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

#include <RNA_BaseCentroidChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker:
Inheritance graph
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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::Sizemoving_residues_
 
utility::vector1< core::Sizefixed_residues_
 
utility::vector1
< core::kinematics::Stub
base_stub_list_
 
utility::vector1< core::Sizeterminal_res_
 
utility::vector1< core::Sizeblock_stack_below_res_
 
utility::vector1< core::Sizeblock_stack_above_res_
 
ObjexxFCL::FArray1D< boolis_terminal_res_
 
ObjexxFCL::FArray1D< boolis_fixed_res_
 
ObjexxFCL::FArray1D< boolis_moving_res_
 
ObjexxFCL::FArray1D< boolis_virtual_base_
 
ObjexxFCL::FArray2D< boolstacked_on_terminal_res_in_original_pose_
 

Constructor & Destructor Documentation

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

Member Function Documentation

bool const& protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::allow_base_pair_only_screen ( ) const
inline
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
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
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
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
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
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_stack ( core::Size const &  pos1,
core::Size const &  pos2,
bool const  verbose = false 
)
private
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
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
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
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
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction ( core::kinematics::Stub const &  moving_res_base_stub,
StepWiseRNA_CountStruct count_data 
)
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction ( StepWiseRNA_CountStruct count_data)
private
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
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked ( bool const  verbose = false)
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::found_centroid_interaction ( ) const
inline
void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list ( core::pose::Pose const &  pose,
bool const  verbose = false 
)
private
void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base ( core::pose::Pose const &  pose,
bool const  verbose = false 
)
private
void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_terminal_res ( core::pose::Pose const &  pose)
private
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
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_strong_base_stack ( core::kinematics::Stub const &  moving_res_base) const
private
void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_allow_base_pair_only_screen ( bool const  setting)
inline
void protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_floating_base ( bool const  setting)
inline

References floating_base_.

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

Member Data Documentation

bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::allow_base_pair_only_screen_
private
core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_axis_cutoff_
private
core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_dist_max_
private

Referenced by check_base_pair().

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_dist_min_
private
core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_planarity_cutoff_
private
core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_pair_rho_max_
private

Referenced by check_base_pair().

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

Referenced by check_base_pair().

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

Referenced by check_base_stack().

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

Referenced by check_base_stack().

core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_z_offset_max_
private
core::Real const protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stack_z_offset_min_
private
utility::vector1< core::kinematics::Stub > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::base_stub_list_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::block_stack_above_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::block_stack_below_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::fixed_residues_
private
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::floating_base_
private
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::found_centroid_interaction_
private
ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_fixed_res_
private
ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_moving_res_
private
ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_terminal_res_
private

Referenced by Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::is_virtual_base_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::moving_residues_
private
core::scoring::rna::RNA_CentroidInfoOP protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::rna_centroid_info_
private
ObjexxFCL::FArray2D< bool > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::stacked_on_terminal_res_in_original_pose_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::terminal_res_
private
bool protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::tether_jump_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::working_parameters_
private

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