off_range_atom_bin_, update_VDW_screen_bin(), user_inputted_VDW_screen_pose_, VDW_screen_bin_, and write_to_file_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::Add_virtual_O2Star_hydrogen(), create_VDW_rep_screen_pose(), protocols::swa::rna::VDW_RepScreeninfo::full_align_res, protocols::swa::rna::VDW_RepScreeninfo::import_ID, protocols::swa::rna::VDW_RepScreeninfo::input_string, protocols::swa::rna::Output_title_text(), protocols::swa::rna::VDW_RepScreeninfo::pose_name, protocols::swa::rna::string_to_int(), protocols::swa::rna::Tokenize(), core::pose::Pose::total_residue(), use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, protocols::swa::rna::VDW_RepScreeninfo::VDW_align_res, VDW_rep_screen_info_list_, and protocols::swa::rna::VDW_RepScreeninfo::working_align_res.

Atom_Bin protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_atom_bin ( numeric::xyzVector< core::Real > const &  atom_pos) const

private

References atom_bin_size_, bin_offset_, Is_reference_xyz_setup_, reference_xyz_, protocols::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by update_VDW_screen_bin(), and VDW_rep_screen().

numeric::xyzVector< core::Real > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_atom_pos ( Atom_Bin const &  atom_bin) const

private

References atom_bin_size_, bin_offset_, Is_reference_xyz_setup_, reference_xyz_, protocols::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by output_atom_bin(), and update_VDW_screen_bin().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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(), core::conformation::Residue::atom_type(), protocols::swa::rna::Contain_seq_num(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), core::pose::Pose::residue(), protocols::swa::rna::string_to_int(), protocols::swa::rna::Tokenize(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_ignore_matching_res_, and core::conformation::Residue::xyz().

Referenced by create_VDW_rep_screen_pose().

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::Is_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin) const

private

References bin_max_, protocols::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by check_atom_bin_in_range(), and update_VDW_screen_bin().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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_, VDW_screen_bin_, protocols::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::reference_xyz_consistency_check

(

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

inputted_reference_xyz)

const

References Is_reference_xyz_setup_, and reference_xyz_.

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

inline

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_physical_pose_clash_dist_cutoff ( core::Real const &  setting)

inline

References physical_pose_clash_dist_cutoff_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_reference_xyz ( numeric::xyzVector< core::Real > const &  reference_xyz)

private

References Is_reference_xyz_setup_, and reference_xyz_.

Referenced by create_VDW_screen_bin().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting)

inline

References VDW_rep_alignment_RMSD_CUTOFF_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting)

inline

References VDW_rep_ignore_matching_res_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose	(	utility::vector1< std::string > const &	VDW_rep_screen_pose_info,
		core::pose::Pose const &	const_working_pose,
		StepWiseRNA_JobParametersCOP const &	job_parameters
	)

References protocols::swa::rna::Add_virtual_O2Star_hydrogen(), protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::Contain_seq_num(), create_VDW_rep_screen_pose(), create_VDW_screen_bin(), core::pose::Pose::fold_tree(), protocols::swa::rna::VDW_RepScreeninfo::full_align_res, core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::VDW_RepScreeninfo::import_ID, protocols::swa::rna::VDW_RepScreeninfo::input_string, protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::VDW_RepScreeninfo::pose_name, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::swa::rna::string_to_int(), protocols::swa::rna::Tokenize(), use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, protocols::swa::rna::VDW_RepScreeninfo::VDW_align_res, VDW_rep_screen_info_list_, and protocols::swa::rna::VDW_RepScreeninfo::working_align_res.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose	(	core::pose::Pose const &	const_working_pose,
		StepWiseRNA_JobParametersCOP const &	job_parameters
	)

References protocols::swa::rna::Add_virtual_O2Star_hydrogen(), create_VDW_screen_bin(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::Output_title_text(), and core::pose::Pose::residue().

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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 core::io::serialization::at(), atom_bin_size_, core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), protocols::swa::rna::Contain_seq_num(), get_atom_bin(), get_atom_pos(), Is_atom_bin_in_range(), core::chemical::AtomType::lj_radius(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), protocols::swa::rna::Output_seq_num_list(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), VDW_screen_bin_, write_to_file_, protocols::swa::rna::Atom_Bin::x, core::conformation::Residue::xyz(), protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::user_inputted_VDW_screen_pose

(

)

const

References user_inputted_VDW_screen_pose_.

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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 core::io::serialization::at(), core::conformation::Residue::atom_type(), check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), get_atom_bin(), protocols::swa::rna::get_atom_coordinates(), core::chemical::AtomType::name(), num_clash_atom_cutoff_, core::pose::Pose::residue(), VDW_screen_bin_, protocols::swa::rna::Atom_Bin::x, protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen	(	core::pose::Pose const &	screening_pose,
		core::Size const &	moving_res
	)

References core::io::serialization::at(), core::conformation::Residue::atom_type(), check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), get_atom_bin(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), num_clash_atom_cutoff_, core::pose::Pose::residue(), VDW_screen_bin_, protocols::swa::rna::Atom_Bin::x, core::conformation::Residue::xyz(), protocols::swa::rna::Atom_Bin::y, and protocols::swa::rna::Atom_Bin::z.

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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(), protocols::swa::rna::Contain_seq_num(), protocols::swa::rna::Is_residues_in_contact(), num_clash_atom_cutoff_, protocols::swa::rna::Output_seq_num_list(), physical_pose_clash_dist_cutoff_, core::pose::Pose::total_residue(), use_VDW_rep_pose_for_screening_, protocols::swa::rna::VDW_RepScreeninfo::VDW_align_res, protocols::swa::rna::VDW_RepScreeninfo::VDW_ignore_res, protocols::swa::rna::VDW_RepScreeninfo::VDW_pose, VDW_rep_screen_info_list_, VDW_rep_screen_with_physical_pose_verbose_, and protocols::swa::rna::VDW_RepScreeninfo::working_align_res.

Member Data Documentation

core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::atom_bin_size_

private

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

int const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::bin_min_

private

Referenced by create_VDW_screen_bin().

int const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::bin_offset_

private

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

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::Is_VDW_screen_bin_setup_

private

Referenced by check_VDW_screen_bin_is_setup(), and create_VDW_screen_bin().

core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::max_distance_

private

Referenced by create_VDW_screen_bin().

int protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::num_atom_pos_bin_out_of_range_message_outputted_

private

Referenced by check_atom_bin_in_range().

core::Size const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::num_clash_atom_cutoff_

private

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

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::output_pdb_

private

Referenced by align_VDW_rep_screen_pose(), and set_output_pdb().

core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::reference_xyz_

private

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

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::tolerate_off_range_atom_bin_

private

Referenced by check_atom_bin_in_range(), and create_VDW_screen_bin().

bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_physical_pose_verbose_

private

Referenced by VDW_rep_screen_with_act_pose().

utility::vector1< utility::vector1< utility::vector1< bool > > > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::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::swa::rna::StepWiseRNA_VDW_Bin_Screener::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/swa/rna/StepWiseRNA_VDW_Bin_Screener.hh
• src/protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.cc