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core::scoring::methods::MMLJEnergyInter Member List

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

atomic_interaction_cutoff() const overridecore::scoring::methods::MMLJEnergyIntervirtual
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 core::scoring::methods::TwoBodyEnergyvirtual
backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const core::scoring::methods::TwoBodyEnergyvirtual
bump_energy_backbone(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::methods::MMLJEnergyIntervirtual
bump_energy_full(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::methods::MMLJEnergyIntervirtual
clone() const overridecore::scoring::methods::MMLJEnergyIntervirtual
ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentTwoBodyEnergy
create_rotamer_trie(conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const core::scoring::methods::MMLJEnergyInter
create_rotamer_trie(conformation::Residue const &res, pose::Pose const &pose) const core::scoring::methods::MMLJEnergyInter
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::methods::MMLJEnergyIntervirtual
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 core::scoring::methods::ShortRangeTwoBodyEnergyvirtual
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const overridecore::scoring::methods::MMLJEnergyIntervirtual
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 &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const overridecore::scoring::methods::MMLJEnergyIntervirtual
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_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::TwoBodyEnergyvirtual
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::methods::MMLJEnergyIntervirtual
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::methods::MMLJEnergyIntervirtual
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 &sfxn, EnergyMap &total_energy) const core::scoring::methods::EnergyMethodvirtual
get_count_pair_function(Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::methods::MMLJEnergyInter
get_count_pair_function(conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::methods::MMLJEnergyInter
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::methods::MMLJEnergyInter
get_count_pair_function_trie(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::methods::MMLJEnergyInter
get_intrares_countpair(conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const core::scoring::methods::MMLJEnergyInter
heavyatom_heavyatom_energy(core::scoring::mm::mmtrie::MMEnergyTableAtom const &at1, core::scoring::mm::mmtrie::MMEnergyTableAtom const &at2, DistanceSquared &d2, Size &path_dist) const core::scoring::methods::MMLJEnergyInterinline
heavyatom_hydrogenatom_energy(core::scoring::mm::mmtrie::MMEnergyTableAtom const &at1, core::scoring::mm::mmtrie::MMEnergyTableAtom const &at2, Size &path_dist, core::scoring::trie::TrieVsTrieCachedDataContainerBase const *const ) const core::scoring::methods::MMLJEnergyInterinline
hydrogen_interaction_cutoff() const core::scoring::methods::MMLJEnergyInterinline
hydrogen_interaction_cutoff2() const core::scoring::methods::MMLJEnergyInterinline
hydrogenatom_heavyatom_energy(core::scoring::mm::mmtrie::MMEnergyTableAtom const &at1, core::scoring::mm::mmtrie::MMEnergyTableAtom const &at2, Size &path_dist, core::scoring::trie::TrieVsTrieCachedDataContainerBase const *const ) const core::scoring::methods::MMLJEnergyInterinline
hydrogenatom_hydrogenatom_energy(core::scoring::mm::mmtrie::MMEnergyTableAtom const &at1, core::scoring::mm::mmtrie::MMEnergyTableAtom const &at2, Size &path_dist, core::scoring::trie::TrieVsTrieCachedDataContainerBase const *const ) const core::scoring::methods::MMLJEnergyInterinline
indicate_required_context_graphs(utility::vector1< bool > &) const overridecore::scoring::methods::MMLJEnergyIntervirtual
method_type() const overridecore::scoring::methods::ContextIndependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const core::scoring::methods::EnergyMethodvirtual
MMLJEnergyInter()core::scoring::methods::MMLJEnergyInter
parent typedefcore::scoring::methods::MMLJEnergyInter
potential_core::scoring::methods::MMLJEnergyInterprivate
prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &set) const overridecore::scoring::methods::MMLJEnergyIntervirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const core::scoring::methods::EnergyMethodvirtual
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
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 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::methods::MMLJEnergyIntervirtual
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
score_types() const core::scoring::methods::EnergyMethodinline
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const core::scoring::methods::EnergyMethodvirtual
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::TwoBodyEnergyvirtual
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::methods::MMLJEnergyIntervirtual
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::TwoBodyEnergyvirtual
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::TwoBodyEnergyvirtual
setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const overridecore::scoring::methods::MMLJEnergyIntervirtual
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 &, ScoreFunction const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const core::scoring::methods::TwoBodyEnergyvirtual
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
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 core::scoring::methods::TwoBodyEnergyvirtual
TwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::TwoBodyEnergy
update_residue_for_packing(pose::Pose &pose, Size resid) const overridecore::scoring::methods::MMLJEnergyIntervirtual
use_extended_intrares_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
version() const overridecore::scoring::methods::MMLJEnergyInterprivatevirtual
~ContextIndependentTwoBodyEnergy() overridecore::scoring::methods::ContextIndependentTwoBodyEnergy
~ShortRangeTwoBodyEnergy() overridecore::scoring::methods::ShortRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy