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core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper Class Reference

#include <LK_DomeHelper.hh>

Public Member Functions

 LK_DomeHelper (core::scoring::lkball::LK_DomeEnergyCOP const &lk_dome, Real lk_dome_weight, Real lk_dome_iso_weight, Real lk_dome_bridge_weight, Real lk_dome_bridge_uncpl_weight, Real lk_ball_bridge2_weight, Real lk_ball_bridge_uncpl2_weight)
 
core::Real calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &current_rotamer_ids, core::Size const substitution_position)
 
void commit_considered_substitution ()
 
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
 

Protected Member Functions

void restore_from_shadow ()
 
void save_to_shadow ()
 
void reinit_with_resvect (utility::vector1< core::Size > const &current_rotamer_ids, bool skip_reset=false)
 
void reset_calculation ()
 
void resize_arrays (core::pose::Pose const &pose)
 
void init ()
 
void add_remove_rotamer (utility::vector1< core::Size > const &current_rotamer_ids, Size const substitution_position, bool add)
 
void add_waters (Size position, Size rotamer)
 
void init_water_scores (Size position)
 
uint32_t get_score_data_offset (uint32_t water_seqpos, uint16_t water_id, uint32_t other_seqpos, uint32_t other_rotamer)
 
void update_other_waters_inner (int8_t occlusion_delta, int16_t interact_delta, uint32_t water_seqpos, uint32_t total_water_offset)
 
void update_other_waters (Size position, bool adding)
 
void prepare_lkd_infos_and_assign_waters (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets, utility::vector1< utility::vector0< core::scoring::lkball::LKD_ResidueInfo >> &lkd_infos, utility::vector1< utility::vector0< MyWaterHolder >> &waters, utility::vector1< utility::vector0< utility::vector0< Size >>> &water_assignments)
 
void prepare_simple_rotamer_values (utility::vector1< utility::vector0< MyWaterHolder >> &waters, utility::vector1< utility::vector0< utility::vector0< Size >>> const &water_assignments)
 
void prepare_score_data (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets, utility::vector1< utility::vector0< core::scoring::lkball::LKD_ResidueInfo >> const &lkd_infos, utility::vector1< utility::vector0< MyWaterHolder >> const &waters, utility::vector1< utility::vector0< utility::vector0< Size >>> const &water_assignments)
 
core::scoring::lkball::LK_DomeEnergyCOP lk_dome () const
 
Size memory_use () const
 

Private Attributes

core::scoring::ScoreFunctionOP fake_lr_scorefxn_
 
core::scoring::lkball::LK_DomeEnergyCOP lk_dome_
 
Real lk_dome_weight_
 
Real lk_dome_iso_weight_
 
Real lk_dome_bridge_weight_
 
Real lk_dome_bridge_uncpl_weight_
 
Real lk_ball_bridge2_weight_
 
Real lk_ball_bridge_uncpl2_weight_
 
int64_t total_score_
 
utility::vector1< Size > current_rotamer_at_seqpos_
 
utility::vector1< int32_t > current_score_at_seqpos_
 
utility::vector1< int16_t > current_waters_
 
utility::vector1< int16_t > current_water_occl_sum_
 
utility::vector1< int32_t > current_water_interact_sum_
 
utility::vector1< bool > shadow_mismatch_
 
int64_t shadow_total_score_
 
utility::vector1< Size > shadow_current_rotamer_at_seqpos_
 
utility::vector1< int32_t > shadow_current_score_at_seqpos_
 
utility::vector1< int16_t > shadow_current_waters_
 
utility::vector1< int16_t > shadow_current_water_occl_sum_
 
utility::vector1< int32_t > shadow_current_water_interact_sum_
 
Real partial_score_scaler_
 
Real score_scaler_
 
uint8_t occlusion_min_
 
uint8_t occlusion_span_
 
uint32_t waters_per_seqpos_
 
utility::vector1< uint32_t > seqpos_to_rotamer_to_waters_masks_
 
utility::vector1< uint32_t > seqpos_to_water_to_pwp_index_list_
 
utility::vector1< uint32_t > seqpos_to_riww_at_pos_index_list_
 
utility::vector1< uint16_t > seqpos_num_unique_waters_
 
utility::vector1< uint8_t > seqpos_num_rotamers_32_
 
utility::vector1< uint32_t > rotamer_to_waters_masks_
 
utility::vector1< uint32_t > water_to_pwp_index_list_
 
utility::vector1< uint32_t > pos_water_pair_to_score_
 
utility::vector1< int8_t > score_data_
 
utility::vector1< uint32_t > riww_at_pos_index_list_
 
utility::vector1< uint32_t > rotamer_interacts_with_waters_at_pos_
 
bool debug_store_waters_
 
utility::pointer::shared_ptr< utility::vector1< utility::vector0< MyWaterHolder > > > debug_waters_
 

