Rosetta Protocols  2014.16.56682
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker Class Reference

#include <ChainClosableGeometryChecker.hh>

Public Member Functions

 ChainClosableGeometryChecker (Size const five_prime_chain_break_res, Size const gap_size)
 
 ChainClosableGeometryChecker (Size const five_prime_chain_break_res, Size const three_prime_chain_break_res, Size const gap_size)
 
 ~ChainClosableGeometryChecker ()
 
bool check_screen (pose::Pose const &pose, bool const strict=false) const
 
bool check_screen (pose::Pose const &moving_pose, pose::Pose const &reference_pose, bool const is_prepend, bool const strict=false) const
 
bool check_screen (pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, 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, 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
 
Size const & five_prime_chain_break_res () const
 
Size const & three_prime_chain_break_res () const
 
Real const & dist_squared () const
 
Real const & max_dist_squared () const
 

Private Member Functions

bool check_chain_closable_geometry (pose::Pose const &five_prime_pose, pose::Pose const &three_prime_pose) const
 
bool check_chain_closable_geometry (pose::Pose const &five_prime_pose, 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 (pose::Pose const &five_prime_pose, pose::Pose const &three_prime_pose) const
 
void get_C4_C3_distance_range (conformation::Residue const &five_prime_rsd, conformation::Residue const &three_prime_rsd, Distance &C4_C3_dist_min, Distance &C4_C3_dist_max) const
 
void initialize_distance_range ()
 

Private Attributes

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

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::ChainClosableGeometryChecker ( Size const  five_prime_chain_break_res,
Size const  gap_size 
)

References initialize_distance_range().

protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::ChainClosableGeometryChecker ( Size const  five_prime_chain_break_res,
Size const  three_prime_chain_break_res,
Size const  gap_size 
)

References initialize_distance_range().

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

Member Function Documentation

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

References dist_squared_, numeric::xyzVector< class >::length_squared(), max_dist_squared_, and min_dist_squared_.

Referenced by check_chain_closable_geometry(), protocols::stepwise::screener::ChainClosableGeometryResidueBasedScreener::check_screen(), and check_screen().

bool protocols::stepwise::sampling::rna::checker::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(), and core::conformation::Residue::xyz().

bool protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::check_chain_closable_geometry ( pose::Pose const &  five_prime_pose,
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::sampling::rna::checker::ChainClosableGeometryChecker::check_chain_closable_geometry ( pose::Pose const &  five_prime_pose,
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::sampling::rna::checker::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::sampling::rna::checker::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::rotamer_sampler::rigid_body::get_specific_atom_coordinate(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

bool protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::check_chain_closable_geometry_strict ( pose::Pose const &  five_prime_pose,
pose::Pose const &  three_prime_pose 
) const
private

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

Referenced by check_chain_closable_geometry().

bool protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::check_screen ( pose::Pose const &  pose,
bool const  strict = false 
) const

Referenced by protocols::stepwise::screener::ChainClosableGeometryScreener::check_screen(), protocols::stepwise::screener::ChainClosableGeometryStubBasedScreener::check_screen(), check_screen(), protocols::stepwise::screener::AnchorSugarScreener::check_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

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

References check_chain_closable_geometry().

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

References check_chain_closable_geometry(), five_prime_chain_break_res_, and runtime_assert.

bool protocols::stepwise::sampling::rna::checker::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,
Size const &  reference_res 
) const

References check_screen().

Real const& protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::dist_squared ( ) const
inline
Size const& protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::five_prime_chain_break_res ( ) const
inline
void protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::get_C4_C3_distance_range ( conformation::Residue const &  five_prime_rsd,
conformation::Residue const &  three_prime_rsd,
Distance &  C4_C3_dist_min,
Distance &  C4_C3_dist_max 
) const
private

References dot(), dot_product(), numeric::xyzVector< class >::normalize(), protocols::TR, utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by check_chain_closable_geometry_strict().

void protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::initialize_distance_range ( )
private

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

Referenced by ChainClosableGeometryChecker().

Real const& protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::max_dist_squared ( ) const
inline
Size const& protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::three_prime_chain_break_res ( ) const
inline

Member Data Documentation

Real protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::dist_squared_
mutableprivate

Referenced by check_chain_closable_geometry(), and initialize_distance_range().

Size const protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::five_prime_chain_break_res_
private

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

Size const protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::gap_size_
private

Referenced by check_chain_closable_geometry_strict(), and initialize_distance_range().

Real protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::max_dist_squared_
private

Referenced by check_chain_closable_geometry(), and initialize_distance_range().

Real protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::min_dist_squared_
private

Referenced by check_chain_closable_geometry(), and initialize_distance_range().

Size const protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::three_prime_chain_break_res_
private

Referenced by check_chain_closable_geometry(), and check_chain_closable_geometry_strict().

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