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core::scoring::vdwaals::VDW_Energy Member List

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

__pad0__core::scoring::vdwaals::VDW_Energy
atom_pair_energy(VDWAtom const &at1, VDWAtom const &at2, Real &d2) constcore::scoring::vdwaals::VDW_Energyinline
atom_type_set_name_core::scoring::vdwaals::VDW_Energyprivate
atom_vdw_core::scoring::vdwaals::VDW_Energyprivate
atomic_interaction_cutoff() const overridecore::scoring::vdwaals::VDW_Energyvirtual
atomistic_energy(core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) constcore::scoring::methods::EnergyMethodvirtual
atomistic_pair_energy(core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) constcore::scoring::methods::EnergyMethodvirtual
atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &p) constcore::scoring::methods::TwoBodyEnergyvirtual
backbone_backbone_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) constcore::scoring::methods::TwoBodyEnergyvirtual
backbone_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) constcore::scoring::methods::TwoBodyEnergyvirtual
bump_energy_backbone(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) constcore::scoring::methods::TwoBodyEnergyvirtual
bump_energy_full(conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) constcore::scoring::methods::TwoBodyEnergyvirtual
calculate_hydrogen_interaction_cutoff()core::scoring::vdwaals::VDW_Energyprivate
clone() const overridecore::scoring::vdwaals::VDW_Energyvirtual
ContextIndependentTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentTwoBodyEnergy
create_rotamer_trie(conformation::RotamerSetBase const &rotset) constcore::scoring::vdwaals::VDW_Energyprivate
defines_high_order_terms(pose::Pose const &) constcore::scoring::methods::EnergyMethodvirtual
defines_intrares_dof_derivatives(pose::Pose const &p) constcore::scoring::methods::TwoBodyEnergyvirtual
defines_intrares_energy(EnergyMap const &) const overridecore::scoring::vdwaals::VDW_Energyinlinevirtual
defines_intrares_energy_for_residue(conformation::Residue const &res) constcore::scoring::methods::TwoBodyEnergyvirtual
defines_score_for_residue_pair(conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) constcore::scoring::methods::TwoBodyEnergyvirtual
divides_backbone_and_sidechain_energetics() constcore::scoring::methods::ShortRangeTwoBodyEnergyvirtual
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 &scorefxn, EnergyMap const &weights, Vector &F1, Vector &F2) const overridecore::scoring::vdwaals::VDW_Energyvirtual
eval_intrares_derivatives(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) constcore::scoring::methods::TwoBodyEnergyvirtual
eval_intrares_energy(conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const overridecore::scoring::vdwaals::VDW_Energyinlinevirtual
eval_intrares_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) constcore::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) constcore::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) constcore::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::ShortRangeTwoBodyEnergyvirtual
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) constcore::scoring::methods::TwoBodyEnergyvirtual
evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) constcore::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::vdwaals::VDW_Energyvirtual
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) constcore::scoring::methods::EnergyMethodvirtual
finalize_after_minimizing(pose::Pose &pose) constcore::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) constcore::scoring::methods::EnergyMethodvirtual
get_count_pair_function_trie(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose) constcore::scoring::vdwaals::VDW_Energyprivate
get_count_pair_function_trie(conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2) constcore::scoring::vdwaals::VDW_Energyprivate
has_atomistic_energies() constcore::scoring::methods::EnergyMethodvirtual
has_atomistic_pairwise_energies() constcore::scoring::methods::EnergyMethodvirtual
hydrogen_interaction_cutoff2_core::scoring::vdwaals::VDW_Energyprivate
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const overridecore::scoring::vdwaals::VDW_Energyvirtual
method_type() const overridecore::scoring::methods::ContextIndependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) constcore::scoring::methods::EnergyMethodvirtual
parent typedefcore::scoring::methods::ContextIndependentTwoBodyEnergy
prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &set) const overridecore::scoring::vdwaals::VDW_Energyvirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) constcore::scoring::methods::EnergyMethodvirtual
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) constcore::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_derivatives_for_residue_pair_opportunity(pose::Pose const &pose) constcore::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) constcore::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) constcore::scoring::methods::EnergyMethodvirtual
requires_a_setup_for_scoring_for_residue_pair_opportunity(pose::Pose const &pose) constcore::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::vdwaals::VDW_Energyvirtual
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) constcore::scoring::methods::TwoBodyEnergyvirtual
score_types() constcore::scoring::methods::EnergyMethodinline
score_types_core::scoring::methods::EnergyMethodprivate
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &) const overridecore::scoring::vdwaals::VDW_Energyvirtual
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) constcore::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) constcore::scoring::methods::TwoBodyEnergyvirtual
setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) constcore::scoring::methods::EnergyMethodvirtual
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) constcore::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) constcore::scoring::methods::TwoBodyEnergyvirtual
setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) constcore::scoring::methods::EnergyMethodvirtual
setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) constcore::scoring::methods::EnergyMethodvirtual
setup_for_scoring(pose::Pose &pose, ScoreFunction const &) const overridecore::scoring::vdwaals::VDW_Energyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) constcore::scoring::methods::TwoBodyEnergyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) constcore::scoring::methods::TwoBodyEnergy
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) constcore::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) constcore::scoring::methods::TwoBodyEnergyvirtual
ShortRangeTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ShortRangeTwoBodyEnergy
show_additional_info(std::ostream &, pose::Pose &, bool) constcore::scoring::methods::EnergyMethodvirtual
sidechain_sidechain_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) constcore::scoring::methods::TwoBodyEnergyvirtual
TwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::TwoBodyEnergy
update_residue_for_packing(pose::Pose &, Size resid) constcore::scoring::methods::EnergyMethodvirtual
use_extended_intrares_energy_interface() constcore::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() constcore::scoring::methods::TwoBodyEnergyvirtual
VDW_Energy(methods::EnergyMethodOptions const &options)core::scoring::vdwaals::VDW_Energy
VDW_Energy()core::scoring::vdwaals::VDW_Energyprivate
vdw_scale_factor_core::scoring::vdwaals::VDW_Energyprivate
version() const overridecore::scoring::vdwaals::VDW_Energyvirtual
~ContextIndependentTwoBodyEnergy() overridecore::scoring::methods::ContextIndependentTwoBodyEnergy
~ShortRangeTwoBodyEnergy() overridecore::scoring::methods::ShortRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy