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core::pack::guidance_scoreterms::sap::SapConstraintHelper Class Reference

#include <SapConstraintHelper.hh>

Public Member Functions

 SapConstraintHelper (SapConstraintOptionsCOP const &options)
 
core::Real calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position)
 
void commit_considered_substitution ()
 
SapConstraintOptionsCOP options () const
 
core::pack::rotamer_set::RotamerSets init_with_pose (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
Real current_score () const
 
Real set_accurate_sasa_and_recalc (pose::Pose const &pose)
 
void report ()
 
void report_final_score (Real actual_sap) const
 
core::id::AtomID_Map< Real > get_per_atom_sap (pose::Pose const &pose) const
 

Protected Types

typedef std::pair< Size, uint8_t[ATOM_WITHIN_5_ELEMS]> atom_within_5_value
 
typedef std::unordered_map< std::pair< conformation::Residue const *, conformation::Residue const * >, atom_within_5_value, RotamerRotamerHasher > type_atom_within_5_map
 
typedef float atom_sasa_score_value[ATOM_SASA_SCORE_ELEMS]
 
typedef std::unordered_map< conformation::Residue const *, atom_sasa_score_value > atom_sasa_score_map
 

Protected Member Functions

void restore_from_shadow ()
 
void save_to_shadow ()
 
core::Real symm_calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position)
 
void recalculate_saps (utility::vector1< Size > const &positions_to_update)
 
void recalculate_sasa ()
 
void update_neighbors_sap (float const *delta_sasa_score, Size seqpos, bool invert, bool skip_self)
 
void add_to_sap (float amount, Size seqpos, Size iat)
 
void add_remove_rotamer (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void add_remove_rotamer_fast (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void add_remove_rotamer_lightning (utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add)
 
void lightning_update_neighbors_sap (Size seqpos, bool invert, bool dont_update_self)
 
void lightning_add_to_sap (float amount, Size seqpos)
 
void store_sasa_blocks (Size &offset, Size seqpos, bool add, bool mark_dirty)
 
void reinit_with_resvect (utility::vector1< core::conformation::ResidueCOP > const &resvect, bool skip_reset=false)
 
void reset_calculation ()
 
void apply_residue_selectors (core::pose::Pose const &pose)
 
void resize_arrays (core::pose::Pose const &pose)
 
void fill_block_params (core::pose::Pose const &pose, pack::rotamer_set::RotamerSets const &rotamer_sets)
 
Real calculate_block (Real dist2, Real radius_us, Real radius_them)
 
void fill_atom_neighbor_stuff (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void convert_block_sasa_to_sasa_score (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
float & lightning_1b_lookup (chemical::AA aa, Size seqpos)
 
std::pair< float, float > & lightning_2b_lookup (chemical::AA aa1, Size seqpos1, chemical::AA aa2, Size seqpos2, bool create=false)
 
Real find_lightning_2b (conformation::ResidueCOP const &from_rot, conformation::ResidueCOP const &to_rot)
 
core::pack::rotamer_set::RotamerSets setup_lightning (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void setup_fast (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets)
 
void add_sap_data (conformation::Residue const *key1, conformation::Residue const *key2, utility::vector1< utility::vector1< uint8_t >> const &sap_positions, Size natoms, Size first_sidechain)
 
core::pack::rotamer_set::RotamerSets setup_for_symmetry (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotsets)
 
Size my_natoms (core::conformation::ResidueCOP const &res) const
 
Size my_natoms (core::conformation::Residue const *res) const
 
Real my_hydrophobic_weight (SapDatabase *db, char aa) const
 
void init ()
 

Private Attributes

SapConstraintOptionsCOP options_
 
bool fast_
 
bool lightning_
 
bool heavy_
 
utility::vector1< bool > score_positions_
 
utility::vector1< bool > sap_calculate_positions_
 
utility::vector1< bool > sasa_positions_
 
core::conformation::ResidueCOP fake_rotamer_
 
core::scoring::ScoreFunctionOP fake_lr_scorefxn_
 
core::scoring::ScoreFunctionOP fake_sr_scorefxn_
 
Size max_rotamer_atoms_
 
utility::vector1< utility::vector1< Size > > check_positions_sap_
 
utility::vector1< utility::vector1< Size > > check_positions_block_
 
std::unordered_map< conformation::Residue const *, Size > rotamer_to_block_param_offset_
 
utility::vector1< BlockParam > all_block_params_
 
atom_sasa_score_map rotamer_to_sasa_data_
 
std::unordered_map< std::pair< conformation::Residue const *, conformation::Residue const * >, Size, RotamerRotamerHasher > interacting_block_offset_
 
utility::vector1< uint8_t > interacting_block_
 
type_atom_within_5_map atom_within_5_map_
 
utility::vector1< uint8_t > atom_within_5_
 
utility::vector1< core::conformation::ResidueCOP > internal_resvect_
 
utility::vector1< Size > block_param_offset_
 
utility::vector1< utility::vector0< uint16_t > > sasa_blocks_
 
utility::vector1< utility::vector0< float > > atom_sasa_score_
 
utility::vector1< utility::vector0< float > > atom_sap_
 
float current_score_
 
utility::vector1< float * > atom_sasa_score_fast_
 
utility::vector1< bool > shadow_mismatch_
 
utility::vector1< utility::vector0< bool > > dirty_sasa_
 
utility::vector1< utility::vector0< float > > atom_sasa_score_shadow_
 
utility::vector1< utility::vector0< uint16_t > > sasa_blocks_shadow_
 
utility::vector1< utility::vector0< float > > atom_sap_shadow_
 
float current_score_shadow_
 
utility::vector1< Size > block_param_offset_shadow_
 
utility::vector1< core::conformation::ResidueCOP > internal_resvect_shadow_
 
utility::vector1< float * > atom_sasa_score_fast_shadow_
 
utility::vector1< uint16_t > lightning_aa_2_index_
 
Size lightning_num_aas_
 
Size lightning_num_aas_sq_
 
utility::vector1< uint32_t > lightning_seqpos_2_index_
 
Size lightning_num_seqpos_
 
utility::vector0< float > lightning_rotamer_1b_sap_
 
utility::vector0< std::pair< float, float > > lightning_rotamer_2b_sap_
 
bool use_2b_map_
 
std::unordered_map< basic::datacache::ResRotPair, std::pair< float, float >, basic::datacache::ResRotPairHasher > lightning_rotamer_2b_sap_map_
 
std::pair< float, float > default_2b_
 
utility::vector1< Real > lightning_current_res_sap_
 
utility::vector1< Real > lightning_current_res_sap_shadow_
 
utility::vector1< Size > recalc_positions_scratch_
 
utility::vector0< float > delta_sasa_scratch_
 
utility::vector0< float > delta_sasa_zeros_
 
conformation::symmetry::SymmetryInfoCOP symm_info_
 
std::unordered_map< core::conformation::Residue const *, utility::vector1< core::conformation::ResidueCOP > > symm_rotamer_to_other_rotamers_
 
utility::vector1< core::conformation::ResidueCOP > symm_work_resvect_
 
utility::vector1< core::conformation::ResidueCOP > symm_work_resvect_shadow_
 
bool symm_debug_
 
bool symm_debug_force_map_
 

Friends

class ::SapConstraintEnergyTests
 

Member Typedef Documentation

◆ atom_sasa_score_map

typedef std::unordered_map< conformation::Residue const*, atom_sasa_score_value > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_map
protected

◆ atom_sasa_score_value

typedef float core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_value[ATOM_SASA_SCORE_ELEMS]
protected

◆ atom_within_5_value

typedef std::pair< Size, uint8_t[ATOM_WITHIN_5_ELEMS]> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_within_5_value
protected

◆ type_atom_within_5_map

typedef std::unordered_map< std::pair< conformation::Residue const *, conformation::Residue const * >, atom_within_5_value, RotamerRotamerHasher > core::pack::guidance_scoreterms::sap::SapConstraintHelper::type_atom_within_5_map
protected

Constructor & Destructor Documentation

◆ SapConstraintHelper()

core::pack::guidance_scoreterms::sap::SapConstraintHelper::SapConstraintHelper ( SapConstraintOptionsCOP const &  options)

References init().

Member Function Documentation

◆ add_remove_rotamer()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected

References protocols::mean_field::add(), atom_sap_, atom_sasa_score_, block_param_offset_, check_positions_block_, current_score_, dirty_sasa_, interacting_block_offset_, internal_resvect_, my_natoms(), rotamer_to_block_param_offset_, sasa_blocks_, score_positions_, shadow_mismatch_, store_sasa_blocks(), and update_neighbors_sap().

Referenced by calculate_energy(), reinit_with_resvect(), and symm_calculate_energy().

◆ add_remove_rotamer_fast()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_fast ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected

References protocols::mean_field::add(), atom_sap_, atom_sasa_score_fast_, current_score_, internal_resvect_, my_natoms(), rotamer_to_sasa_data_, score_positions_, shadow_mismatch_, and update_neighbors_sap().

Referenced by calculate_energy(), reinit_with_resvect(), and symm_calculate_energy().

◆ add_remove_rotamer_lightning()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_lightning ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
Size const  substitution_position,
bool  add 
)
protected

References protocols::mean_field::add(), current_score_, internal_resvect_, lightning_1b_lookup(), lightning_current_res_sap_, lightning_update_neighbors_sap(), score_positions_, and shadow_mismatch_.

Referenced by calculate_energy(), reinit_with_resvect(), and symm_calculate_energy().

◆ add_sap_data()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_sap_data ( conformation::Residue const *  key1,
conformation::Residue const *  key2,
utility::vector1< utility::vector1< uint8_t >> const &  sap_positions,
Size  natoms,
Size  first_sidechain 
)
protected

References atom_within_5_, ATOM_WITHIN_5_ELEMS, and atom_within_5_map_.

Referenced by fill_atom_neighbor_stuff().

◆ add_to_sap()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_to_sap ( float  amount,
Size  seqpos,
Size  iat 
)
protected

References atom_sap_, current_score_, internal_resvect_, and score_positions_.

Referenced by update_neighbors_sap().

◆ apply_residue_selectors()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::apply_residue_selectors ( core::pose::Pose const &  pose)
protected

References core::conformation::Residue::is_virtual_residue(), options_, core::pose::Pose::residue(), sap_calculate_positions_, sasa_positions_, score_positions_, and core::pose::Pose::size().

Referenced by init_with_pose().

◆ calculate_block()

Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_block ( Real  dist2,
Real  radius_us,
Real  radius_them 
)
protected

References core::kinematics::distance().

Referenced by fill_atom_neighbor_stuff().

◆ calculate_energy()

core::Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_energy ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
core::Size const  substitution_position 
)

References protocols::cluster::calibur::aa, add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), current_score_, fast_, internal_resvect_, lightning_, recalc_positions_scratch_, recalculate_saps(), recalculate_sasa(), reinit_with_resvect(), restore_from_shadow(), sap_calculate_positions_, sasa_positions_, symm_calculate_energy(), and symm_info_.

◆ commit_considered_substitution()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::commit_considered_substitution ( )

References save_to_shadow().

◆ convert_block_sasa_to_sasa_score()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected

References all_block_params_, ATOM_SASA_SCORE_ELEMS, core::pack::guidance_scoreterms::sap::BlockParam::full_block, core::conformation::Residue::get_self_ptr(), core::pack::guidance_scoreterms::sap::BlockParam::max_sasa_score, my_natoms(), core::pack::guidance_scoreterms::sap::BlockParam::no_block, core::pack::rotamer_set::RotamerSets::nrotamers(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer(), rotamer_to_block_param_offset_, rotamer_to_sasa_data_, core::pack::guidance_scoreterms::sap::SAP_BLOCK_STORE_SCALE, and core::pose::Pose::size().

Referenced by setup_fast(), and setup_lightning().

◆ current_score()

Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score ( ) const

References current_score_shadow_.

◆ fill_atom_neighbor_stuff()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected

References core::pose::motif::a(), add_sap_data(), core::conformation::Residue::atom_is_backbone(), ATOM_SASA_SCORE_ELEMS, core::conformation::Residue::atom_type(), atom_within_5_, atom_within_5_map_, calculate_block(), check_positions_block_, check_positions_sap_, core::pack::create_packer_graph(), fake_lr_scorefxn_, fast_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::get_self_ptr(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), interacting_block_, interacting_block_offset_, core::chemical::AtomType::lj_radius(), core::pose::symmetry::make_asymmetric_pose(), core::pack::guidance_scoreterms::sap::MAX_BLOCK_INTERACTION, max_rotamer_atoms_, my_natoms(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::pack::rotamer_set::RotamerSets::nrotamers(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), rotamer_to_sasa_data_, core::pack::guidance_scoreterms::sap::SAP_BLOCK_STORE_SCALE, sap_calculate_positions_, sasa_positions_, core::pose::Pose::size(), symm_info_, core::pack::rotamer_set::RotamerSets::task(), and core::conformation::Residue::xyz().

Referenced by init_with_pose(), and setup_lightning().

◆ fill_block_params()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params ( core::pose::Pose const &  pose,
pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected

References all_block_params_, core::pack::guidance_scoreterms::sap::SapDatabase::atomtype_to_block_param(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::conformation::Residue::get_self_ptr(), max_rotamer_atoms_, my_hydrophobic_weight(), my_natoms(), core::pack::rotamer_set::RotamerSets::nrotamers(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer(), rotamer_to_block_param_offset_, sap_calculate_positions_, score_positions_, core::pose::Pose::size(), and core::pack::guidance_scoreterms::sap::TR().

Referenced by init_with_pose(), and setup_lightning().

◆ find_lightning_2b()

Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::find_lightning_2b ( conformation::ResidueCOP const &  from_rot,
conformation::ResidueCOP const &  to_rot 
)
protected

References ATOM_SASA_SCORE_ELEMS, ATOM_WITHIN_5_ELEMS, atom_within_5_map_, my_natoms(), and rotamer_to_sasa_data_.

Referenced by setup_lightning().

◆ get_per_atom_sap()

core::id::AtomID_Map< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap ( pose::Pose const &  pose) const

References atom_sap_, core::conformation::Residue::first_sidechain_atom(), core::pose::initialize_atomid_map(), internal_resvect_, my_natoms(), core::conformation::Residue::name3(), core::pose::Pose::residue(), sap_calculate_positions_, score_positions_, and core::pose::Pose::size().

