#include <RNA_BaseCentroidChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker:

Public Member Functions
	RNA_BaseCentroidChecker (core::pose::Pose const &pose, working_parameters::StepWiseWorkingParametersCOP &working_parameters, bool const tether_jump=false)

	~RNA_BaseCentroidChecker () override

bool	update_base_stub_list_and_check_centroid_interaction (core::pose::Pose const &pose, StepWiseRNA_CountStruct &count_data)

bool	update_base_stub_list_and_check_that_terminal_res_are_unstacked (core::pose::Pose const &pose, bool const reinitialize=false)

bool	check_that_terminal_res_are_unstacked (bool const verbose=false)

bool	check_centroid_interaction (core::kinematics::Stub const &moving_res_base_stub, StepWiseRNA_CountStruct &count_data)

void	set_allow_base_pair_only_screen (bool const setting)

bool const &	allow_base_pair_only_screen () const

void	set_floating_base (bool const setting)

bool	found_centroid_interaction () const

Private Member Functions
void	Initialize_is_virtual_base (core::pose::Pose const &pose, bool const verbose=false)

void	Initialize_base_stub_list (core::pose::Pose const &pose, bool const verbose=false)

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

bool	check_base_stack (core::kinematics::Stub const &moving_residue_base_stub, core::kinematics::Stub const &other_base_stub, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF, core::chemical::rna::BaseStackWhichSide &base_stack_side, bool const verbose=false) const

bool	check_base_stack (core::kinematics::Stub const &moving_residue_base_stub, core::kinematics::Stub const &other_base_stub, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF, bool const verbose=false) const

bool	check_base_stack (core::kinematics::Stub const &moving_residue_base_stub, core::kinematics::Stub const &other_base_stub, core::chemical::rna::BaseStackWhichSide &base_stack_side)

bool	check_base_stack (core::Size const &pos1, core::Size const &pos2, bool const verbose=false)

bool	check_base_stack (core::kinematics::Stub const &moving_res_base, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF) const

bool	check_base_pair (core::kinematics::Stub const &moving_residue_base_stub, core::kinematics::Stub const &other_base_stub, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF) const

bool	check_base_pair (core::kinematics::Stub const &moving_residue_base_stub, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF) const

bool	check_base_stack (core::kinematics::Stub const &moving_residue_base_stub, core::kinematics::Stub const &other_base_stub, bool const verbose=false) const

bool	check_centroid_interaction_floating_base (core::kinematics::Stub const &moving_res_base_stub, StepWiseRNA_CountStruct &count_data) const

bool	check_centroid_interaction (StepWiseRNA_CountStruct &count_data)

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

bool	is_strong_base_stack (core::kinematics::Stub const &moving_res_base) const

bool	is_medium_base_stack_and_medium_base_pair (core::kinematics::Stub const &moving_res_base) const

bool	check_block_stack_res (utility::vector1< core::Size > const &block_stack_res, core::chemical::rna::BaseStackWhichSide const &block_stack_side) const

bool	check_base_stack_in_partition (core::Size const &block_stack_res, utility::vector1< core::Size > const &other_res, core::chemical::rna::BaseStackWhichSide const &block_stack_side) const

Private Attributes
working_parameters::StepWiseWorkingParametersCOP	working_parameters_

core::scoring::rna::RNA_CentroidInfoOP	rna_centroid_info_

core::Real const	base_stack_dist_cutoff_

core::Real const	base_stack_z_offset_max_

core::Real const	base_stack_z_offset_min_

core::Real const	base_stack_axis_cutoff_

core::Real const	base_stack_planarity_cutoff_

core::Real const	base_pair_dist_min_

core::Real const	base_pair_dist_max_

core::Real const	base_pair_z_offset_cutoff_

core::Real const	base_pair_axis_cutoff_

core::Real const	base_pair_planarity_cutoff_

core::Real const	base_pair_rho_min_

core::Real const	base_pair_rho_max_

bool	allow_base_pair_only_screen_

bool	floating_base_

bool	found_centroid_interaction_

bool	tether_jump_

utility::vector1< core::Size >	moving_residues_

utility::vector1< core::Size >	fixed_residues_

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

utility::vector1< core::Size >	terminal_res_

utility::vector1< core::Size >	block_stack_below_res_

utility::vector1< core::Size >	block_stack_above_res_

ObjexxFCL::FArray1D< bool >	is_terminal_res_

ObjexxFCL::FArray1D< bool >	is_fixed_res_

ObjexxFCL::FArray1D< bool >	is_moving_res_

ObjexxFCL::FArray1D< bool >	is_virtual_base_

ObjexxFCL::FArray2D< bool >	stacked_on_terminal_res_in_original_pose_

Constructor & Destructor Documentation

◆ RNA_BaseCentroidChecker()

protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::RNA_BaseCentroidChecker	(	core::pose::Pose const &	pose,
		working_parameters::StepWiseWorkingParametersCOP &	working_parameters,
		bool const	tether_jump = `false`
	)

References Initialize_base_stub_list(), Initialize_is_virtual_base(), and Initialize_terminal_res().

