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

#include <RNA_VDW_BinChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker:
Inheritance graph
[legend]

Public Member Functions

 RNA_VDW_BinChecker (core::pose::Pose const &pose)
 
 RNA_VDW_BinChecker ()
 
 ~RNA_VDW_BinChecker () override
 
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 FARFAR_setup_using_user_input_VDW_pose (utility::vector1< std::string > const &All_VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, bool const include_side_chains)
 
void setup_using_user_input_VDW_pose (utility::vector1< std::string > const &All_VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
void setup_using_working_pose (core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_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< core::pose::rna::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)
 
void align_working_pose (core::pose::Pose &working_pose) const
 
void setup_working_alignment (core::pose::Pose &working_pose)
 
utility::vector1< core::Sizeget_VDW_align_res ()
 
void set_num_clash_atom_cutoff (core::Size const setting)
 

Private Member Functions

void check_VDW_screen_bin_is_setup () const
 
bool check_atom_bin_in_range (core::pose::rna::Atom_Bin const &atom_pos_bin)
 
core::Vector get_reference_xyz (core::pose::Pose const &pose, core::Size const reference_res)
 
core::Vector get_reference_xyz_average (core::pose::Pose const &pose)
 
void set_reference_xyz (numeric::xyzVector< core::Real > const &reference_xyz)
 
numeric::xyzVector< core::Realget_atom_pos (core::pose::rna::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)
 
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, bool const setup_working_align)
 
void read_in_VDW_rep_screen_pose (core::pose::rna::VDW_RepScreenInfo &VDW_rep_screen_info) const
 
void create_VDW_rep_screen_pose (core::pose::rna::VDW_RepScreenInfo &VDW_rep_screen_info, core::pose::Pose const &working_pose, std::map< core::Size, core::Size > &full_to_sub, bool const verbose)
 

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 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_
 
core::pose::rna::VDW_GridCOP VDW_screen_bin_
 
utility::vector1
< core::pose::rna::Atom_Bin
occupied_xyz_bins_
 
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_
 
bool output_pdb_
 
bool align_pose_
 
bool include_side_chains_
 
bool vdw_align_res_set_
 
utility::vector1< core::Sizevdw_align_res_
 
core::id::AtomID_Map
< core::id::AtomID
stored_align_working_atom_id_map_
 
bool optimize_memory_usage_
 
bool optimize_speed_
 
bool verbose_
 
utility::vector1< std::string > VDW_rep_ignore_matching_res_
 
bool use_VDW_rep_pose_for_screening_
 
utility::vector1
< core::pose::rna::VDW_RepScreenInfo
VDW_rep_screen_info_list_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker ( core::pose::Pose const &  pose)
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker ( )
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::~RNA_VDW_BinChecker ( )
override

Member Function Documentation

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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 
)
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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,
bool const  setup_working_align 
)
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_working_pose ( core::pose::Pose working_pose) const
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_atom_bin_in_range ( core::pose::rna::Atom_Bin const &  atom_pos_bin)
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_VDW_screen_bin_is_setup ( ) const
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose ( core::pose::rna::VDW_RepScreenInfo VDW_rep_screen_info,
core::pose::Pose const &  working_pose,
std::map< core::Size, core::Size > &  full_to_sub,
bool const  verbose 
)
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin ( utility::vector1< core::pose::rna::VDW_RepScreenInfo > const &  VDW_rep_screen_info_list,
numeric::xyzVector< core::Real > const &  reference_xyz,
bool const  verbose 
)
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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 protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose ( utility::vector1< std::string > const &  All_VDW_rep_screen_pose_info,
core::pose::Pose const &  const_working_pose,
bool const  include_side_chains 
)
numeric::xyzVector< core::Real > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_atom_pos ( core::pose::rna::Atom_Bin const &  atom_bin) const
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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
core::Vector protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz ( core::pose::Pose const &  pose,
core::Size const  reference_res 
)
private
core::Vector protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average ( core::pose::Pose const &  pose)
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_VDW_align_res ( )
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_atom_bin ( std::string const  filename) const
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose ( core::pose::rna::VDW_RepScreenInfo VDW_rep_screen_info) const
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_consistency_check ( numeric::xyzVector< core::Real > const &  inputted_reference_xyz) const
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_num_clash_atom_cutoff ( core::Size const  setting)
inline
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_physical_pose_clash_dist_cutoff ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_reference_xyz ( numeric::xyzVector< core::Real > const &  reference_xyz)
private
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting)
inline
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose ( utility::vector1< std::string > const &  All_VDW_rep_screen_pose_info,
core::pose::Pose const &  const_working_pose,
working_parameters::StepWiseWorkingParametersCOP const &  working_parameters 
)
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose ( core::pose::Pose const &  const_working_pose,
working_parameters::StepWiseWorkingParametersCOP const &  working_parameters 
)
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_working_alignment ( core::pose::Pose working_pose)
void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose ( ) const
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen ( core::pose::Pose const &  screening_pose,
core::Size const &  moving_res 
)
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::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

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_pose_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::atom_bin_size_
private
int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_max_
private
int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_min_
private

Referenced by create_VDW_screen_bin().

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_offset_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::include_side_chains_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_reference_xyz_setup_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_VDW_screen_bin_setup_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::max_distance_
private

Referenced by create_VDW_screen_bin().

int protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::num_atom_pos_bin_out_of_range_message_outputted_
private

Referenced by check_atom_bin_in_range().

core::Size protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::num_clash_atom_cutoff_
private
utility::vector1< core::pose::rna::Atom_Bin > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::occupied_xyz_bins_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::optimize_memory_usage_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::optimize_speed_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_pdb_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::physical_pose_clash_dist_cutoff_
private
numeric::xyzVector< core::Real > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_
private
core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::stored_align_working_atom_id_map_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::tolerate_off_range_atom_bin_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::use_VDW_rep_pose_for_screening_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::vdw_align_res_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::vdw_align_res_set_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_alignment_RMSD_CUTOFF_
private
utility::vector1< std::string > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_ignore_matching_res_
private
utility::vector1< core::pose::rna::VDW_RepScreenInfo > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_info_list_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_physical_pose_verbose_
private
core::pose::rna::VDW_GridCOP protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_screen_bin_
private
bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::verbose_
private
bool const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::write_to_file_
private

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