| ::SapConstraintEnergyTests class | core::pack::guidance_scoreterms::sap::SapConstraintHelper | friend |
| add_remove_rotamer(utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| add_remove_rotamer_fast(utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| add_remove_rotamer_lightning(utility::vector1< core::conformation::ResidueCOP > const &resvect, Size const substitution_position, bool add) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| 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::guidance_scoreterms::sap::SapConstraintHelper | protected |
| add_to_sap(float amount, Size seqpos, Size iat) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| all_block_params_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| apply_residue_selectors(core::pose::Pose const &pose) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| atom_sap_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sap_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sasa_score_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sasa_score_fast_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sasa_score_fast_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sasa_score_map typedef | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| atom_sasa_score_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_sasa_score_value typedef | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| atom_within_5_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_within_5_map_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| atom_within_5_value typedef | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| block_param_offset_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| block_param_offset_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| calculate_block(Real dist2, Real radius_us, Real radius_them) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| calculate_energy(utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| check_positions_block_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| check_positions_sap_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| commit_considered_substitution() | 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) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| current_score() const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| current_score_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| current_score_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| delta_sasa_scratch_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| delta_sasa_zeros_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| dirty_sasa_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| fake_lr_scorefxn_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| fake_rotamer_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| fake_sr_scorefxn_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| fast_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| fill_atom_neighbor_stuff(core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| fill_block_params(core::pose::Pose const &pose, pack::rotamer_set::RotamerSets const &rotamer_sets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| find_lightning_2b(conformation::ResidueCOP const &from_rot, conformation::ResidueCOP const &to_rot) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| get_per_atom_sap(pose::Pose const &pose) const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| heavy_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| init() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| init_with_pose(core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| interacting_block_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| interacting_block_offset_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| internal_resvect_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| internal_resvect_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_1b_lookup(chemical::AA aa, Size seqpos) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| lightning_2b_lookup(chemical::AA aa1, Size seqpos1, chemical::AA aa2, Size seqpos2) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| lightning_aa_2_index_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_add_to_sap(float amount, Size seqpos) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| lightning_current_res_sap_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_current_res_sap_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_num_aas_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_num_aas_sq_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_num_seqpos_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_rotamer_1b_sap_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_rotamer_2b_sap_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_seqpos_2_index_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| lightning_update_neighbors_sap(Size seqpos, bool invert, bool dont_update_self) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| max_rotamer_atoms_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| my_natoms(core::conformation::ResidueCOP const &res) const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| my_natoms(core::conformation::Residue const *res) const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| options() const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| options_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| recalc_positions_scratch_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| recalculate_saps(utility::vector1< Size > const &positions_to_update) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| recalculate_sasa() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| reinit_with_resvect(utility::vector1< core::conformation::ResidueCOP > const &resvect, bool skip_reset=false) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| report() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| report_final_score(Real actual_sap) const | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| reset_calculation() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| resize_arrays(core::pose::Pose const &pose) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| restore_from_shadow() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| rotamer_to_block_param_offset_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| rotamer_to_sasa_data_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| sap_calculate_positions_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| SapConstraintHelper(SapConstraintOptionsCOP const &options) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| sasa_blocks_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| sasa_blocks_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| sasa_positions_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| save_to_shadow() | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| score_positions_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| set_accurate_sasa_and_recalc(pose::Pose const &pose) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | |
| setup_fast(core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| setup_for_symmetry(core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotsets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| setup_lightning(core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamer_sets) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| shadow_mismatch_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| store_sasa_blocks(Size &offset, Size seqpos, bool add, bool mark_dirty) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| symm_calculate_energy(utility::vector1< core::conformation::ResidueCOP > const &resvect, core::Size const substitution_position) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| symm_debug_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| symm_info_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| symm_rotamer_to_other_rotamers_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| symm_work_resvect_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| symm_work_resvect_shadow_ | core::pack::guidance_scoreterms::sap::SapConstraintHelper | private |
| type_atom_within_5_map typedef | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
| update_neighbors_sap(float const *delta_sasa_score, Size seqpos, bool invert, bool skip_self) | core::pack::guidance_scoreterms::sap::SapConstraintHelper | protected |
1.8.7