protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker Class Reference

#include <RNA_BaseCentroidChecker.hh>

Public Member Functions
	RNA_BaseCentroidChecker (core::pose::Pose const &pose, StepWiseRNA_JobParametersCOP &job_parameters, bool const tether_jump=false)
virtual	~RNA_BaseCentroidChecker ()
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, bool const verbose=false) const
bool	check_base_stack (Size const &pos1, 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

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_
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_
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

protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::RNA_BaseCentroidChecker	(	core::pose::Pose const &	pose,
		StepWiseRNA_JobParametersCOP &	job_parameters,
		bool const	tether_jump = false
	)

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

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

virtual

Member Function Documentation

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

inline

References allow_base_pair_only_screen_.

Referenced by protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::get_num_pose_kept(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

bool protocols::stepwise::sampling::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_, numeric::xyzMatrix< class >::col_z(), dot(), numeric::xyzVector< class >::length(), core::kinematics::Stub::M, 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().

bool protocols::stepwise::sampling::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_.

bool protocols::stepwise::sampling::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 base_stack_dist_cutoff_, base_stack_z_offset_max_, base_stack_z_offset_min_, numeric::xyzMatrix< class >::col_z(), dot(), numeric::xyzVector< class >::length(), core::kinematics::Stub::M, subtract(), protocols::TR, and core::kinematics::Stub::v.

Referenced by check_base_stack(), 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().

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

private

References base_stub_list_, check_base_stack(), is_virtual_base_, and utility_exit_with_message.

bool protocols::stepwise::sampling::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_.

bool protocols::stepwise::sampling::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().

bool protocols::stepwise::sampling::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_, moving_residues_, and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::BaseCentroidScreener::check_screen(), and update_base_stub_list_and_check_centroid_interaction().

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

private

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

bool protocols::stepwise::sampling::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::sampling::rna::StepWiseRNA_CountStruct::base_pairing_count, protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::base_stack_count, check_base_pair(), is_medium_base_stack_and_medium_base_pair(), is_strong_base_stack(), protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::pass_base_centroid_screen, and protocols::stepwise::sampling::rna::StepWiseRNA_CountStruct::strict_base_pairing_count.

Referenced by check_centroid_interaction().

bool protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked

(

bool const

verbose = false

)

References check_base_stack(), fixed_res, fixed_residues_, moving_residues_, stacked_on_terminal_res_in_original_pose_, terminal_res, terminal_res_, and protocols::TR.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::BaseCentroidScreener::check_screen(), and update_base_stub_list_and_check_that_terminal_res_are_unstacked().

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

inline

References found_centroid_interaction_.

Referenced by protocols::stepwise::screener::BulgeApplier::bulge_variant_decision().

void protocols::stepwise::sampling::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_, centroid, fixed_residues_, is_fixed_res_, is_moving_res_, is_virtual_base_, job_parameters_, moving_residues_, nres, core::pose::Pose::residue(), rna_centroid_info_, runtime_assert, tether_jump_, and core::pose::Pose::total_residue().

Referenced by RNA_BaseCentroidChecker(), and update_base_stub_list_and_check_that_terminal_res_are_unstacked().

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

private

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

Referenced by RNA_BaseCentroidChecker().

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

private

References check_base_stack(), is_fixed_res_, is_moving_res_, is_terminal_res_, is_virtual_base_, job_parameters_, nres, stacked_on_terminal_res_in_original_pose_, terminal_res, terminal_res_, core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by RNA_BaseCentroidChecker().

bool protocols::stepwise::sampling::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().

bool protocols::stepwise::sampling::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().

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

inline

References allow_base_pair_only_screen_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

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

inline

References floating_base_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

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

private

References base_stub_list_, centroid, 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::stepwise::sampling::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().

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), and protocols::stepwise::screener::BaseCentroidScreener::check_screen().

bool protocols::stepwise::sampling::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().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

Member Data Documentation

bool protocols::stepwise::sampling::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().

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

private

Referenced by check_centroid_interaction().

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

private

Referenced by check_base_pair().

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

private

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

private

Referenced by check_centroid_interaction().

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

private

Referenced by check_base_pair().

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

private

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

private

Referenced by check_base_pair().

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

private

Referenced by check_base_stack().

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

private

Referenced by check_base_stack().

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

private

Referenced by check_base_stack().

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

private

Referenced by check_base_stack().

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

private

Referenced by check_base_stack().

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

private

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

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

private

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

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

private

Referenced by check_centroid_interaction(), and set_floating_base().

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

private

Referenced by check_centroid_interaction(), and found_centroid_interaction().

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

private

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

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

private

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

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

private

Referenced by Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::stepwise::sampling::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().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::job_parameters_

private

Referenced by Initialize_base_stub_list(), and Initialize_terminal_res().

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

private

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::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::rna_centroid_info_

private

Referenced by Initialize_base_stub_list(), and update_base_stub_list().

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

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

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

private

Referenced by check_that_terminal_res_are_unstacked(), and Initialize_terminal_res().

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

private

Referenced by Initialize_base_stub_list().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/checker/RNA_BaseCentroidChecker.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/checker/RNA_BaseCentroidChecker.cc