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Public Member Functions | Private Member Functions | Private Attributes | List of all members
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:
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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::Size > get_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::Real > get_atom_pos (core::pose::rna::Atom_Bin const &atom_bin) const
 
void output_atom_bin (std::string const filename) const
 
utility::vector1< core::Size > 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
 
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::Real > reference_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::Size > vdw_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

◆ RNA_VDW_BinChecker() [1/2]

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

References protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(), optimize_memory_usage_, protocols::TR(), protocols::scoring::VDW_CachedRepScreenInfo::VDW_screen_bin(), and VDW_screen_bin_.

◆ RNA_VDW_BinChecker() [2/2]

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::RNA_VDW_BinChecker ( )

References optimize_memory_usage_, and VDW_screen_bin_.

◆ ~RNA_VDW_BinChecker()

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::~RNA_VDW_BinChecker ( )
override

References occupied_xyz_bins_, optimize_memory_usage_, optimize_speed_, and VDW_screen_bin_.

Member Function Documentation

◆ align_VDW_rep_screen_pose() [1/2]

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

Referenced by create_VDW_rep_screen_pose(), setup_working_alignment(), and VDW_rep_screen_with_act_pose().

◆ align_VDW_rep_screen_pose() [2/2]

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

References protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), core::pose::Pose::dump_pdb(), output_pdb_, protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::size(), stored_align_working_atom_id_map_, core::scoring::superimpose_pose(), protocols::TR(), and VDW_rep_alignment_RMSD_CUTOFF_.

◆ align_working_pose()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_working_pose ( core::pose::Pose &  working_pose) const

References stored_align_working_atom_id_map_, core::scoring::superimpose_pose(), core::pose::rna::VDW_RepScreenInfo::VDW_pose, and VDW_rep_screen_info_list_.

◆ check_atom_bin_in_range()

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_atom_bin_in_range ( core::pose::rna::Atom_Bin const &  atom_pos_bin)
private

References bin_max_, core::pose::rna::is_atom_bin_in_range(), num_atom_pos_bin_out_of_range_message_outputted_, tolerate_off_range_atom_bin_, protocols::TR(), core::pose::rna::Atom_Bin::x, core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by VDW_rep_screen().

◆ check_VDW_screen_bin_is_setup()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::check_VDW_screen_bin_is_setup ( ) const
private

References is_VDW_screen_bin_setup_, and VDW_screen_bin_.

Referenced by output_atom_bin(), and VDW_rep_screen().

◆ create_VDW_rep_screen_pose()

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

References align_pose_, align_VDW_rep_screen_pose(), core::pose::full_model_info::full_to_sub(), get_matching_res_in_VDW_rep_screen_pose(), read_in_VDW_rep_screen_pose(), core::pose::rna::VDW_RepScreenInfo::VDW_align_res, core::pose::rna::VDW_RepScreenInfo::VDW_ignore_res, core::pose::rna::VDW_RepScreenInfo::VDW_pose, and core::pose::rna::VDW_RepScreenInfo::working_align_res.

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and setup_using_user_input_VDW_pose().

◆ create_VDW_screen_bin() [1/3]

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 
)

Referenced by create_VDW_screen_bin(), FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and setup_using_working_pose().

◆ create_VDW_screen_bin() [2/3]

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 
)

References atom_bin_size_, bin_max_, bin_min_, bin_offset_, is_VDW_screen_bin_setup_, max_distance_, num_clash_atom_cutoff_, output_atom_bin(), protocols::stepwise::modeler::output_boolean(), reference_xyz_, set_reference_xyz(), tolerate_off_range_atom_bin_, protocols::TR(), update_VDW_screen_bin(), user_inputted_VDW_screen_pose_, VDW_screen_bin_, verbose_, and write_to_file_.

◆ create_VDW_screen_bin() [3/3]

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 
)

References create_VDW_screen_bin().

◆ FARFAR_setup_using_user_input_VDW_pose() [1/2]

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 
)

References FARFAR_setup_using_user_input_VDW_pose(), and include_side_chains_.

◆ FARFAR_setup_using_user_input_VDW_pose() [2/2]

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 
)

References core::pose::rna::add_virtual_O2Prime_hydrogen(), align_pose_, protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(), create_VDW_rep_screen_pose(), create_VDW_screen_bin(), core::pose::Pose::data(), core::pose::rna::VDW_RepScreenInfo::full_align_res, core::pose::full_model_info::full_to_sub(), core::pose::get_center_of_mass(), core::pose::rna::VDW_RepScreenInfo::import_ID, core::pose::rna::VDW_RepScreenInfo::input_string, protocols::stepwise::modeler::rna::output_title_text(), core::pose::rna::VDW_RepScreenInfo::pose_name, setup_working_alignment(), core::pose::Pose::size(), stored_align_working_atom_id_map_, protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR(), use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, core::pose::rna::VDW_RepScreenInfo::VDW_align_res, vdw_align_res_, vdw_align_res_set_, core::pose::datacache::CacheableDataType::VDW_REP_SCREEN_INFO, protocols::scoring::VDW_CachedRepScreenInfo::VDW_rep_screen_info_list(), VDW_rep_screen_info_list_, verbose_, and core::pose::rna::VDW_RepScreenInfo::working_align_res.

Referenced by FARFAR_setup_using_user_input_VDW_pose().

◆ get_atom_pos()

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

References atom_bin_size_, bin_offset_, is_reference_xyz_setup_, reference_xyz_, core::pose::rna::Atom_Bin::x, core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by output_atom_bin(), and update_VDW_screen_bin().

◆ get_matching_res_in_VDW_rep_screen_pose()

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

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), core::pose::Pose::dump_pdb(), core::conformation::Residue::first_sidechain_atom(), core::pose::full_model_info::full_to_sub(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), protocols::stepwise::modeler::output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR(), core::conformation::Residue::type(), VDW_rep_alignment_RMSD_CUTOFF_, VDW_rep_ignore_matching_res_, verbose_, and core::conformation::Residue::xyz().

Referenced by create_VDW_rep_screen_pose().

◆ get_reference_xyz()

core::Vector protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz ( core::pose::Pose const &  pose,
core::Size const  reference_res 
)
private

References core::chemical::rna::get_rna_base_centroid(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by setup_using_user_input_VDW_pose(), and setup_using_working_pose().

◆ get_reference_xyz_average()

core::Vector protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average ( core::pose::Pose const &  pose)
private

References core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::full_model_info::const_full_model_info(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by setup_using_user_input_VDW_pose().

◆ get_VDW_align_res()

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_VDW_align_res ( )

References align_pose_, vdw_align_res_, and vdw_align_res_set_.

◆ output_atom_bin()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_atom_bin ( std::string const  filename) const
private

References bin_max_, check_VDW_screen_bin_is_setup(), protocols::abinitio::filename(), get_atom_pos(), is_reference_xyz_setup_, VDW_screen_bin_, core::pose::rna::Atom_Bin::x, core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

◆ read_in_VDW_rep_screen_pose()

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

References core::pose::rna::add_virtual_O2Prime_hydrogen(), core::chemical::FA_STANDARD, include_side_chains_, core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::rna::VDW_RepScreenInfo::pose_name, protocols::TR(), core::pose::rna::VDW_RepScreenInfo::VDW_pose, and protocols::stepwise::modeler::virtualize_side_chains().

Referenced by create_VDW_rep_screen_pose(), and setup_using_user_input_VDW_pose().

◆ reference_xyz_consistency_check()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_consistency_check ( numeric::xyzVector< core::Real > const &  inputted_reference_xyz) const

References is_reference_xyz_setup_, reference_xyz_, and protocols::TR().

◆ set_num_clash_atom_cutoff()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_num_clash_atom_cutoff ( core::Size const  setting)
inline

References num_clash_atom_cutoff_.

◆ set_output_pdb()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

◆ set_physical_pose_clash_dist_cutoff()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_physical_pose_clash_dist_cutoff ( core::Real const &  setting)
inline

References physical_pose_clash_dist_cutoff_.

◆ set_reference_xyz()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_reference_xyz ( numeric::xyzVector< core::Real > const &  reference_xyz)
private

References is_reference_xyz_setup_, reference_xyz_, and protocols::TR().

Referenced by create_VDW_screen_bin().

◆ set_VDW_rep_alignment_RMSD_CUTOFF()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_alignment_RMSD_CUTOFF ( core::Real const &  setting)
inline

References VDW_rep_alignment_RMSD_CUTOFF_.

◆ set_VDW_rep_delete_matching_res()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_delete_matching_res ( utility::vector1< std::string > const &  setting)
inline

References VDW_rep_ignore_matching_res_.

