ApproximateBuriedUnsatPenalty()=delete | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | |
ApproximateBuriedUnsatPenalty(core::scoring::methods::EnergyMethodOptions const &options) | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | |
assume_const_backbone_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
atomic_interaction_cutoff() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
backbone_backbone_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
bump_energy_backbone(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const | core::scoring::methods::TwoBodyEnergy | virtual |
bump_energy_full(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const | core::scoring::methods::TwoBodyEnergy | virtual |
burial_atomic_depth_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
burial_probe_radius_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
burial_resolution_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
clone() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
ContextDependentTwoBodyEnergy(EnergyMethodCreatorOP creator) | core::scoring::methods::ContextDependentTwoBodyEnergy | |
cor_opt_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
defines_intrares_dof_derivatives(pose::Pose const &p) const | core::scoring::methods::TwoBodyEnergy | virtual |
defines_intrares_energy(scoring::EnergyMap const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
defines_intrares_energy_for_residue(conformation::Residue const &res) const | core::scoring::methods::TwoBodyEnergy | virtual |
defines_score_for_residue_pair(conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const | core::scoring::methods::TwoBodyEnergy | virtual |
divides_backbone_and_sidechain_energetics() const | core::scoring::methods::ShortRangeTwoBodyEnergy | virtual |
energy_method_is_unpublished() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
energy_method_provides_citation_info() const | core::scoring::methods::EnergyMethod | virtual |
EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const | core::scoring::methods::EnergyMethod | virtual |
eval_intrares_derivatives(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const | core::scoring::methods::TwoBodyEnergy | virtual |
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &emap) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
eval_intrares_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
eval_intraresidue_dof_derivative(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const | core::scoring::methods::TwoBodyEnergy | virtual |
eval_residue_pair_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const | core::scoring::methods::TwoBodyEnergy | virtual |
evaluate_rotamer_background_energies(conformation::RotamerSetBase const &, conformation::Residue const &, pose::Pose const &, scoring::ScoreFunction const &, scoring::EnergyMap const &, utility::vector1< core::PackerEnergy > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
evaluate_rotamer_background_energy_maps(conformation::RotamerSetBase const &, conformation::Residue const &, pose::Pose const &, scoring::ScoreFunction const &, scoring::EnergyMap const &, utility::vector1< scoring::EnergyMap > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
evaluate_rotamer_intrares_energies(conformation::RotamerSetBase const &set, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, utility::vector1< scoring::EnergyMap > &emaps) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
evaluate_rotamer_pair_energies(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
finalize_after_minimizing(pose::Pose &pose) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
finalize_total_energy(pose::Pose &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &total_energy) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
get_energies_cache(pose::Pose const &pose) const | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
hbond_bonus_opt_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
hbond_energy_threshold_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
IDLE enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
indicate_required_context_graphs(utility::vector1< bool > &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
method_type() const override | core::scoring::methods::ContextDependentTwoBodyEnergy | virtual |
minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
MINIMIZING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
Mode enum name | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
mode_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
oversat_penalty_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
PACKING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
parent typedef | core::scoring::methods::ContextDependentTwoBodyEnergy | |
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
provide_authorship_info_for_unpublished() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
provide_citation_info() const | core::scoring::methods::EnergyMethod | virtual |
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
requires_a_setup_for_derivatives_for_residue_pair_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
requires_a_setup_for_scoring_for_residue_pair_opportunity(pose::Pose const &pose) const | core::scoring::methods::TwoBodyEnergy | virtual |
residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap &emap) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
residue_pair_energy_ext(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
score_types() const | core::scoring::methods::EnergyMethod | inline |
scorefxn_bb_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
scorefxn_hbond_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
scorefxn_sc_ | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
SCORING enum value | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | private |
set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
setup_for_derivatives_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
setup_for_minimizing(pose::Pose &, scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, basic::datacache::BasicDataCache &residue_data_cache, ResSingleMinimizationData &res_data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
setup_for_minimizing_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, scoring::ScoreFunction const &sfxn) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
setup_for_scoring(pose::Pose &, scoring::ScoreFunction const &) const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | virtual |
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const | core::scoring::methods::TwoBodyEnergy | virtual |
core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const | core::scoring::methods::EnergyMethod | virtual |
setup_for_scoring_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const | core::scoring::methods::TwoBodyEnergy | virtual |
ShortRangeTwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::ShortRangeTwoBodyEnergy | |
show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
sidechain_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const | core::scoring::methods::TwoBodyEnergy | virtual |
symm_vs_self_asu_resnum1 | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
symm_vs_self_asu_resnum2 | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
symm_vs_self_rotamer_count | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | mutableprivate |
TwoBodyEnergy(EnergyMethodCreatorOP) | core::scoring::methods::TwoBodyEnergy | |
update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
use_extended_intrares_energy_interface() const | core::scoring::methods::TwoBodyEnergy | virtual |
use_extended_residue_pair_energy_interface() const | core::scoring::methods::TwoBodyEnergy | virtual |
version() const override | core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty | inlinevirtual |
~ContextDependentTwoBodyEnergy() override | core::scoring::methods::ContextDependentTwoBodyEnergy | |
~ShortRangeTwoBodyEnergy() override | core::scoring::methods::ShortRangeTwoBodyEnergy | |
~TwoBodyEnergy() override | core::scoring::methods::TwoBodyEnergy | |