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core::scoring::lkball::LK_BallEnergy Member List

This is the complete list of members for core::scoring::lkball::LK_BallEnergy, including all inherited members.

__pad0__core::scoring::lkball::LK_BallEnergy
accumulate_single_atom_contributions(Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, AtomWeights const &atom1_wts, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const core::scoring::lkball::LK_BallEnergy
atom_type_is_charged_core::scoring::lkball::LK_BallEnergyprivate
atomic_interaction_cutoff() const overridecore::scoring::lkball::LK_BallEnergyvirtual
atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &p) const core::scoring::methods::TwoBodyEnergyvirtual
backbone_backbone_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::lkball::LK_BallEnergyvirtual
backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::lkball::LK_BallEnergyvirtual
bump_energy_backbone(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const core::scoring::methods::TwoBodyEnergyvirtual
bump_energy_full(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const core::scoring::methods::TwoBodyEnergyvirtual
calculate_lk_ball_atom_energies(Size const atom1, conformation::Residue const &rsd1, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const core::scoring::lkball::LK_BallEnergy
calculate_lk_ball_atom_energies_cp(Size const atom1, conformation::Residue const &rsd1, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, etable::count_pair::CPCrossoverBehavior const &cp_crossover, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const core::scoring::lkball::LK_BallEnergy
calculate_lk_desolvation_of_single_atom_by_residue(Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)core::scoring::lkball::LK_BallEnergy
calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)core::scoring::lkball::LK_BallEnergy
clone() const overridecore::scoring::lkball::LK_BallEnergyvirtual
ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentTwoBodyEnergy
create_rotamer_trie(conformation::RotamerSetBase const &rotset) const core::scoring::lkball::LK_BallEnergyprivate
create_rotamer_trie(conformation::Residue const &res) const core::scoring::lkball::LK_BallEnergyprivate
d2_low_core::scoring::lkball::LK_BallEnergyprivate
defines_high_order_terms(pose::Pose const &) const core::scoring::methods::EnergyMethodvirtual
defines_intrares_dof_derivatives(pose::Pose const &p) const core::scoring::methods::TwoBodyEnergyvirtual
defines_intrares_energy(EnergyMap const &) const overridecore::scoring::lkball::LK_BallEnergyinlinevirtual
defines_intrares_energy_for_residue(conformation::Residue const &res) const core::scoring::methods::TwoBodyEnergyvirtual
defines_score_for_residue_pair(conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const core::scoring::methods::TwoBodyEnergyvirtual
divides_backbone_and_sidechain_energetics() const overridecore::scoring::lkball::LK_BallEnergyvirtual
dsolv1_core::scoring::lkball::LK_BallEnergyprivate
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
etable() const core::scoring::lkball::LK_BallEnergy
etable_core::scoring::lkball::LK_BallEnergyprivate
etable_bins_per_A2() const core::scoring::lkball::LK_BallEnergyinline
etable_bins_per_A2_core::scoring::lkball::LK_BallEnergyprivate
eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const overridecore::scoring::lkball::LK_BallEnergyvirtual
eval_d_lk_fraction_dr_over_r(Real const d2_delta, Real const width) const core::scoring::lkball::LK_BallEnergy
eval_desolvation_derivs_no_count_pair(Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv)core::scoring::lkball::LK_BallEnergy
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::TwoBodyEnergyvirtual
eval_intrares_energy(conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const overridecore::scoring::lkball::LK_BallEnergyinlinevirtual
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::TwoBodyEnergyvirtual
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::TwoBodyEnergyvirtual
eval_lk_fraction(Real const d2_delta, Real const width) const core::scoring::lkball::LK_BallEnergy
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 overridecore::scoring::lkball::LK_BallEnergyvirtual
evaluate_rotamer_background_energies(conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const overridecore::scoring::lkball::LK_BallEnergyvirtual
evaluate_rotamer_background_energy_maps(conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const overridecore::scoring::methods::ShortRangeTwoBodyEnergyvirtual
evaluate_rotamer_intrares_energies(conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const core::scoring::methods::TwoBodyEnergyvirtual
evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const core::scoring::methods::TwoBodyEnergyvirtual
evaluate_rotamer_pair_energies(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const overridecore::scoring::lkball::LK_BallEnergyvirtual
fasol_max_dis2() const core::scoring::lkball::LK_BallEnergyinline
fasol_max_dis2_core::scoring::lkball::LK_BallEnergyprivate
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const core::scoring::methods::EnergyMethodvirtual
finalize_after_minimizing(pose::Pose &pose) const core::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const overridecore::scoring::lkball::LK_BallEnergyvirtual
get_count_pair_function_trie(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::lkball::LK_BallEnergyprivate
get_count_pair_function_trie(conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::lkball::LK_BallEnergyprivate
get_d2_low(core::Size idx) const core::scoring::lkball::LK_BallEnergyinline
get_lk_fractional_contribution(Vector const &atom2_xyz, Size const atom2_type_index, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, WaterDerivContributions &d_weighted_d2_d_di, Real &weighted_water_dis2) const core::scoring::lkball::LK_BallEnergy
get_lk_fractional_contribution(Vector const &atom2_xyz, Size const atom2_type_index, Size const atom1_n_attached_waters, Size const atom1_water_offset, WaterCoords const &rsd1_waters) const core::scoring::lkball::LK_BallEnergy
get_lk_fractional_contribution_for_single_water(Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const core::scoring::lkball::LK_BallEnergy
get_lkbr_fractional_contribution(Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const core::scoring::lkball::LK_BallEnergy
