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protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener Class Reference

#include <StepWiseRNA_VDW_Bin_Screener.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener:
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Collaboration diagram for protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener:
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Public Member Functions

 StepWiseRNA_VDW_Bin_Screener ()
 
virtual ~StepWiseRNA_VDW_Bin_Screener ()
 
void FARFAR_setup_using_user_input_VDW_pose (utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose)
 
void setup_using_user_input_VDW_pose (utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, StepWiseRNA_JobParametersCOP const &job_parameters)
 
void setup_using_working_pose (core::pose::Pose const &const_working_pose, StepWiseRNA_JobParametersCOP const &job_parameters)
 
void update_VDW_screen_bin (core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const Is_prepend, std::ofstream &outfile_act)
 
void create_VDW_screen_bin (core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const Is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose=false)
 
void create_VDW_screen_bin (utility::vector1< VDW_RepScreeninfo > const &VDW_rep_screen_info_list, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose)
 
void create_VDW_screen_bin (utility::vector1< core::pose::Pose > const &pose_list, utility::vector1< utility::vector1< core::Size > > const &list_of_ignore_res_list, utility::vector1< bool > const list_of_Is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose)
 
bool VDW_rep_screen (core::pose::Pose const &screening_pose, core::Size const &moving_res, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
 
bool VDW_rep_screen (core::pose::Pose const &screening_pose, core::Size const &moving_res)
 
bool VDW_rep_screen_with_act_pose (core::pose::Pose const &screening_pose, utility::vector1< core::Size > const &moving_res_list, bool const local_verbose=true)
 Warning, this version is very SLOW! More...
 
bool user_inputted_VDW_screen_pose () const
 
void reference_xyz_consistency_check (numeric::xyzVector< core::Real > const &inputted_reference_xyz) const
 
void set_VDW_rep_alignment_RMSD_CUTOFF (core::Real const &setting)
 
void set_VDW_rep_delete_matching_res (utility::vector1< std::string > const &setting)
 
void set_physical_pose_clash_dist_cutoff (core::Real const &setting)
 
void set_output_pdb (bool const setting)
 

Private Member Functions

void check_VDW_screen_bin_is_setup () const
 
bool Is_atom_bin_in_range (Atom_Bin const &atom_pos_bin) const
 
bool check_atom_bin_in_range (Atom_Bin const &atom_pos_bin)
 
void set_reference_xyz (numeric::xyzVector< core::Real > const &reference_xyz)
 
Atom_Bin get_atom_bin (numeric::xyzVector< core::Real > const &atom_pos) const
 
numeric::xyzVector< core::Realget_atom_pos (Atom_Bin const &atom_bin) const
 
void output_atom_bin (std::string const filename) const
 
utility::vector1< core::Sizeget_matching_res_in_VDW_rep_screen_pose (core::pose::Pose const &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, std::map< core::Size, core::Size > &full_to_sub) const
 
void align_VDW_rep_screen_pose (core::pose::Pose &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, bool const verbose) const
 
void create_VDW_rep_screen_pose (VDW_RepScreeninfo &VDW_rep_screen_info, core::pose::Pose const &working_pose, std::map< core::Size, core::Size > &full_to_sub, bool const verbose) const
 

Private Attributes

core::Real max_distance_
 
core::Real atom_bin_size_
 
int const bin_min_
 
int const bin_max_
 
int const bin_offset_
 
core::Size const num_clash_atom_cutoff_
 
bool const write_to_file_
 
bool Is_reference_xyz_setup_
 
bool Is_VDW_screen_bin_setup_
 
bool user_inputted_VDW_screen_pose_
 
utility::vector1
< utility::vector1
< utility::vector1< bool > > > 
VDW_screen_bin_
 
numeric::xyzVector< core::Realreference_xyz_
 
core::Real VDW_rep_alignment_RMSD_CUTOFF_
 
bool tolerate_off_range_atom_bin_
 
int num_atom_pos_bin_out_of_range_message_outputted_
 
bool VDW_rep_screen_with_physical_pose_verbose_
 
core::Real physical_pose_clash_dist_cutoff_
 
utility::vector1< std::string > VDW_rep_ignore_matching_res_
 
bool use_VDW_rep_pose_for_screening_
 
utility::vector1
< VDW_RepScreeninfo
VDW_rep_screen_info_list_
 
bool output_pdb_
 

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::StepWiseRNA_VDW_Bin_Screener ( )
protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::~StepWiseRNA_VDW_Bin_Screener ( )
virtual