◆ init()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::init ( )
protected

References core::scoring::methods::EnergyMethodOptions::etable_options(), core::scoring::fa_rep, fake_lr_scorefxn_, fake_rotamer_, fast_, core::conformation::get_residue_from_name1(), heavy_, lightning_, core::pack::guidance_scoreterms::sap::MAX_BLOCK_INTERACTION, core::scoring::etable::EtableOptions::max_dis, options_, recalc_positions_scratch_, symm_debug_, and symm_debug_force_map_.

Referenced by SapConstraintHelper().

◆ init_with_pose()

core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::init_with_pose ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)

References apply_residue_selectors(), fast_, fill_atom_neighbor_stuff(), fill_block_params(), lightning_, resize_arrays(), setup_fast(), setup_for_symmetry(), setup_lightning(), and symm_info_.

◆ lightning_1b_lookup()

float & core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_1b_lookup ( chemical::AA  aa,
Size  seqpos 
)
protected

References protocols::cluster::calibur::aa, BAD_AA_INDEX, BAD_SEQPOS_INDEX, lightning_aa_2_index_, lightning_num_aas_, lightning_rotamer_1b_sap_, and lightning_seqpos_2_index_.

Referenced by add_remove_rotamer_lightning(), and setup_lightning().

◆ lightning_2b_lookup()

std::pair< float, float > & core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_2b_lookup ( chemical::AA  aa1,
Size  seqpos1,
chemical::AA  aa2,
Size  seqpos2,
bool  create = false 
)
protected

References BAD_AA_INDEX, BAD_SEQPOS_INDEX, default_2b_, lightning_aa_2_index_, lightning_num_aas_, lightning_num_aas_sq_, lightning_num_seqpos_, lightning_rotamer_2b_sap_, lightning_rotamer_2b_sap_map_, lightning_seqpos_2_index_, core::pack::guidance_scoreterms::sap::upper_triangle_offset(), and use_2b_map_.

Referenced by lightning_update_neighbors_sap(), and setup_lightning().

◆ lightning_add_to_sap()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_add_to_sap ( float  amount,
Size  seqpos 
)
protected

References current_score_, lightning_current_res_sap_, and score_positions_.

Referenced by lightning_update_neighbors_sap().

◆ lightning_update_neighbors_sap()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_update_neighbors_sap ( Size  seqpos,
bool  invert,
bool  dont_update_self 
)
protected

References check_positions_sap_, fake_rotamer_, internal_resvect_, lightning_2b_lookup(), lightning_add_to_sap(), score_positions_, and shadow_mismatch_.

Referenced by add_remove_rotamer_lightning().

◆ my_hydrophobic_weight()

Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_hydrophobic_weight ( SapDatabase *  db,
char  aa 
) const
protected

References protocols::cluster::calibur::aa, core::pack::guidance_scoreterms::sap::SapDatabase::hydrophobic_weight(), and options_.

Referenced by fill_block_params(), and set_accurate_sasa_and_recalc().

◆ my_natoms() [1/2]

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms ( core::conformation::Residue const *  res) const
protected

References heavy_, core::conformation::Residue::natoms(), and core::conformation::Residue::nheavyatoms().

◆ my_natoms() [2/2]

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms ( core::conformation::ResidueCOP const &  res) const
protected

References heavy_.

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), convert_block_sasa_to_sasa_score(), fill_atom_neighbor_stuff(), fill_block_params(), find_lightning_2b(), get_per_atom_sap(), recalculate_saps(), recalculate_sasa(), report(), set_accurate_sasa_and_recalc(), store_sasa_blocks(), and update_neighbors_sap().

◆ options()

SapConstraintOptionsCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::options ( ) const

References options_.

◆ recalculate_saps()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalculate_saps ( utility::vector1< Size > const &  positions_to_update)
protected

References atom_sap_, atom_sasa_score_, atom_sasa_score_fast_, atom_within_5_, ATOM_WITHIN_5_ELEMS, atom_within_5_map_, check_positions_sap_, current_score_, fast_, internal_resvect_, my_natoms(), and score_positions_.

Referenced by calculate_energy(), reinit_with_resvect(), set_accurate_sasa_and_recalc(), and symm_calculate_energy().

◆ recalculate_sasa()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalculate_sasa ( )
protected

References all_block_params_, atom_sasa_score_, block_param_offset_, delta_sasa_scratch_, dirty_sasa_, core::pack::guidance_scoreterms::sap::BlockParam::full_block, internal_resvect_, core::pack::guidance_scoreterms::sap::BlockParam::max_sasa_score, my_natoms(), core::pack::guidance_scoreterms::sap::BlockParam::no_block, sasa_blocks_, shadow_mismatch_, and update_neighbors_sap().

Referenced by calculate_energy(), reinit_with_resvect(), and symm_calculate_energy().

◆ reinit_with_resvect()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::reinit_with_resvect ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
bool  skip_reset = false 
)
protected

References add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), fake_rotamer_, fast_, lightning_, recalculate_saps(), recalculate_sasa(), reset_calculation(), sap_calculate_positions_, sasa_positions_, and save_to_shadow().

Referenced by calculate_energy(), and symm_calculate_energy().

◆ report()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::report ( )

References atom_sap_, internal_resvect_, my_natoms(), restore_from_shadow(), sap_calculate_positions_, and core::simple_metrics::metrics::sum.

◆ report_final_score()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::report_final_score ( Real  actual_sap) const

References current_score_shadow_, protocols::kinmatch::str(), and core::pack::guidance_scoreterms::sap::TR().

◆ reset_calculation()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::reset_calculation ( )
protected

References atom_sap_, atom_sap_shadow_, atom_sasa_score_, atom_sasa_score_fast_, atom_sasa_score_fast_shadow_, atom_sasa_score_shadow_, block_param_offset_, block_param_offset_shadow_, current_score_, current_score_shadow_, delta_sasa_zeros_, dirty_sasa_, fake_rotamer_, fast_, internal_resvect_, internal_resvect_shadow_, lightning_current_res_sap_, lightning_current_res_sap_shadow_, max_rotamer_atoms_, sasa_blocks_, sasa_blocks_shadow_, score_positions_, shadow_mismatch_, symm_work_resvect_, and symm_work_resvect_shadow_.

Referenced by reinit_with_resvect(), and symm_calculate_energy().

◆ resize_arrays()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::resize_arrays ( core::pose::Pose const &  pose)
protected

References check_positions_block_, check_positions_sap_, delta_sasa_scratch_, delta_sasa_zeros_, core::pack::guidance_scoreterms::sap::find_mismatch(), lightning_, max_rotamer_atoms_, sap_calculate_positions_, sasa_positions_, score_positions_, and core::pose::Pose::size().

Referenced by init_with_pose().

◆ restore_from_shadow()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::restore_from_shadow ( )
protected

References atom_sap_, atom_sap_shadow_, atom_sasa_score_, atom_sasa_score_fast_, atom_sasa_score_fast_shadow_, atom_sasa_score_shadow_, block_param_offset_, block_param_offset_shadow_, current_score_, current_score_shadow_, internal_resvect_, internal_resvect_shadow_, lightning_, lightning_current_res_sap_, lightning_current_res_sap_shadow_, sasa_blocks_, sasa_blocks_shadow_, shadow_mismatch_, symm_info_, symm_work_resvect_, and symm_work_resvect_shadow_.

Referenced by calculate_energy(), report(), and symm_calculate_energy().

◆ save_to_shadow()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::save_to_shadow ( )
protected

References atom_sap_, atom_sap_shadow_, atom_sasa_score_, atom_sasa_score_fast_, atom_sasa_score_fast_shadow_, atom_sasa_score_shadow_, block_param_offset_, block_param_offset_shadow_, current_score_, current_score_shadow_, internal_resvect_, internal_resvect_shadow_, lightning_, lightning_current_res_sap_, lightning_current_res_sap_shadow_, sasa_blocks_, sasa_blocks_shadow_, shadow_mismatch_, symm_info_, symm_work_resvect_, and symm_work_resvect_shadow_.

Referenced by commit_considered_substitution(), reinit_with_resvect(), and set_accurate_sasa_and_recalc().

◆ set_accurate_sasa_and_recalc()

Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc ( pose::Pose const &  pose)

References atom_sap_, atom_sasa_score_, current_score_, fast_, core::conformation::Residue::first_sidechain_atom(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::conformation::Residue::get_self_ptr(), internal_resvect_, core::pack::guidance_scoreterms::sap::SapDatabase::max_sasa(), my_hydrophobic_weight(), my_natoms(), core::conformation::Residue::name3(), recalculate_saps(), core::pose::Pose::residue(), core::pack::guidance_scoreterms::sap::sap_atom_sasa(), sap_calculate_positions_, sasa_positions_, save_to_shadow(), protocols::hybridization::score, and core::pose::Pose::size().

◆ setup_fast()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_fast ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected

References convert_block_sasa_to_sasa_score(), dirty_sasa_, and max_rotamer_atoms_.

Referenced by init_with_pose().

◆ setup_for_symmetry()

core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotsets 
)
protected

References core::pose::Pose::conformation(), core::select::get_residue_selector_from_subset(), core::conformation::Residue::get_self_ptr(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::pose::symmetry::is_symmetric(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::pack::rotamer_set::RotamerSets::resid_2_moltenres(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), sap_calculate_positions_, sasa_positions_, score_positions_, core::pack::rotamer_set::RotamerSets::set_explicit_rotamers(), core::pack::rotamer_set::RotamerSets::set_task(), core::pose::Pose::size(), symm_debug_, symm_info_, symm_rotamer_to_other_rotamers_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pack::rotamer_set::RotamerSets::task(), core::pack::guidance_scoreterms::sap::TR(), and core::pack::rotamer_set::RotamerSets::update_offset_data().

Referenced by init_with_pose().

◆ setup_lightning()

core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_lightning ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)
protected

References BAD_AA_INDEX, BAD_SEQPOS_INDEX, check_positions_sap_, convert_block_sasa_to_sasa_score(), default_2b_, fill_atom_neighbor_stuff(), fill_block_params(), find_lightning_2b(), core::conformation::Residue::get_self_ptr(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), lightning_1b_lookup(), lightning_2b_lookup(), lightning_aa_2_index_, lightning_num_aas_, lightning_num_aas_sq_, lightning_num_seqpos_, lightning_rotamer_1b_sap_, lightning_rotamer_2b_sap_, lightning_rotamer_2b_sap_map_, lightning_seqpos_2_index_, core::chemical::num_aa_types, core::pack::rotamer_set::RotamerSets::resid_2_moltenres(), core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), sap_calculate_positions_, core::pack::rotamer_set::RotamerSets::set_explicit_rotamers(), core::pack::rotamer_set::RotamerSets::set_task(), core::pose::Pose::size(), symm_debug_force_map_, core::pack::rotamer_set::RotamerSets::task(), core::pack::guidance_scoreterms::sap::TR(), core::pack::rotamer_set::RotamerSets::update_offset_data(), and use_2b_map_.

Referenced by init_with_pose().

◆ store_sasa_blocks()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::store_sasa_blocks ( Size &  offset,
Size  seqpos,
bool  add,
bool  mark_dirty 
)
protected

References protocols::mean_field::add(), dirty_sasa_, interacting_block_, internal_resvect_, my_natoms(), and sasa_blocks_.

Referenced by add_remove_rotamer().

◆ symm_calculate_energy()

core::Real core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_calculate_energy ( utility::vector1< core::conformation::ResidueCOP > const &  resvect,
core::Size const  substitution_position 
)
protected

References protocols::cluster::calibur::aa, add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), current_score_, fast_, internal_resvect_, lightning_, recalculate_saps(), recalculate_sasa(), reinit_with_resvect(), reset_calculation(), restore_from_shadow(), sap_calculate_positions_, sasa_positions_, shadow_mismatch_, symm_info_, symm_rotamer_to_other_rotamers_, and symm_work_resvect_.

Referenced by calculate_energy().

◆ update_neighbors_sap()

void core::pack::guidance_scoreterms::sap::SapConstraintHelper::update_neighbors_sap ( float const *  delta_sasa_score,
Size  seqpos,
bool  invert,
bool  skip_self 
)
protected

References add_to_sap(), atom_within_5_, ATOM_WITHIN_5_ELEMS, atom_within_5_map_, check_positions_sap_, dirty_sasa_, internal_resvect_, my_natoms(), score_positions_, and shadow_mismatch_.

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), and recalculate_sasa().

Friends And Related Function Documentation

◆ ::SapConstraintEnergyTests

friend class ::SapConstraintEnergyTests
friend

Member Data Documentation

◆ all_block_params_

utility::vector1<BlockParam> core::pack::guidance_scoreterms::sap::SapConstraintHelper::all_block_params_
private

Referenced by convert_block_sasa_to_sasa_score(), fill_block_params(), and recalculate_sasa().

◆ atom_sap_

utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sap_
private

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), add_to_sap(), get_per_atom_sap(), recalculate_saps(), report(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and set_accurate_sasa_and_recalc().

◆ atom_sap_shadow_

utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sap_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ atom_sasa_score_

utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_
private

Referenced by add_remove_rotamer(), recalculate_saps(), recalculate_sasa(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and set_accurate_sasa_and_recalc().

◆ atom_sasa_score_fast_

utility::vector1<float *> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_fast_
private

Referenced by add_remove_rotamer_fast(), recalculate_saps(), reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ atom_sasa_score_fast_shadow_

utility::vector1<float *> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_fast_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ atom_sasa_score_shadow_

utility::vector1<utility::vector0<float> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_sasa_score_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ atom_within_5_

utility::vector1<uint8_t> core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_within_5_
private

Referenced by add_sap_data(), fill_atom_neighbor_stuff(), recalculate_saps(), and update_neighbors_sap().

◆ atom_within_5_map_

type_atom_within_5_map core::pack::guidance_scoreterms::sap::SapConstraintHelper::atom_within_5_map_
private

Referenced by add_sap_data(), fill_atom_neighbor_stuff(), find_lightning_2b(), recalculate_saps(), and update_neighbors_sap().

◆ block_param_offset_

utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::block_param_offset_
private

Referenced by add_remove_rotamer(), recalculate_sasa(), reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ block_param_offset_shadow_

utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::block_param_offset_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ check_positions_block_

utility::vector1<utility::vector1<Size> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::check_positions_block_
private

Referenced by add_remove_rotamer(), fill_atom_neighbor_stuff(), and resize_arrays().

◆ check_positions_sap_

utility::vector1<utility::vector1<Size> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::check_positions_sap_
private

Referenced by fill_atom_neighbor_stuff(), lightning_update_neighbors_sap(), recalculate_saps(), resize_arrays(), setup_lightning(), and update_neighbors_sap().

◆ current_score_

float core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score_
private

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), add_to_sap(), calculate_energy(), lightning_add_to_sap(), recalculate_saps(), reset_calculation(), restore_from_shadow(), save_to_shadow(), set_accurate_sasa_and_recalc(), and symm_calculate_energy().

◆ current_score_shadow_

float core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score_shadow_
private

Referenced by current_score(), report_final_score(), reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ default_2b_

std::pair< float, float > core::pack::guidance_scoreterms::sap::SapConstraintHelper::default_2b_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

◆ delta_sasa_scratch_

utility::vector0<float> core::pack::guidance_scoreterms::sap::SapConstraintHelper::delta_sasa_scratch_
private

Referenced by recalculate_sasa(), and resize_arrays().

◆ delta_sasa_zeros_

utility::vector0<float> core::pack::guidance_scoreterms::sap::SapConstraintHelper::delta_sasa_zeros_
private

Referenced by reset_calculation(), and resize_arrays().

◆ dirty_sasa_

utility::vector1<utility::vector0<bool> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::dirty_sasa_
private

Referenced by add_remove_rotamer(), recalculate_sasa(), reset_calculation(), setup_fast(), store_sasa_blocks(), and update_neighbors_sap().

◆ fake_lr_scorefxn_

core::scoring::ScoreFunctionOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_lr_scorefxn_
private

Referenced by fill_atom_neighbor_stuff(), and init().

◆ fake_rotamer_

core::conformation::ResidueCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_rotamer_
private

Referenced by init(), lightning_update_neighbors_sap(), reinit_with_resvect(), and reset_calculation().

◆ fake_sr_scorefxn_

core::scoring::ScoreFunctionOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::fake_sr_scorefxn_
private

◆ fast_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::fast_
private

Referenced by calculate_energy(), fill_atom_neighbor_stuff(), init(), init_with_pose(), recalculate_saps(), reinit_with_resvect(), reset_calculation(), set_accurate_sasa_and_recalc(), and symm_calculate_energy().

◆ heavy_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::heavy_
private

Referenced by init(), and my_natoms().

◆ interacting_block_

utility::vector1<uint8_t> core::pack::guidance_scoreterms::sap::SapConstraintHelper::interacting_block_
private

Referenced by fill_atom_neighbor_stuff(), and store_sasa_blocks().

◆ interacting_block_offset_

std::unordered_map< std::pair< conformation::Residue const *, conformation::Residue const *>, Size, RotamerRotamerHasher > core::pack::guidance_scoreterms::sap::SapConstraintHelper::interacting_block_offset_
private

Referenced by add_remove_rotamer(), and fill_atom_neighbor_stuff().

◆ internal_resvect_

utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::internal_resvect_
private

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), add_to_sap(), calculate_energy(), get_per_atom_sap(), lightning_update_neighbors_sap(), recalculate_saps(), recalculate_sasa(), report(), reset_calculation(), restore_from_shadow(), save_to_shadow(), set_accurate_sasa_and_recalc(), store_sasa_blocks(), symm_calculate_energy(), and update_neighbors_sap().

◆ internal_resvect_shadow_

utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::internal_resvect_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ lightning_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_
private

Referenced by calculate_energy(), init(), init_with_pose(), reinit_with_resvect(), resize_arrays(), restore_from_shadow(), save_to_shadow(), and symm_calculate_energy().

◆ lightning_aa_2_index_

utility::vector1< uint16_t > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_aa_2_index_
private

Referenced by lightning_1b_lookup(), lightning_2b_lookup(), and setup_lightning().

◆ lightning_current_res_sap_

utility::vector1< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_current_res_sap_
private

Referenced by add_remove_rotamer_lightning(), lightning_add_to_sap(), reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ lightning_current_res_sap_shadow_

utility::vector1< Real > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_current_res_sap_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ lightning_num_aas_

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_aas_
private

Referenced by lightning_1b_lookup(), lightning_2b_lookup(), and setup_lightning().

◆ lightning_num_aas_sq_

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_aas_sq_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

◆ lightning_num_seqpos_

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_num_seqpos_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

◆ lightning_rotamer_1b_sap_

utility::vector0< float > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_rotamer_1b_sap_
private

Referenced by lightning_1b_lookup(), and setup_lightning().