◆ ~RNA_BaseCentroidChecker()

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

overridedefault

Member Function Documentation

◆ allow_base_pair_only_screen()

bool const& protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::allow_base_pair_only_screen ( ) const

inline

References allow_base_pair_only_screen_.

◆ check_base_pair() [1/2]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_pair	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::kinematics::Stub const &	other_base_stub,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF
	)		const

private

References base_pair_dist_max_, base_pair_rho_max_, base_pair_z_offset_cutoff_, core::kinematics::Stub::M, protocols::mean_field::subtract(), and core::kinematics::Stub::v.

Referenced by check_base_pair(), check_centroid_interaction(), check_centroid_interaction_floating_base(), and is_medium_base_stack_and_medium_base_pair().

◆ check_base_pair() [2/2]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_pair	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF
	)		const

private

References base_stub_list_, check_base_pair(), and fixed_residues_.

◆ check_base_stack() [1/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::kinematics::Stub const &	moving_res_base,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF
	)		const

private

References base_stub_list_, check_base_stack(), and fixed_residues_.

◆ check_base_stack() [2/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::kinematics::Stub const &	other_base_stub,
		bool const	verbose = `false`
	)		const

private

References base_stack_axis_cutoff_, base_stack_planarity_cutoff_, and check_base_stack().

◆ check_base_stack() [3/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::kinematics::Stub const &	other_base_stub,
		core::chemical::rna::BaseStackWhichSide &	base_stack_side
	)

private

◆ check_base_stack() [4/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::kinematics::Stub const &	other_base_stub,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF,
		bool const	verbose = `false`
	)		const

private

References core::chemical::rna::ANY_BASE_STACK_SIDE, and check_base_stack().

◆ check_base_stack() [5/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::kinematics::Stub const &	moving_residue_base_stub,
		core::kinematics::Stub const &	other_base_stub,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF,
		core::chemical::rna::BaseStackWhichSide &	base_stack_side,
		bool const	verbose = `false`
	)		const

private

Referenced by check_base_stack(), check_base_stack_in_partition(), check_centroid_interaction(), check_that_terminal_res_are_unstacked(), Initialize_terminal_res(), is_medium_base_stack_and_medium_base_pair(), and is_strong_base_stack().

◆ check_base_stack() [6/6]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack	(	core::Size const &	pos1,
		core::Size const &	pos2,
		bool const	verbose = `false`
	)

private

References base_stub_list_, check_base_stack(), and is_virtual_base_.

◆ check_base_stack_in_partition()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack_in_partition	(	core::Size const &	block_stack_res,
		utility::vector1< core::Size > const &	other_res,
		core::chemical::rna::BaseStackWhichSide const &	block_stack_side
	)		const

private

References core::chemical::rna::ANY_BASE_STACK_SIDE, base_stub_list_, and check_base_stack().

Referenced by check_block_stack_res().

◆ check_block_stack_res()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_block_stack_res	(	utility::vector1< core::Size > const &	block_stack_res,
		core::chemical::rna::BaseStackWhichSide const &	block_stack_side
	)		const

private

References check_base_stack_in_partition(), fixed_residues_, is_moving_res_, and moving_residues_.

Referenced by check_that_terminal_res_are_unstacked().

◆ check_centroid_interaction() [1/2]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction	(	core::kinematics::Stub const &	moving_res_base_stub,
		StepWiseRNA_CountStruct &	count_data
	)

References base_stub_list_, check_centroid_interaction_floating_base(), floating_base_, found_centroid_interaction_, and moving_residues_.

Referenced by update_base_stub_list_and_check_centroid_interaction().

◆ check_centroid_interaction() [2/2]

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction ( StepWiseRNA_CountStruct & count_data )

private

References base_pair_axis_cutoff_, base_pair_planarity_cutoff_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_pairing_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_stack_count, base_stub_list_, check_base_pair(), check_base_stack(), fixed_residues_, moving_residues_, and protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::pass_base_centroid_screen.

◆ check_centroid_interaction_floating_base()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction_floating_base	(	core::kinematics::Stub const &	moving_res_base_stub,
		StepWiseRNA_CountStruct &	count_data
	)		const

private

References allow_base_pair_only_screen_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_pairing_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_stack_count, check_base_pair(), is_medium_base_stack_and_medium_base_pair(), is_strong_base_stack(), protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::pass_base_centroid_screen, and protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::strict_base_pairing_count.

Referenced by check_centroid_interaction().

◆ check_that_terminal_res_are_unstacked()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked ( bool const verbose = false )

References core::chemical::rna::ABOVE, core::chemical::rna::BELOW, block_stack_above_res_, block_stack_below_res_, check_base_stack(), check_block_stack_res(), fixed_residues_, is_fixed_res_, moving_residues_, stacked_on_terminal_res_in_original_pose_, terminal_res_, and protocols::TR().

Referenced by update_base_stub_list_and_check_that_terminal_res_are_unstacked().

◆ found_centroid_interaction()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::found_centroid_interaction ( ) const

inline

References found_centroid_interaction_.

◆ Initialize_base_stub_list()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list	(	core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, base_stub_list_, fixed_residues_, is_fixed_res_, is_moving_res_, core::conformation::Residue::is_NA(), is_virtual_base_, moving_residues_, core::pose::Pose::residue(), rna_centroid_info_, core::pose::Pose::size(), tether_jump_, and working_parameters_.

Referenced by RNA_BaseCentroidChecker(), and update_base_stub_list_and_check_that_terminal_res_are_unstacked().

◆ Initialize_is_virtual_base()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base	(	core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)

private

References core::chemical::BULGE, core::conformation::Residue::has_variant_type(), is_virtual_base_, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by RNA_BaseCentroidChecker().

◆ Initialize_terminal_res()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_terminal_res ( core::pose::Pose const & pose )

private

References core::pose::Pose::annotated_sequence(), block_stack_above_res_, block_stack_below_res_, check_base_stack(), core::pose::Pose::fold_tree(), is_fixed_res_, is_moving_res_, is_terminal_res_, is_virtual_base_, core::pose::Pose::size(), stacked_on_terminal_res_in_original_pose_, terminal_res_, protocols::TR(), and working_parameters_.

Referenced by RNA_BaseCentroidChecker().

◆ is_medium_base_stack_and_medium_base_pair()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_medium_base_stack_and_medium_base_pair ( core::kinematics::Stub const & moving_res_base ) const

private

References check_base_pair(), and check_base_stack().

Referenced by check_centroid_interaction_floating_base().

◆ is_strong_base_stack()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_strong_base_stack ( core::kinematics::Stub const & moving_res_base ) const

private

References check_base_stack().

Referenced by check_centroid_interaction_floating_base().

◆ set_allow_base_pair_only_screen()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_allow_base_pair_only_screen ( bool const setting )

inline

References allow_base_pair_only_screen_.

◆ set_floating_base()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_floating_base ( bool const setting )

inline

References floating_base_.

◆ update_base_stub_list()

void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list ( core::pose::Pose const & pose )

private

References base_stub_list_, core::chemical::ResidueType::is_NA(), moving_residues_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and rna_centroid_info_.

Referenced by update_base_stub_list_and_check_centroid_interaction(), and update_base_stub_list_and_check_that_terminal_res_are_unstacked().

◆ update_base_stub_list_and_check_centroid_interaction()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list_and_check_centroid_interaction	(	core::pose::Pose const &	pose,
		StepWiseRNA_CountStruct &	count_data
	)

References check_centroid_interaction(), and update_base_stub_list().

◆ update_base_stub_list_and_check_that_terminal_res_are_unstacked()

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list_and_check_that_terminal_res_are_unstacked	(	core::pose::Pose const &	pose,
		bool const	reinitialize = `false`
	)

References check_that_terminal_res_are_unstacked(), Initialize_base_stub_list(), and update_base_stub_list().

Member Data Documentation

◆ allow_base_pair_only_screen_

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::allow_base_pair_only_screen_

private

Referenced by allow_base_pair_only_screen(), check_centroid_interaction_floating_base(), and set_allow_base_pair_only_screen().

◆ base_pair_axis_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_axis_cutoff_

private

Referenced by check_centroid_interaction().

◆ base_pair_dist_max_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_dist_max_

private

Referenced by check_base_pair().

◆ base_pair_dist_min_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_dist_min_

private

◆ base_pair_planarity_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_planarity_cutoff_

private

Referenced by check_centroid_interaction().

◆ base_pair_rho_max_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_rho_max_

private

Referenced by check_base_pair().

◆ base_pair_rho_min_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_rho_min_

private

◆ base_pair_z_offset_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_z_offset_cutoff_

private

Referenced by check_base_pair().

◆ base_stack_axis_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_axis_cutoff_

private

Referenced by check_base_stack().

◆ base_stack_dist_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_dist_cutoff_

private

◆ base_stack_planarity_cutoff_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_planarity_cutoff_

private

Referenced by check_base_stack().