◆ setup_using_user_input_VDW_pose()

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 
)

References core::pose::rna::add_virtual_O2Prime_hydrogen(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(), create_VDW_rep_screen_pose(), create_VDW_screen_bin(), core::pose::Pose::fold_tree(), core::pose::rna::VDW_RepScreenInfo::full_align_res, core::pose::full_model_info::full_to_sub(), get_reference_xyz(), get_reference_xyz_average(), core::pose::rna::VDW_RepScreenInfo::import_ID, core::pose::rna::VDW_RepScreenInfo::input_string, optimize_speed_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::rna::VDW_RepScreenInfo::pose_name, read_in_VDW_rep_screen_pose(), core::kinematics::FoldTree::root(), protocols::kinmatch::str(), protocols::stepwise::modeler::rna::string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR(), use_VDW_rep_pose_for_screening_, user_inputted_VDW_screen_pose_, core::pose::rna::VDW_RepScreenInfo::VDW_align_res, core::pose::rna::VDW_RepScreenInfo::VDW_pose, protocols::scoring::VDW_CachedRepScreenInfo::VDW_rep_screen_info_list(), VDW_rep_screen_info_list_, VDW_screen_bin_, verbose_, and core::pose::rna::VDW_RepScreenInfo::working_align_res.

◆ setup_using_working_pose()

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 
)

References create_VDW_screen_bin(), get_reference_xyz(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR(), and protocols::stepwise::modeler::virtualize_side_chains().

◆ setup_working_alignment()

void protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_working_alignment ( core::pose::Pose &  working_pose)

References align_VDW_rep_screen_pose(), core::pose::rna::VDW_RepScreenInfo::VDW_align_res, core::pose::rna::VDW_RepScreenInfo::VDW_pose, VDW_rep_screen_info_list_, and core::pose::rna::VDW_RepScreenInfo::working_align_res.

Referenced by FARFAR_setup_using_user_input_VDW_pose().

◆ update_VDW_screen_bin()

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 
)

References atom_bin_size_, core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), bin_max_, bin_offset_, core::pose::rna::get_atom_bin(), get_atom_pos(), core::pose::rna::is_atom_bin_in_range(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), occupied_xyz_bins_, optimize_memory_usage_, protocols::stepwise::modeler::rna::output_seq_num_list(), reference_xyz_, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), core::conformation::Residue::type(), VDW_screen_bin_, write_to_file_, core::pose::rna::Atom_Bin::x, core::conformation::Residue::xyz(), core::pose::rna::Atom_Bin::y, and core::pose::rna::Atom_Bin::z.

Referenced by create_VDW_screen_bin().

◆ user_inputted_VDW_screen_pose()

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose ( ) const

References user_inputted_VDW_screen_pose_.

◆ VDW_rep_screen() [1/2]

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen ( core::pose::Pose const &  screening_pose,
core::Size const &  moving_res 
)

References atom_bin_size_, bin_offset_, check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), core::pose::rna::get_atom_bin(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), num_clash_atom_cutoff_, reference_xyz_, core::pose::Pose::residue(), VDW_screen_bin_, and core::conformation::Residue::xyz().

◆ VDW_rep_screen() [2/2]

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 
)

References atom_bin_size_, bin_offset_, check_atom_bin_in_range(), check_VDW_screen_bin_is_setup(), core::pose::rna::get_atom_bin(), protocols::toolbox::rigid_body::get_atom_coordinates(), core::conformation::Residue::is_virtual(), num_clash_atom_cutoff_, reference_xyz_, core::pose::Pose::residue(), protocols::TR(), VDW_screen_bin_, and protocols::kinmatch::xyz().

◆ VDW_rep_screen_with_act_pose()

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 
)

Warning, this version is very SLOW!

References align_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::is_residues_in_contact(), num_clash_atom_cutoff_, protocols::stepwise::modeler::rna::output_seq_num_list(), physical_pose_clash_dist_cutoff_, core::pose::Pose::size(), protocols::TR(), use_VDW_rep_pose_for_screening_, VDW_rep_screen_info_list_, and VDW_rep_screen_with_physical_pose_verbose_.

Member Data Documentation

◆ align_pose_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_pose_
private

Referenced by create_VDW_rep_screen_pose(), FARFAR_setup_using_user_input_VDW_pose(), and get_VDW_align_res().

◆ atom_bin_size_

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::atom_bin_size_
private

Referenced by create_VDW_screen_bin(), get_atom_pos(), update_VDW_screen_bin(), and VDW_rep_screen().

◆ bin_max_

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_max_
private

Referenced by check_atom_bin_in_range(), create_VDW_screen_bin(), output_atom_bin(), and update_VDW_screen_bin().

◆ bin_min_

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_min_
private

Referenced by create_VDW_screen_bin().

◆ bin_offset_

int const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::bin_offset_
private

Referenced by create_VDW_screen_bin(), get_atom_pos(), update_VDW_screen_bin(), and VDW_rep_screen().

◆ include_side_chains_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::include_side_chains_
private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and read_in_VDW_rep_screen_pose().

◆ is_reference_xyz_setup_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_reference_xyz_setup_
private

Referenced by get_atom_pos(), output_atom_bin(), reference_xyz_consistency_check(), and set_reference_xyz().

◆ is_VDW_screen_bin_setup_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::is_VDW_screen_bin_setup_
private

Referenced by check_VDW_screen_bin_is_setup(), and create_VDW_screen_bin().

◆ max_distance_

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::max_distance_
private

Referenced by create_VDW_screen_bin().

◆ num_atom_pos_bin_out_of_range_message_outputted_

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().

◆ num_clash_atom_cutoff_

core::Size protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::num_clash_atom_cutoff_
private

Referenced by create_VDW_screen_bin(), set_num_clash_atom_cutoff(), VDW_rep_screen(), and VDW_rep_screen_with_act_pose().

◆ occupied_xyz_bins_

utility::vector1< core::pose::rna::Atom_Bin > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::occupied_xyz_bins_
private

Referenced by update_VDW_screen_bin(), and ~RNA_VDW_BinChecker().

◆ optimize_memory_usage_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::optimize_memory_usage_
private

Referenced by RNA_VDW_BinChecker(), update_VDW_screen_bin(), and ~RNA_VDW_BinChecker().

◆ optimize_speed_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::optimize_speed_
private

Referenced by setup_using_user_input_VDW_pose(), and ~RNA_VDW_BinChecker().

◆ output_pdb_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_pdb_
private

Referenced by align_VDW_rep_screen_pose(), and set_output_pdb().

◆ physical_pose_clash_dist_cutoff_

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::physical_pose_clash_dist_cutoff_
private

Referenced by set_physical_pose_clash_dist_cutoff(), and VDW_rep_screen_with_act_pose().

◆ reference_xyz_

numeric::xyzVector< core::Real > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_
private

Referenced by create_VDW_screen_bin(), get_atom_pos(), reference_xyz_consistency_check(), set_reference_xyz(), update_VDW_screen_bin(), and VDW_rep_screen().

◆ stored_align_working_atom_id_map_

core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::stored_align_working_atom_id_map_
private

Referenced by align_VDW_rep_screen_pose(), align_working_pose(), and FARFAR_setup_using_user_input_VDW_pose().

◆ tolerate_off_range_atom_bin_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::tolerate_off_range_atom_bin_
private

Referenced by check_atom_bin_in_range(), and create_VDW_screen_bin().

◆ use_VDW_rep_pose_for_screening_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::use_VDW_rep_pose_for_screening_
private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and VDW_rep_screen_with_act_pose().

◆ user_inputted_VDW_screen_pose_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose_
private

Referenced by create_VDW_screen_bin(), FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), and user_inputted_VDW_screen_pose().

◆ vdw_align_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::vdw_align_res_
private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and get_VDW_align_res().

◆ vdw_align_res_set_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::vdw_align_res_set_
private

Referenced by FARFAR_setup_using_user_input_VDW_pose(), and get_VDW_align_res().

◆ VDW_rep_alignment_RMSD_CUTOFF_

core::Real protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_alignment_RMSD_CUTOFF_
private

Referenced by align_VDW_rep_screen_pose(), get_matching_res_in_VDW_rep_screen_pose(), and set_VDW_rep_alignment_RMSD_CUTOFF().

◆ VDW_rep_ignore_matching_res_

utility::vector1< std::string > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_ignore_matching_res_
private

Referenced by get_matching_res_in_VDW_rep_screen_pose(), and set_VDW_rep_delete_matching_res().

◆ VDW_rep_screen_info_list_

utility::vector1< core::pose::rna::VDW_RepScreenInfo > protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_info_list_
private

Referenced by align_working_pose(), FARFAR_setup_using_user_input_VDW_pose(), setup_using_user_input_VDW_pose(), setup_working_alignment(), and VDW_rep_screen_with_act_pose().

◆ VDW_rep_screen_with_physical_pose_verbose_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_physical_pose_verbose_
private

Referenced by VDW_rep_screen_with_act_pose().

◆ VDW_screen_bin_

core::pose::rna::VDW_GridCOP protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_screen_bin_
private

Referenced by check_VDW_screen_bin_is_setup(), create_VDW_screen_bin(), output_atom_bin(), RNA_VDW_BinChecker(), setup_using_user_input_VDW_pose(), update_VDW_screen_bin(), VDW_rep_screen(), and ~RNA_VDW_BinChecker().

◆ verbose_

bool protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::verbose_
private

Referenced by create_VDW_screen_bin(), FARFAR_setup_using_user_input_VDW_pose(), get_matching_res_in_VDW_rep_screen_pose(), and setup_using_user_input_VDW_pose().

◆ write_to_file_

bool const protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::write_to_file_
private

Referenced by create_VDW_screen_bin(), and update_VDW_screen_bin().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 11:03:15 for Rosetta by doxygen 1.9.1