#include <StepWiseRNA_BaseCentroidScreener.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_BaseCentroidScreener:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_BaseCentroidScreener:

Public Member Functions
	StepWiseRNA_BaseCentroidScreener (core::pose::Pose const &pose, StepWiseRNA_JobParametersCOP &job_parameters)

virtual	~StepWiseRNA_BaseCentroidScreener ()

bool	Update_base_stub_list_and_Check_centroid_interaction (core::pose::Pose const &pose, SillyCountStruct &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)

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_stack_base (core::kinematics::Stub const &rebuild_residue_base_stub, core::kinematics::Stub const &base_stub, bool const verbose=false) const

bool	check_stack_base (Size const &pos1, Size const &pos2, bool const verbose=false)

bool	check_base_pairing (core::kinematics::Stub const &rebuild_residue_base_stub, core::kinematics::Stub const &base_stub) const

bool	Check_centroid_interaction (SillyCountStruct &count_data) const

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

Private Attributes
StepWiseRNA_JobParametersCOP	job_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_

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_

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_

Detailed Description

Definition at line 40 of file StepWiseRNA_BaseCentroidScreener.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::StepWiseRNA_BaseCentroidScreener	(	core::pose::Pose const &	pose,
		StepWiseRNA_JobParametersCOP &	job_parameters
	)

Definition at line 48 of file StepWiseRNA_BaseCentroidScreener.cc.

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

protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::~StepWiseRNA_BaseCentroidScreener ( )

virtual

Definition at line 69 of file StepWiseRNA_BaseCentroidScreener.cc.

Member Function Documentation

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_base_pairing	(	core::kinematics::Stub const &	rebuild_residue_base_stub,
		core::kinematics::Stub const &	base_stub
	)		const

private

Definition at line 256 of file StepWiseRNA_BaseCentroidScreener.cc.

References base_pair_axis_cutoff_, base_pair_dist_max_, base_pair_planarity_cutoff_, base_pair_rho_max_, base_pair_z_offset_cutoff_, core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by Check_centroid_interaction().

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Check_centroid_interaction ( SillyCountStruct & count_data) const

private

Definition at line 323 of file StepWiseRNA_BaseCentroidScreener.cc.

References protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, base_stub_list_, check_base_pairing(), check_stack_base(), fixed_residues_, moving_residues_, and protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen.

Referenced by Update_base_stub_list_and_Check_centroid_interaction().

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_stack_base	(	core::kinematics::Stub const &	rebuild_residue_base_stub,
		core::kinematics::Stub const &	base_stub,
		bool const	verbose = `false`
	)		const

private

Definition at line 217 of file StepWiseRNA_BaseCentroidScreener.cc.

References base_stack_axis_cutoff_, base_stack_dist_cutoff_, base_stack_planarity_cutoff_, base_stack_z_offset_max_, base_stack_z_offset_min_, core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by Check_centroid_interaction(), check_stack_base(), Check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_stack_base	(	Size const &	pos1,
		Size const &	pos2,
		bool const	verbose = `false`
	)

private

Definition at line 378 of file StepWiseRNA_BaseCentroidScreener.cc.

References base_stub_list_, check_stack_base(), and is_virtual_base_.

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Check_that_terminal_res_are_unstacked ( bool const verbose = false)

Definition at line 391 of file StepWiseRNA_BaseCentroidScreener.cc.

References check_stack_base(), fixed_residues_, moving_residues_, stacked_on_terminal_res_in_original_pose_, and terminal_res_.

Referenced by Update_base_stub_list_and_Check_that_terminal_res_are_unstacked().

void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_base_stub_list	(	core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)

private

Definition at line 96 of file StepWiseRNA_BaseCentroidScreener.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, base_stub_list_, fixed_residues_, is_fixed_res_, is_moving_res_, is_virtual_base_, job_parameters_, moving_residues_, protocols::swa::rna::Output_seq_num_list(), core::pose::Pose::residue(), rna_centroid_info_, and core::pose::Pose::total_residue().

Referenced by StepWiseRNA_BaseCentroidScreener(), and Update_base_stub_list_and_Check_that_terminal_res_are_unstacked().

void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_is_virtual_base	(	core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)

private

Definition at line 73 of file StepWiseRNA_BaseCentroidScreener.cc.

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

Referenced by StepWiseRNA_BaseCentroidScreener().

void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_terminal_res ( core::pose::Pose const & pose)

private

Definition at line 174 of file StepWiseRNA_BaseCentroidScreener.cc.

References check_stack_base(), is_fixed_res_, is_moving_res_, is_terminal_res_, is_virtual_base_, job_parameters_, stacked_on_terminal_res_in_original_pose_, terminal_res_, and core::pose::Pose::total_residue().

Referenced by StepWiseRNA_BaseCentroidScreener().

void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Update_base_stub_list ( core::pose::Pose const & pose)

private

Definition at line 304 of file StepWiseRNA_BaseCentroidScreener.cc.

References base_stub_list_, moving_residues_, core::pose::Pose::residue(), 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().

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Update_base_stub_list_and_Check_centroid_interaction	(	core::pose::Pose const &	pose,
		SillyCountStruct &	count_data
	)

Definition at line 296 of file StepWiseRNA_BaseCentroidScreener.cc.

References Check_centroid_interaction(), and Update_base_stub_list().

bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Update_base_stub_list_and_Check_that_terminal_res_are_unstacked	(	core::pose::Pose const &	pose,
		bool const	reinitialize = `false`
	)

Definition at line 365 of file StepWiseRNA_BaseCentroidScreener.cc.

References Check_that_terminal_res_are_unstacked(), Initialize_base_stub_list(), and Update_base_stub_list().

Member Data Documentation

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_axis_cutoff_

private

Definition at line 102 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_base_pairing().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_dist_max_

private

Definition at line 100 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_base_pairing().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_dist_min_

private

Definition at line 99 of file StepWiseRNA_BaseCentroidScreener.hh.

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_planarity_cutoff_

private

Definition at line 103 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_base_pairing().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_rho_max_

private

Definition at line 105 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_base_pairing().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_rho_min_

private

Definition at line 104 of file StepWiseRNA_BaseCentroidScreener.hh.

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_pair_z_offset_cutoff_

private

Definition at line 101 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_base_pairing().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stack_axis_cutoff_

private

Definition at line 97 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_stack_base().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stack_dist_cutoff_

private

Definition at line 94 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_stack_base().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stack_planarity_cutoff_

private

Definition at line 98 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_stack_base().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stack_z_offset_max_

private

Definition at line 95 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_stack_base().

core::Real const protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stack_z_offset_min_

private

Definition at line 96 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by check_stack_base().

utility::vector1< core::kinematics::Stub > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stub_list_

private

Definition at line 109 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Check_centroid_interaction(), check_stack_base(), Initialize_base_stub_list(), and Update_base_stub_list().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::fixed_residues_

private

Definition at line 108 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Check_centroid_interaction(), Check_that_terminal_res_are_unstacked(), and Initialize_base_stub_list().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_fixed_res_

private

Definition at line 113 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_moving_res_

private

Definition at line 114 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_terminal_res_

private

Definition at line 112 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_virtual_base_

private

Definition at line 115 of file StepWiseRNA_BaseCentroidScreener.hh.

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

StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::job_parameters_

private

Definition at line 91 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::moving_residues_

private

Definition at line 107 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Check_centroid_interaction(), Check_that_terminal_res_are_unstacked(), Initialize_base_stub_list(), and Update_base_stub_list().

core::scoring::rna::RNA_CentroidInfoOP protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::rna_centroid_info_

private

Definition at line 92 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Initialize_base_stub_list(), and Update_base_stub_list().

ObjexxFCL::FArray2D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::stacked_on_terminal_res_in_original_pose_

private

Definition at line 116 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::terminal_res_

private

Definition at line 111 of file StepWiseRNA_BaseCentroidScreener.hh.

Referenced by Check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

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

src/protocols/swa/rna/StepWiseRNA_BaseCentroidScreener.hh
src/protocols/swa/rna/StepWiseRNA_BaseCentroidScreener.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation