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core::scoring::elec::FA_ElecEnergy Member List

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

__pad0__core::scoring::elec::FA_ElecEnergy
atomic_interaction_cutoff() const overridecore::scoring::elec::FA_ElecEnergyvirtual
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::elec::FA_ElecEnergyvirtual
backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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
clone() const overridecore::scoring::elec::FA_ElecEnergyvirtual
ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentTwoBodyEnergy
coulomb() const core::scoring::elec::FA_ElecEnergyinline
coulomb_core::scoring::elec::FA_ElecEnergyprivate
count_pair_full_core::scoring::elec::FA_ElecEnergyprivate
count_pair_hybrid_core::scoring::elec::FA_ElecEnergyprivate
cp_rep_map_core::scoring::elec::FA_ElecEnergyprivate
create_rotamer_trie(conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const core::scoring::elec::FA_ElecEnergyprivate
create_rotamer_trie(conformation::Residue const &res, pose::Pose const &) const core::scoring::elec::FA_ElecEnergyprivate
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::elec::FA_ElecEnergyvirtual
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 overridecore::scoring::elec::FA_ElecEnergyvirtual
divides_backbone_and_sidechain_energetics() const overridecore::scoring::elec::FA_ElecEnergyinlinevirtual
elec_weight(bool intra_res, bool at1isbb, bool at2isbb, weight_triple const &wts) const core::scoring::elec::FA_ElecEnergyinline
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
eval_atom_derivative(id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const overridecore::scoring::elec::FA_ElecEnergy
core::scoring::methods::ContextIndependentTwoBodyEnergy::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::EnergyMethodvirtual
eval_intrares_derivatives(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const overridecore::scoring::elec::FA_ElecEnergyvirtual
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sf, EnergyMap &emap) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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_intrares_ST_only() const core::scoring::elec::FA_ElecEnergyinline
eval_intrares_ST_only_core::scoring::elec::FA_ElecEnergyprivate
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_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::elec::FA_ElecEnergyvirtual
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::elec::FA_ElecEnergyvirtual
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 overridecore::scoring::elec::FA_ElecEnergyvirtual
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::elec::FA_ElecEnergyvirtual
exclude_DNA_DNA_core::scoring::elec::FA_ElecEnergyprivate
exclude_monomer_core::scoring::elec::FA_ElecEnergyprivate
exclude_protein_protein_core::scoring::elec::FA_ElecEnergyprivate
exclude_RNA_protein_core::scoring::elec::FA_ElecEnergyprivate
exclude_RNA_RNA_core::scoring::elec::FA_ElecEnergyprivate
FA_ElecEnergy()=deletecore::scoring::elec::FA_ElecEnergy
FA_ElecEnergy(methods::EnergyMethodOptions const &options)core::scoring::elec::FA_ElecEnergy
FA_ElecEnergy(FA_ElecEnergy const &src)core::scoring::elec::FA_ElecEnergy
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::elec::FA_ElecEnergyvirtual
get_count_pair_function(Size const, Size const, pose::Pose const &, ScoreFunction const &) const core::scoring::elec::FA_ElecEnergy
get_count_pair_function(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::scoring::elec::FA_ElecEnergy
get_count_pair_function_trie(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::elec::FA_ElecEnergyprivate
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::elec::FA_ElecEnergyprivate
get_countpair_representative_atom(core::chemical::ResidueType const &restype, core::Size atm_i) const core::scoring::elec::FA_ElecEnergy
get_intrares_countpair(conformation::Residue const &, pose::Pose const &, ScoreFunction const &sf) const core::scoring::elec::FA_ElecEnergy
hydrogen_interaction_cutoff() const core::scoring::elec::FA_ElecEnergyinline
hydrogen_interaction_cutoff2() const core::scoring::elec::FA_ElecEnergyinline
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const overridecore::scoring::elec::FA_ElecEnergyvirtual
initialize()core::scoring::elec::FA_ElecEnergy
method_type() const overridecore::scoring::methods::ContextIndependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &pose) const overridecore::scoring::elec::FA_ElecEnergyvirtual
monomer_test(Size irsd, Size jrsd) const core::scoring::elec::FA_ElecEnergyprivate
nres_monomer_core::scoring::elec::FA_ElecEnergymutableprivate
parent typedefcore::scoring::methods::ContextIndependentTwoBodyEnergy
prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &set) const overridecore::scoring::elec::FA_ElecEnergyvirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const core::scoring::methods::EnergyMethodvirtual
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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 &) const overridecore::scoring::elec::FA_ElecEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const core::scoring::methods::EnergyMethodvirtual
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 &, EnergyMap &emap) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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 overridecore::scoring::elec::FA_ElecEnergyvirtual
score_atom_pair(conformation::Residue const &res1, conformation::Residue const &res2, Size const at1, Size const at2, EnergyMap &emap, Real const cpweight, Real &d2) const core::scoring::elec::FA_ElecEnergyinlineprivate
score_types() const core::scoring::methods::EnergyMethodinline
set_nres_mono(core::pose::Pose const &pose) const core::scoring::elec::FA_ElecEnergyprivate
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &) const overridecore::scoring::elec::FA_ElecEnergyvirtual
setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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 &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const overridecore::scoring::elec::FA_ElecEnergyvirtual
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, basic::datacache::BasicDataCache &, ResSingleMinimizationData &resdata) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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 overridecore::scoring::elec::FA_ElecEnergyvirtual
setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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::elec::FA_ElecEnergyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &sfxn, ResSingleMinimizationData &resdata) const overridecore::scoring::elec::FA_ElecEnergyvirtual
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::EnergyMethodvirtual
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
setup_weight_triple(EnergyMap const &weights, weight_triple &wttrip) const core::scoring::elec::FA_ElecEnergyprivate
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::elec::FA_ElecEnergyvirtual
TwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::TwoBodyEnergy
update_residue_for_packing(pose::Pose &pose, Size resid) const overridecore::scoring::elec::FA_ElecEnergyvirtual
use_cp_rep_core::scoring::elec::FA_ElecEnergyprivate
use_extended_intrares_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() const overridecore::scoring::elec::FA_ElecEnergyvirtual
version() const overridecore::scoring::elec::FA_ElecEnergyprivatevirtual
~ContextIndependentTwoBodyEnergy() overridecore::scoring::methods::ContextIndependentTwoBodyEnergy
~ShortRangeTwoBodyEnergy() overridecore::scoring::methods::ShortRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy
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