Friends

class ::LK_DomeEnergyTests
 

Constructor & Destructor Documentation

◆ LK_DomeHelper()

core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::LK_DomeHelper ( core::scoring::lkball::LK_DomeEnergyCOP const &  lk_dome,
Real  lk_dome_weight,
Real  lk_dome_iso_weight,
Real  lk_dome_bridge_weight,
Real  lk_dome_bridge_uncpl_weight,
Real  lk_ball_bridge2_weight,
Real  lk_ball_bridge_uncpl2_weight 
)

References init().

Member Function Documentation

◆ add_remove_rotamer()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::add_remove_rotamer ( utility::vector1< core::Size > const &  current_rotamer_ids,
Size const  substitution_position,
bool  add 
)
protected

References protocols::mean_field::add(), add_waters(), current_rotamer_at_seqpos_, current_score_at_seqpos_, init_water_scores(), shadow_mismatch_, total_score_, and update_other_waters().

Referenced by calculate_energy().

◆ add_waters()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::add_waters ( Size  position,
Size  rotamer 
)
protected

References current_waters_, rotamer_to_waters_masks_, seqpos_num_unique_waters_, seqpos_to_rotamer_to_waters_masks_, and waters_per_seqpos_.

Referenced by add_remove_rotamer(), and reinit_with_resvect().

◆ calculate_energy()

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

References add_remove_rotamer(), current_rotamer_at_seqpos_, reinit_with_resvect(), restore_from_shadow(), score_scaler_, and total_score_.

◆ commit_considered_substitution()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::commit_considered_substitution ( )

References save_to_shadow().

◆ current_score()

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_score ( ) const

References score_scaler_, and shadow_total_score_.

◆ get_score_data_offset()

uint32_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::get_score_data_offset ( uint32_t  water_seqpos,
uint16_t  water_id,
uint32_t  other_seqpos,
uint32_t  other_rotamer 
)
protected

References core::pack::guidance_scoreterms::lk_dome::bit_test(), core::pack::guidance_scoreterms::lk_dome::popcount_until_bit(), pos_water_pair_to_score_, PWP_BITFIELDS, PWP_OFFSET_INTO_SCORE_DATA, PWP_OTHER_SEQPOS, seqpos_num_rotamers_32_, seqpos_to_water_to_pwp_index_list_, and water_to_pwp_index_list_.

Referenced by update_other_waters().

◆ init()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::init ( )
protected

References core::scoring::methods::EnergyMethodOptions::etable_options(), core::scoring::fa_rep, fake_lr_scorefxn_, lk_dome_, and core::scoring::etable::EtableOptions::max_dis.

Referenced by LK_DomeHelper().

◆ init_water_scores()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::init_water_scores ( Size  position)
protected

References core::pack::guidance_scoreterms::lk_dome::bit_test(), current_rotamer_at_seqpos_, current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, current_waters_, FULLY_OCCLUDED, occlusion_min_, occlusion_span_, core::pack::guidance_scoreterms::lk_dome::popcount_until_bit(), pos_water_pair_to_score_, PWP_BITFIELDS, PWP_OFFSET_INTO_SCORE_DATA, PWP_OTHER_SEQPOS, score_data_, seqpos_num_rotamers_32_, seqpos_to_water_to_pwp_index_list_, shadow_mismatch_, total_score_, water_to_pwp_index_list_, and waters_per_seqpos_.

Referenced by add_remove_rotamer(), and reinit_with_resvect().

◆ init_with_pose()

core::pack::rotamer_set::RotamerSets core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::init_with_pose ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets 
)

References debug_store_waters_, debug_waters_, prepare_lkd_infos_and_assign_waters(), prepare_score_data(), prepare_simple_rotamer_values(), and resize_arrays().

◆ lk_dome()

core::scoring::lkball::LK_DomeEnergyCOP core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome ( ) const
protected

References lk_dome_.

◆ memory_use()

Size core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::memory_use ( ) const
protected

References current_rotamer_at_seqpos_, current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, current_waters_, pos_water_pair_to_score_, riww_at_pos_index_list_, rotamer_interacts_with_waters_at_pos_, rotamer_to_waters_masks_, score_data_, seqpos_num_rotamers_32_, seqpos_num_unique_waters_, seqpos_to_riww_at_pos_index_list_, seqpos_to_rotamer_to_waters_masks_, seqpos_to_water_to_pwp_index_list_, shadow_current_rotamer_at_seqpos_, shadow_current_score_at_seqpos_, shadow_current_water_interact_sum_, shadow_current_water_occl_sum_, shadow_current_waters_, shadow_mismatch_, water_to_pwp_index_list_, and waters_per_seqpos_.

Referenced by prepare_score_data().

◆ prepare_lkd_infos_and_assign_waters()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets,
utility::vector1< utility::vector0< core::scoring::lkball::LKD_ResidueInfo >> &  lkd_infos,
utility::vector1< utility::vector0< MyWaterHolder >> &  waters,
utility::vector1< utility::vector0< utility::vector0< Size >>> &  water_assignments 
)
protected

References core::conformation::Residue::atom_is_backbone(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::scoring::lkball::LKB_ResidueInfo::has_waters(), lk_dome_, core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::conformation::Residue::nheavyatoms(), core::scoring::pair, core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::pose::Pose::size(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), core::scoring::lkball::LKD_ResidueInfo::water_sol_values(), core::scoring::lkball::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by init_with_pose().

◆ prepare_score_data()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSets const &  rotamer_sets,
utility::vector1< utility::vector0< core::scoring::lkball::LKD_ResidueInfo >> const &  lkd_infos,
utility::vector1< utility::vector0< MyWaterHolder >> const &  waters,
utility::vector1< utility::vector0< utility::vector0< Size >>> const &  water_assignments 
)
protected

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_type_index(), core::pack::guidance_scoreterms::lk_dome::MyWaterHolder::base_xyz, core::pack::guidance_scoreterms::lk_dome::bit_set(), core::pack::create_packer_graph(), fake_lr_scorefxn_, core::pack::find_residue_max_radii(), FULLY_OCCLUDED, core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::conformation::Residue::is_protein(), protocols::stepwise::modeler::is_protein(), lk_ball_bridge2_weight_, lk_ball_bridge_uncpl2_weight_, lk_dome_, lk_dome_bridge_uncpl_weight_, lk_dome_bridge_weight_, lk_dome_iso_weight_, lk_dome_weight_, protocols::mean_field::max(), memory_use(), core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), occlusion_min_, occlusion_span_, partial_score_scaler_, pos_water_pair_to_score_, core::pose::Pose::residue(), riww_at_pos_index_list_, rotamer_interacts_with_waters_at_pos_, core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), score_data_, score_scaler_, seqpos_num_rotamers_32_, seqpos_to_riww_at_pos_index_list_, seqpos_to_water_to_pwp_index_list_, core::pose::Pose::size(), core::pack::guidance_scoreterms::lk_dome::MyWaterHolder::sol_value, core::scoring::electron_density::square(), core::pack::rotamer_set::RotamerSets::task(), core::pack::guidance_scoreterms::lk_dome::TR(), core::conformation::Residue::type(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), water_to_pwp_index_list_, core::pack::guidance_scoreterms::lk_dome::MyWaterHolder::water_xyz, core::scoring::lkball::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by init_with_pose().

◆ prepare_simple_rotamer_values()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_simple_rotamer_values ( utility::vector1< utility::vector0< MyWaterHolder >> &  waters,
utility::vector1< utility::vector0< utility::vector0< Size >>> const &  water_assignments 
)
protected

References core::pack::guidance_scoreterms::lk_dome::bit_set(), rotamer_to_waters_masks_, seqpos_num_rotamers_32_, seqpos_num_unique_waters_, seqpos_to_rotamer_to_waters_masks_, and waters_per_seqpos_.

Referenced by init_with_pose().

◆ reinit_with_resvect()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::reinit_with_resvect ( utility::vector1< core::Size > const &  current_rotamer_ids,
bool  skip_reset = false 
)
protected

References add_waters(), current_rotamer_at_seqpos_, init_water_scores(), reset_calculation(), and save_to_shadow().

Referenced by calculate_energy().