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose ( core::pose::Pose VDW_rep_screen_pose,
core::pose::Pose const &  working_pose,
utility::vector1< core::Size > const &  VDW_rep_screen_align_res,
utility::vector1< core::Size > const &  working_align_res,
bool const  verbose 
) const
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::check_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin)
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::check_VDW_screen_bin_is_setup ( ) const
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose ( VDW_RepScreeninfo VDW_rep_screen_info,
core::pose::Pose const &  working_pose,
std::map< core::Size, core::Size > &  full_to_sub,
bool const  verbose 
) const
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_screen_bin ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ignore_res_list,
bool const  Is_prepend,
numeric::xyzVector< core::Real > const &  reference_xyz,
bool const  verbose = false 
)
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_screen_bin ( utility::vector1< VDW_RepScreeninfo > const &  VDW_rep_screen_info_list,
numeric::xyzVector< core::Real > const &  reference_xyz,
bool const  verbose 
)
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_screen_bin ( utility::vector1< core::pose::Pose > const &  pose_list,
utility::vector1< utility::vector1< core::Size > > const &  list_of_ignore_res_list,
utility::vector1< bool > const  list_of_Is_prepend,
numeric::xyzVector< core::Real > const &  reference_xyz,
bool const  verbose 
)
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose ( utility::vector1< std::string > const &  VDW_rep_screen_pose_info,
core::pose::Pose const &  const_working_pose 
)
Atom_Bin protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_atom_bin ( numeric::xyzVector< core::Real > const &  atom_pos) const
private
numeric::xyzVector< core::Real > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_atom_pos ( Atom_Bin const &  atom_bin) const
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose ( core::pose::Pose const &  VDW_rep_screen_pose,
core::pose::Pose const &  working_pose,
utility::vector1< core::Size > const &  VDW_rep_screen_align_res,
utility::vector1< core::Size > const &  working_align_res,
std::map< core::Size, core::Size > &  full_to_sub 
) const
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::Is_atom_bin_in_range ( Atom_Bin const &  atom_pos_bin) const
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::output_atom_bin ( std::string const  filename) const
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::reference_xyz_consistency_check ( numeric::xyzVector< core::Real > const &  inputted_reference_xyz) const
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_physical_pose_clash_dist_cutoff ( core::Real const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_reference_xyz ( numeric::xyzVector< core::Real > const &  reference_xyz)
private
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose ( utility::vector1< std::string > const &  VDW_rep_screen_pose_info,
core::pose::Pose const &  const_working_pose,
StepWiseRNA_JobParametersCOP const &  job_parameters 
)
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose ( core::pose::Pose const &  const_working_pose,
StepWiseRNA_JobParametersCOP const &  job_parameters 
)
void protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ignore_res_list,
bool const  Is_prepend,
std::ofstream &  outfile_act 
)
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::user_inputted_VDW_screen_pose ( ) const
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen ( core::pose::Pose const &  screening_pose,
core::Size const &  moving_res,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_base_stub 
)
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen ( core::pose::Pose const &  screening_pose,
core::Size const &  moving_res 
)
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_act_pose ( core::pose::Pose const &  screening_pose,
utility::vector1< core::Size > const &  moving_res_list,
bool const  local_verbose = true 
)

Member Data Documentation

core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::atom_bin_size_
private
int const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::bin_max_
private
int const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::bin_min_
private

Referenced by create_VDW_screen_bin().

int const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::bin_offset_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::Is_reference_xyz_setup_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::Is_VDW_screen_bin_setup_
private
core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::max_distance_
private

Referenced by create_VDW_screen_bin().

int protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::num_atom_pos_bin_out_of_range_message_outputted_
private

Referenced by check_atom_bin_in_range().

core::Size const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::num_clash_atom_cutoff_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::output_pdb_
private
core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::physical_pose_clash_dist_cutoff_
private
numeric::xyzVector<core::Real> protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::reference_xyz_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::tolerate_off_range_atom_bin_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::use_VDW_rep_pose_for_screening_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::user_inputted_VDW_screen_pose_
private
core::Real protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_alignment_RMSD_CUTOFF_
private
utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_ignore_matching_res_
private
utility::vector1< VDW_RepScreeninfo > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_info_list_
private
bool protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_physical_pose_verbose_
private
utility::vector1< utility::vector1< utility::vector1< bool > > > protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_screen_bin_
private
bool const protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::write_to_file_
private

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