◆ lightning_rotamer_2b_sap_

utility::vector0< std::pair< float, float > > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_rotamer_2b_sap_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

◆ lightning_rotamer_2b_sap_map_

std::unordered_map< basic::datacache::ResRotPair, std::pair< float, float >, basic::datacache::ResRotPairHasher > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_rotamer_2b_sap_map_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

◆ lightning_seqpos_2_index_

utility::vector1< uint32_t > core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_seqpos_2_index_
private

Referenced by lightning_1b_lookup(), lightning_2b_lookup(), and setup_lightning().

◆ max_rotamer_atoms_

Size core::pack::guidance_scoreterms::sap::SapConstraintHelper::max_rotamer_atoms_
private

Referenced by fill_atom_neighbor_stuff(), fill_block_params(), reset_calculation(), resize_arrays(), and setup_fast().

◆ options_

SapConstraintOptionsCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::options_
private

Referenced by apply_residue_selectors(), init(), my_hydrophobic_weight(), and options().

◆ recalc_positions_scratch_

utility::vector1<Size> core::pack::guidance_scoreterms::sap::SapConstraintHelper::recalc_positions_scratch_
private

Referenced by calculate_energy(), and init().

◆ rotamer_to_block_param_offset_

std::unordered_map< conformation::Residue const*, Size > core::pack::guidance_scoreterms::sap::SapConstraintHelper::rotamer_to_block_param_offset_
private

Referenced by add_remove_rotamer(), convert_block_sasa_to_sasa_score(), and fill_block_params().

◆ rotamer_to_sasa_data_

atom_sasa_score_map core::pack::guidance_scoreterms::sap::SapConstraintHelper::rotamer_to_sasa_data_
private

Referenced by add_remove_rotamer_fast(), convert_block_sasa_to_sasa_score(), fill_atom_neighbor_stuff(), and find_lightning_2b().

◆ sap_calculate_positions_

utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::sap_calculate_positions_
private

Referenced by apply_residue_selectors(), calculate_energy(), fill_atom_neighbor_stuff(), fill_block_params(), get_per_atom_sap(), reinit_with_resvect(), report(), resize_arrays(), set_accurate_sasa_and_recalc(), setup_for_symmetry(), setup_lightning(), and symm_calculate_energy().

◆ sasa_blocks_

utility::vector1<utility::vector0<uint16_t> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_blocks_
private

Referenced by add_remove_rotamer(), recalculate_sasa(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and store_sasa_blocks().

◆ sasa_blocks_shadow_

utility::vector1<utility::vector0<uint16_t> > core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_blocks_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ sasa_positions_

utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::sasa_positions_
private

Referenced by apply_residue_selectors(), calculate_energy(), fill_atom_neighbor_stuff(), reinit_with_resvect(), resize_arrays(), set_accurate_sasa_and_recalc(), setup_for_symmetry(), and symm_calculate_energy().

◆ score_positions_

utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::score_positions_
private

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), add_to_sap(), apply_residue_selectors(), fill_block_params(), get_per_atom_sap(), lightning_add_to_sap(), lightning_update_neighbors_sap(), recalculate_saps(), reset_calculation(), resize_arrays(), setup_for_symmetry(), and update_neighbors_sap().

◆ shadow_mismatch_

utility::vector1<bool> core::pack::guidance_scoreterms::sap::SapConstraintHelper::shadow_mismatch_
private

Referenced by add_remove_rotamer(), add_remove_rotamer_fast(), add_remove_rotamer_lightning(), lightning_update_neighbors_sap(), recalculate_sasa(), reset_calculation(), restore_from_shadow(), save_to_shadow(), symm_calculate_energy(), and update_neighbors_sap().

◆ symm_debug_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_debug_
private

Referenced by init(), and setup_for_symmetry().

◆ symm_debug_force_map_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_debug_force_map_
private

Referenced by init(), and setup_lightning().

◆ symm_info_

conformation::symmetry::SymmetryInfoCOP core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_info_
private

Referenced by calculate_energy(), fill_atom_neighbor_stuff(), init_with_pose(), restore_from_shadow(), save_to_shadow(), setup_for_symmetry(), and symm_calculate_energy().

◆ symm_rotamer_to_other_rotamers_

std::unordered_map< core::conformation::Residue const *, utility::vector1< core::conformation::ResidueCOP > > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_rotamer_to_other_rotamers_
private

Referenced by setup_for_symmetry(), and symm_calculate_energy().

◆ symm_work_resvect_

utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_work_resvect_
private

Referenced by reset_calculation(), restore_from_shadow(), save_to_shadow(), and symm_calculate_energy().

◆ symm_work_resvect_shadow_

utility::vector1< core::conformation::ResidueCOP > core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_work_resvect_shadow_
private

Referenced by reset_calculation(), restore_from_shadow(), and save_to_shadow().

◆ use_2b_map_

bool core::pack::guidance_scoreterms::sap::SapConstraintHelper::use_2b_map_
private

Referenced by lightning_2b_lookup(), and setup_lightning().

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