◆ reset_calculation()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::reset_calculation ( )
protected

References current_rotamer_at_seqpos_, current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, current_waters_, seqpos_to_rotamer_to_waters_masks_, shadow_current_rotamer_at_seqpos_, shadow_current_score_at_seqpos_, shadow_current_water_interact_sum_, shadow_current_water_occl_sum_, shadow_current_waters_, shadow_mismatch_, shadow_total_score_, total_score_, and waters_per_seqpos_.

Referenced by reinit_with_resvect().

◆ resize_arrays()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::resize_arrays ( core::pose::Pose const &  pose)
protected

Referenced by init_with_pose().

◆ restore_from_shadow()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::restore_from_shadow ( )
protected

References current_rotamer_at_seqpos_, current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, current_waters_, shadow_current_rotamer_at_seqpos_, shadow_current_score_at_seqpos_, shadow_current_water_interact_sum_, shadow_current_water_occl_sum_, shadow_current_waters_, shadow_mismatch_, shadow_total_score_, total_score_, and waters_per_seqpos_.

Referenced by calculate_energy().

◆ save_to_shadow()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::save_to_shadow ( )
protected

References current_rotamer_at_seqpos_, current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, current_waters_, shadow_current_rotamer_at_seqpos_, shadow_current_score_at_seqpos_, shadow_current_water_interact_sum_, shadow_current_water_occl_sum_, shadow_current_waters_, shadow_mismatch_, shadow_total_score_, total_score_, and waters_per_seqpos_.

Referenced by commit_considered_substitution(), and reinit_with_resvect().

◆ update_other_waters()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::update_other_waters ( Size  position,
bool  adding 
)
protected

References core::pack::guidance_scoreterms::lk_dome::bit_test(), current_rotamer_at_seqpos_, current_waters_, get_score_data_offset(), riww_at_pos_index_list_, rotamer_interacts_with_waters_at_pos_, score_data_, seqpos_num_unique_waters_, seqpos_to_riww_at_pos_index_list_, update_other_waters_inner(), and waters_per_seqpos_.

Referenced by add_remove_rotamer().

◆ update_other_waters_inner()

void core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::update_other_waters_inner ( int8_t  occlusion_delta,
int16_t  interact_delta,
uint32_t  water_seqpos,
uint32_t  total_water_offset 
)
protected

References current_score_at_seqpos_, current_water_interact_sum_, current_water_occl_sum_, FULLY_OCCLUDED, occlusion_min_, occlusion_span_, shadow_mismatch_, and total_score_.

Referenced by update_other_waters().

Friends And Related Function Documentation

◆ ::LK_DomeEnergyTests

friend class ::LK_DomeEnergyTests
friend

Member Data Documentation

◆ current_rotamer_at_seqpos_

utility::vector1<Size> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_rotamer_at_seqpos_
private

Referenced by add_remove_rotamer(), calculate_energy(), init_water_scores(), memory_use(), reinit_with_resvect(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters().

◆ current_score_at_seqpos_

utility::vector1<int32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_score_at_seqpos_
private

Referenced by add_remove_rotamer(), init_water_scores(), memory_use(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters_inner().

◆ current_water_interact_sum_

utility::vector1<int32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_water_interact_sum_
private

Referenced by init_water_scores(), memory_use(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters_inner().

◆ current_water_occl_sum_

utility::vector1<int16_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_water_occl_sum_
private

Referenced by init_water_scores(), memory_use(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters_inner().

◆ current_waters_

utility::vector1<int16_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::current_waters_
private

Referenced by add_waters(), init_water_scores(), memory_use(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters().

◆ debug_store_waters_

bool core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::debug_store_waters_
private

Referenced by init_with_pose().

◆ debug_waters_

utility::pointer::shared_ptr< utility::vector1<utility::vector0<MyWaterHolder> > > core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::debug_waters_
private

Referenced by init_with_pose().

◆ fake_lr_scorefxn_

core::scoring::ScoreFunctionOP core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::fake_lr_scorefxn_
private

Referenced by init(), and prepare_score_data().

◆ lk_ball_bridge2_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_ball_bridge2_weight_
private

Referenced by prepare_score_data().

◆ lk_ball_bridge_uncpl2_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_ball_bridge_uncpl2_weight_
private

Referenced by prepare_score_data().

◆ lk_dome_

core::scoring::lkball::LK_DomeEnergyCOP core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome_
private

Referenced by init(), lk_dome(), prepare_lkd_infos_and_assign_waters(), and prepare_score_data().

◆ lk_dome_bridge_uncpl_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome_bridge_uncpl_weight_
private

Referenced by prepare_score_data().

◆ lk_dome_bridge_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome_bridge_weight_
private

Referenced by prepare_score_data().

◆ lk_dome_iso_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome_iso_weight_
private

Referenced by prepare_score_data().

◆ lk_dome_weight_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::lk_dome_weight_
private

Referenced by prepare_score_data().

◆ occlusion_min_

uint8_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::occlusion_min_
private

Referenced by init_water_scores(), prepare_score_data(), and update_other_waters_inner().

◆ occlusion_span_

uint8_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::occlusion_span_
private

Referenced by init_water_scores(), prepare_score_data(), and update_other_waters_inner().

◆ partial_score_scaler_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::partial_score_scaler_
private

Referenced by prepare_score_data().

◆ pos_water_pair_to_score_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::pos_water_pair_to_score_
private

Referenced by get_score_data_offset(), init_water_scores(), memory_use(), and prepare_score_data().

◆ riww_at_pos_index_list_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::riww_at_pos_index_list_
private

Referenced by memory_use(), prepare_score_data(), and update_other_waters().

◆ rotamer_interacts_with_waters_at_pos_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::rotamer_interacts_with_waters_at_pos_
private

Referenced by memory_use(), prepare_score_data(), and update_other_waters().

◆ rotamer_to_waters_masks_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::rotamer_to_waters_masks_
private

Referenced by add_waters(), memory_use(), and prepare_simple_rotamer_values().

◆ score_data_

utility::vector1<int8_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::score_data_
private

Referenced by init_water_scores(), memory_use(), prepare_score_data(), and update_other_waters().

◆ score_scaler_

Real core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::score_scaler_
private

Referenced by calculate_energy(), current_score(), and prepare_score_data().

◆ seqpos_num_rotamers_32_

utility::vector1<uint8_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::seqpos_num_rotamers_32_
private

Referenced by get_score_data_offset(), init_water_scores(), memory_use(), prepare_score_data(), and prepare_simple_rotamer_values().

◆ seqpos_num_unique_waters_

utility::vector1<uint16_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::seqpos_num_unique_waters_
private

Referenced by add_waters(), memory_use(), prepare_simple_rotamer_values(), and update_other_waters().

◆ seqpos_to_riww_at_pos_index_list_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::seqpos_to_riww_at_pos_index_list_
private

Referenced by memory_use(), prepare_score_data(), and update_other_waters().

◆ seqpos_to_rotamer_to_waters_masks_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::seqpos_to_rotamer_to_waters_masks_
private

Referenced by add_waters(), memory_use(), prepare_simple_rotamer_values(), and reset_calculation().

◆ seqpos_to_water_to_pwp_index_list_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::seqpos_to_water_to_pwp_index_list_
private

Referenced by get_score_data_offset(), init_water_scores(), memory_use(), and prepare_score_data().

◆ shadow_current_rotamer_at_seqpos_

utility::vector1<Size> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_current_rotamer_at_seqpos_
private

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

◆ shadow_current_score_at_seqpos_

utility::vector1<int32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_current_score_at_seqpos_
private

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

◆ shadow_current_water_interact_sum_

utility::vector1<int32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_current_water_interact_sum_
private

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

◆ shadow_current_water_occl_sum_

utility::vector1<int16_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_current_water_occl_sum_
private

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

◆ shadow_current_waters_

utility::vector1<int16_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_current_waters_
private

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

◆ shadow_mismatch_

utility::vector1<bool> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_mismatch_
private

Referenced by add_remove_rotamer(), init_water_scores(), memory_use(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters_inner().

◆ shadow_total_score_

int64_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::shadow_total_score_
private

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

◆ total_score_

int64_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::total_score_
private

Referenced by add_remove_rotamer(), calculate_energy(), init_water_scores(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters_inner().

◆ water_to_pwp_index_list_

utility::vector1<uint32_t> core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::water_to_pwp_index_list_
private

Referenced by get_score_data_offset(), init_water_scores(), memory_use(), and prepare_score_data().

◆ waters_per_seqpos_

uint32_t core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::waters_per_seqpos_
private

Referenced by add_waters(), init_water_scores(), memory_use(), prepare_simple_rotamer_values(), reset_calculation(), restore_from_shadow(), save_to_shadow(), and update_other_waters().

The documentation for this class was generated from the following files:
Generated on Thu Sep 11 2025 16:58:08 for Rosetta by doxygen 1.9.1