◆ base_stack_z_offset_max_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_z_offset_max_

private

◆ base_stack_z_offset_min_

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_z_offset_min_

private

◆ base_stub_list_

utility::vector1< core::kinematics::Stub > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stub_list_

private

Referenced by check_base_pair(), check_base_stack(), check_base_stack_in_partition(), check_centroid_interaction(), Initialize_base_stub_list(), and update_base_stub_list().

◆ block_stack_above_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::block_stack_above_res_

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

◆ block_stack_below_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::block_stack_below_res_

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

◆ fixed_residues_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::fixed_residues_

private

Referenced by check_base_pair(), check_base_stack(), check_block_stack_res(), check_centroid_interaction(), check_that_terminal_res_are_unstacked(), and Initialize_base_stub_list().

◆ floating_base_

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::floating_base_

private

Referenced by check_centroid_interaction(), and set_floating_base().

◆ found_centroid_interaction_

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::found_centroid_interaction_

private

Referenced by check_centroid_interaction(), and found_centroid_interaction().

◆ is_fixed_res_

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_fixed_res_

private

Referenced by check_that_terminal_res_are_unstacked(), Initialize_base_stub_list(), and Initialize_terminal_res().

◆ is_moving_res_

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_moving_res_

private

Referenced by check_block_stack_res(), Initialize_base_stub_list(), and Initialize_terminal_res().

◆ is_terminal_res_

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_terminal_res_

private

Referenced by Initialize_terminal_res().

◆ is_virtual_base_

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_virtual_base_

private

Referenced by check_base_stack(), Initialize_base_stub_list(), Initialize_is_virtual_base(), and Initialize_terminal_res().

◆ moving_residues_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::moving_residues_

private

Referenced by check_block_stack_res(), check_centroid_interaction(), check_that_terminal_res_are_unstacked(), Initialize_base_stub_list(), and update_base_stub_list().

◆ rna_centroid_info_

core::scoring::rna::RNA_CentroidInfoOP protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::rna_centroid_info_

private

Referenced by Initialize_base_stub_list(), and update_base_stub_list().

◆ stacked_on_terminal_res_in_original_pose_

ObjexxFCL::FArray2D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::stacked_on_terminal_res_in_original_pose_

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

◆ terminal_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::terminal_res_

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

◆ tether_jump_

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::tether_jump_

private

Referenced by Initialize_base_stub_list().

◆ working_parameters_

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::working_parameters_

private

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

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

src/protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.hh
src/protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ RNA_BaseCentroidChecker()

◆ ~RNA_BaseCentroidChecker()

Member Function Documentation

◆ allow_base_pair_only_screen()

◆ check_base_pair() [1/2]

◆ check_base_pair() [2/2]

◆ check_base_stack() [1/6]

◆ check_base_stack() [2/6]

◆ check_base_stack() [3/6]

◆ check_base_stack() [4/6]

◆ check_base_stack() [5/6]

◆ check_base_stack() [6/6]

◆ check_base_stack_in_partition()

◆ check_block_stack_res()

◆ check_centroid_interaction() [1/2]

◆ check_centroid_interaction() [2/2]

◆ check_centroid_interaction_floating_base()

◆ check_that_terminal_res_are_unstacked()

◆ found_centroid_interaction()

◆ Initialize_base_stub_list()

◆ Initialize_is_virtual_base()

◆ Initialize_terminal_res()

◆ is_medium_base_stack_and_medium_base_pair()

◆ is_strong_base_stack()

◆ set_allow_base_pair_only_screen()

◆ set_floating_base()

◆ update_base_stub_list()

◆ update_base_stub_list_and_check_centroid_interaction()

◆ update_base_stub_list_and_check_that_terminal_res_are_unstacked()

Member Data Documentation

◆ allow_base_pair_only_screen_

◆ base_pair_axis_cutoff_

◆ base_pair_dist_max_

◆ base_pair_dist_min_

◆ base_pair_planarity_cutoff_

◆ base_pair_rho_max_

◆ base_pair_rho_min_

◆ base_pair_z_offset_cutoff_

◆ base_stack_axis_cutoff_

◆ base_stack_dist_cutoff_

◆ base_stack_planarity_cutoff_

◆ base_stack_z_offset_max_

◆ base_stack_z_offset_min_

◆ base_stub_list_

◆ block_stack_above_res_

◆ block_stack_below_res_

◆ fixed_residues_

◆ floating_base_

◆ found_centroid_interaction_

◆ is_fixed_res_

◆ is_moving_res_

◆ is_terminal_res_

◆ is_virtual_base_

◆ moving_residues_

◆ rna_centroid_info_

◆ stacked_on_terminal_res_in_original_pose_

◆ terminal_res_

◆ tether_jump_

◆ working_parameters_