Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::swa::rna::StepWiseRNA_BaseCentroidScreener Class Reference

#include <StepWiseRNA_BaseCentroidScreener.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_BaseCentroidScreener:
Inheritance graph
[legend]
Collaboration diagram for protocols::swa::rna::StepWiseRNA_BaseCentroidScreener:
Collaboration graph
[legend]

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::Sizemoving_residues_
 
utility::vector1< core::Sizefixed_residues_
 
utility::vector1
< core::kinematics::Stub
base_stub_list_
 
utility::vector1< core::Sizeterminal_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::swa::rna::StepWiseRNA_BaseCentroidScreener::StepWiseRNA_BaseCentroidScreener ( core::pose::Pose const &  pose,
StepWiseRNA_JobParametersCOP job_parameters 
)
protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::~StepWiseRNA_BaseCentroidScreener ( )
virtual

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
bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Check_centroid_interaction ( SillyCountStruct count_data) const
private
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
bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_stack_base ( Size const &  pos1,
Size const &  pos2,
bool const  verbose = false 
)
private
bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Check_that_terminal_res_are_unstacked ( bool const  verbose = false)
void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_base_stub_list ( core::pose::Pose const &  pose,
bool const  verbose = false 
)
private
void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_is_virtual_base ( core::pose::Pose const &  pose,
bool const  verbose = false 
)
private
void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_terminal_res ( core::pose::Pose const &  pose)
private
void protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Update_base_stub_list ( core::pose::Pose const &  pose)
private
bool protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Update_base_stub_list_and_Check_centroid_interaction ( core::pose::Pose const &  pose,
SillyCountStruct count_data 
)
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 
)

Member Data Documentation

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

Referenced by check_base_pairing().

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

Referenced by check_base_pairing().

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

Referenced by check_base_pairing().

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

Referenced by check_base_pairing().

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

Referenced by check_base_pairing().

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

Referenced by check_stack_base().

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

Referenced by check_stack_base().

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

Referenced by check_stack_base().

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

Referenced by check_stack_base().

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

Referenced by check_stack_base().

utility::vector1< core::kinematics::Stub > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::base_stub_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::fixed_residues_
private
ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_fixed_res_
private
ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_moving_res_
private
ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_terminal_res_
private

Referenced by Initialize_terminal_res().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::is_virtual_base_
private
StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::job_parameters_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::moving_residues_
private
core::scoring::rna::RNA_CentroidInfoOP protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::rna_centroid_info_
private
ObjexxFCL::FArray2D< bool > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::stacked_on_terminal_res_in_original_pose_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::terminal_res_
private

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