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

#include <RNA_ChainClosableGeometryChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker:
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Public Member Functions

 RNA_ChainClosableGeometryChecker (core::Size const five_prime_chain_break_res, core::Size const gap_size)
 
 RNA_ChainClosableGeometryChecker (core::Size const five_prime_chain_break_res, core::Size const three_prime_chain_break_res, core::Size const gap_size)
 
 ~RNA_ChainClosableGeometryChecker () override
 
bool check_screen (core::pose::Pose const &pose, bool const strict=false) const
 
bool check_screen (core::pose::Pose const &moving_pose, core::pose::Pose const &reference_pose, bool const is_prepend, bool const strict=false) const
 
bool check_screen (core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, core::Size const &reference_res) const
 
bool check_screen (utility::vector1< core::pose::PoseOP > const &pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, core::Size const &reference_res) const
 
bool check_chain_closable_geometry (numeric::xyzVector< core::Real > const &xyz_1, numeric::xyzVector< core::Real > const &xyz_2) const
 
bool check_chain_closable_geometry (core::conformation::Residue const &five_prime_residue, core::conformation::Residue const &three_prime_residue) const
 
core::Size const & five_prime_chain_break_res () const
 
core::Size const & three_prime_chain_break_res () const
 
core::Real const & dist_squared () const
 
core::Real const & max_dist_squared () const
 

Private Member Functions

bool check_chain_closable_geometry (core::pose::Pose const &five_prime_pose, core::pose::Pose const &three_prime_pose) const
 
bool check_chain_closable_geometry (core::pose::Pose const &five_prime_pose, core::pose::Pose const &three_prime_pose, bool const strict) const
 
bool check_chain_closable_geometry (core::Size const &reference_res, utility::vector1< core::pose::PoseOP > const &pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const is_prepend) const
 
bool check_chain_closable_geometry (core::Size const &reference_res, core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const is_prepend) const
 
bool check_chain_closable_geometry_strict (core::pose::Pose const &five_prime_pose, core::pose::Pose const &three_prime_pose) const
 
void get_C4_C3_distance_range (core::conformation::Residue const &five_prime_rsd, core::conformation::Residue const &three_prime_rsd, core::Distance &C4_C3_dist_min, core::Distance &C4_C3_dist_max) const
 
void initialize_distance_range ()
 

Private Attributes

core::Size const five_prime_chain_break_res_
 
core::Size const three_prime_chain_break_res_
 
core::Size const gap_size_
 
core::Real min_dist_squared_
 
core::Real max_dist_squared_
 
core::Real dist_squared_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::RNA_ChainClosableGeometryChecker ( core::Size const  five_prime_chain_break_res,
core::Size const  gap_size 
)

References initialize_distance_range().

protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::RNA_ChainClosableGeometryChecker ( core::Size const  five_prime_chain_break_res,
core::Size const  three_prime_chain_break_res,
core::Size const  gap_size 
)

References initialize_distance_range().

protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::~RNA_ChainClosableGeometryChecker ( )
overridedefault

Member Function Documentation

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( numeric::xyzVector< core::Real > const &  xyz_1,
numeric::xyzVector< core::Real > const &  xyz_2 
) const

References dist_squared_, max_dist_squared_, and min_dist_squared_.

Referenced by check_chain_closable_geometry(), and check_screen().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( core::conformation::Residue const &  five_prime_residue,
core::conformation::Residue const &  three_prime_residue 
) const

References check_chain_closable_geometry(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_TNA(), and core::conformation::Residue::xyz().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( core::pose::Pose const &  five_prime_pose,
core::pose::Pose const &  three_prime_pose 
) const
private

References check_chain_closable_geometry(), five_prime_chain_break_res_, core::pose::Pose::residue(), and three_prime_chain_break_res_.

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( core::pose::Pose const &  five_prime_pose,
core::pose::Pose const &  three_prime_pose,
bool const  strict 
) const
private

References check_chain_closable_geometry(), and check_chain_closable_geometry_strict().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( core::Size const &  reference_res,
utility::vector1< core::pose::PoseOP > const &  pose_data_list,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
bool const  is_prepend 
) const
private

References check_chain_closable_geometry().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry ( core::Size const &  reference_res,
core::pose::Pose const &  pose,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
bool const  is_prepend 
) const
private

References check_chain_closable_geometry(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry_strict ( core::pose::Pose const &  five_prime_pose,
core::pose::Pose const &  three_prime_pose 
) const
private

References five_prime_chain_break_res_, gap_size_, get_C4_C3_distance_range(), core::conformation::Residue::is_TNA(), core::pose::Pose::residue(), three_prime_chain_break_res_, and core::conformation::Residue::xyz().

Referenced by check_chain_closable_geometry().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen ( core::pose::Pose const &  pose,
bool const  strict = false 
) const

Referenced by check_screen(), and protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen ( core::pose::Pose const &  moving_pose,
core::pose::Pose const &  reference_pose,
bool const  is_prepend,
bool const  strict = false 
) const

References check_chain_closable_geometry().

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen ( core::pose::Pose const &  pose,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
core::Size const &  reference_res 
) const

References check_chain_closable_geometry(), and five_prime_chain_break_res_.

bool protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen ( utility::vector1< core::pose::PoseOP > const &  pose_data_list,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
core::Size const &  reference_res 
) const

References check_screen().

core::Real const& protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::dist_squared ( ) const
inline

References dist_squared_.

core::Size const& protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::five_prime_chain_break_res ( ) const
inline

References five_prime_chain_break_res_.

void protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range ( core::conformation::Residue const &  five_prime_rsd,
core::conformation::Residue const &  three_prime_rsd,
core::Distance &  C4_C3_dist_min,
core::Distance &  C4_C3_dist_max 
) const
private

References core::conformation::Residue::is_TNA(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by check_chain_closable_geometry_strict().

void protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::initialize_distance_range ( )
private

References dist_squared_, gap_size_, protocols::stepwise::modeler::rna::get_possible_O3prime_C5prime_distance_range(), max_dist_squared_, and min_dist_squared_.

Referenced by RNA_ChainClosableGeometryChecker().

core::Real const& protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::max_dist_squared ( ) const
inline

References max_dist_squared_.

core::Size const& protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::three_prime_chain_break_res ( ) const
inline

References three_prime_chain_break_res_.

Member Data Documentation

core::Real protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::dist_squared_
mutableprivate

Referenced by check_chain_closable_geometry(), dist_squared(), and initialize_distance_range().

core::Size const protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::five_prime_chain_break_res_
private

Referenced by check_chain_closable_geometry(), check_chain_closable_geometry_strict(), check_screen(), and five_prime_chain_break_res().

core::Size const protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::gap_size_
private

Referenced by check_chain_closable_geometry_strict(), and initialize_distance_range().

core::Real protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::max_dist_squared_
private

Referenced by check_chain_closable_geometry(), initialize_distance_range(), and max_dist_squared().

core::Real protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::min_dist_squared_
private

Referenced by check_chain_closable_geometry(), and initialize_distance_range().

core::Size const protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::three_prime_chain_break_res_
private

Referenced by check_chain_closable_geometry(), check_chain_closable_geometry_strict(), and three_prime_chain_break_res().

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