get_lkbr_fractional_contribution(Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters, WaterDerivVectors &d_weighted_d2_d_di1, Real &weighted_d2_water_delta, Real &pointterm_lkbr, Real &angleterm_lkbr, Real &d_angleterm_lkbr_dr, bool compute_derivs=true) const core::scoring::lkball::LK_BallEnergy
get_lkbr_fractional_contribution_noangle(Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const core::scoring::lkball::LK_BallEnergy
get_lkbridge_angle_widthscale() const core::scoring::lkball::LK_BallEnergyinline
get_multi_water_fade() const core::scoring::lkball::LK_BallEnergyinline
get_overlap_gap2() const core::scoring::lkball::LK_BallEnergyinline
get_overlap_target_len2() const core::scoring::lkball::LK_BallEnergyinline
get_overlap_width_A2() const core::scoring::lkball::LK_BallEnergyinline
get_ramp_width_A2() const core::scoring::lkball::LK_BallEnergyinline
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const overridecore::scoring::lkball::LK_BallEnergyvirtual
lk_ball_prefactor_core::scoring::lkball::LK_BallEnergyprivate
LK_BallEnergy(methods::EnergyMethodOptions const &options)core::scoring::lkball::LK_BallEnergy
LK_BallEnergy(LK_BallEnergy const &src)core::scoring::lkball::LK_BallEnergy
lkb_max_dis() const core::scoring::lkball::LK_BallEnergyinline
lkb_max_dis2() const core::scoring::lkball::LK_BallEnergyinline
lkb_max_dis2_core::scoring::lkball::LK_BallEnergyprivate
lkb_max_dis_core::scoring::lkball::LK_BallEnergyprivate
lkbridge_angle_widthscale_core::scoring::lkball::LK_BallEnergyprivate
method_type() const overridecore::scoring::methods::ContextIndependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const overridecore::scoring::lkball::LK_BallEnergyvirtual
multi_water_fade_core::scoring::lkball::LK_BallEnergyprivate
overlap_gap2_core::scoring::lkball::LK_BallEnergyprivate
overlap_target_len2_core::scoring::lkball::LK_BallEnergyprivate
overlap_width_A2_core::scoring::lkball::LK_BallEnergyprivate
parent typedefcore::scoring::methods::ContextIndependentTwoBodyEnergy
prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const overridecore::scoring::lkball::LK_BallEnergyvirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const core::scoring::methods::EnergyMethodvirtual
ramp_width_A2_core::scoring::lkball::LK_BallEnergyprivate
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &) const overridecore::scoring::lkball::LK_BallEnergyvirtual
requires_a_setup_for_derivatives_for_residue_pair_opportunity(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const overridecore::scoring::lkball::LK_BallEnergyvirtual
requires_a_setup_for_scoring_for_residue_pair_opportunity(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::lkball::LK_BallEnergyvirtual
residue_pair_energy(conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, ScoreFunction const &sf, EnergyMap &emap) const core::scoring::lkball::LK_BallEnergy
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::TwoBodyEnergyvirtual
ResidueType typedefcore::scoring::lkball::LK_BallEnergy
score_types() const core::scoring::methods::EnergyMethodinline
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_d2_bounds()core::scoring::lkball::LK_BallEnergy
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &scfxn) const overridecore::scoring::lkball::LK_BallEnergyvirtual
setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &residue_data_cache) const overridecore::scoring::lkball::LK_BallEnergyvirtual
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::TwoBodyEnergyvirtual
setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, basic::datacache::BasicDataCache &res_data_cache, ResSingleMinimizationData &resdata) const overridecore::scoring::lkball::LK_BallEnergyvirtual
setup_for_minimizing_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData const &res1data, ResSingleMinimizationData const &res2data, ResPairMinimizationData &pairdata) const overridecore::scoring::lkball::LK_BallEnergyvirtual
setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const overridecore::scoring::lkball::LK_BallEnergyvirtual
setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const core::scoring::methods::EnergyMethodvirtual
setup_for_scoring(pose::Pose &pose, ScoreFunction const &) const overridecore::scoring::lkball::LK_BallEnergyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const overridecore::scoring::lkball::LK_BallEnergyvirtual
core::scoring::methods::ContextIndependentTwoBodyEnergy::setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const core::scoring::methods::TwoBodyEnergyvirtual
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::TwoBodyEnergyvirtual
ShortRangeTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ShortRangeTwoBodyEnergy
show_additional_info(std::ostream &, pose::Pose &, bool) const core::scoring::methods::EnergyMethodvirtual
sidechain_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::lkball::LK_BallEnergyvirtual
Sizes typedefcore::scoring::lkball::LK_BallEnergy
slim_etable() const core::scoring::lkball::LK_BallEnergyinline
slim_etable_core::scoring::lkball::LK_BallEnergyprivate
solv1() const core::scoring::lkball::LK_BallEnergyinline
solv1_core::scoring::lkball::LK_BallEnergyprivate
solv2() const core::scoring::lkball::LK_BallEnergyinline
solv2_core::scoring::lkball::LK_BallEnergyprivate
sum_deriv_contributions_for_heavyatom_pair(Real const d2, Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &, EnergyMap const &weights, Real const cp_weight, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const core::scoring::lkball::LK_BallEnergy
sum_deriv_contributions_for_heavyatom_pair_one_way(Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap const &weights, Real const weight_factor, Real const d2, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const core::scoring::lkball::LK_BallEnergy
TwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::TwoBodyEnergy
update_residue_for_packing(pose::Pose &, Size resid) const overridecore::scoring::lkball::LK_BallEnergyvirtual
use_extended_intrares_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
Vectors typedefcore::scoring::lkball::LK_BallEnergy
version() const overridecore::scoring::lkball::LK_BallEnergyvirtual
~ContextIndependentTwoBodyEnergy() overridecore::scoring::methods::ContextIndependentTwoBodyEnergy
~ShortRangeTwoBodyEnergy() overridecore::scoring::methods::ShortRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy
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