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core::energy_methods::FA_GrpElecEnergy Member List

This is the complete list of members for core::energy_methods::FA_GrpElecEnergy, including all inherited members.

atomic_interaction_cutoff() const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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 &, 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
burial_deriv(core::Real const nb) const core::energy_methods::FA_GrpElecEnergyinlineprivate
burial_weight(core::Real const nb) const core::energy_methods::FA_GrpElecEnergyinlineprivate
clone() const overridecore::energy_methods::FA_GrpElecEnergyvirtual
context_dependent_core::energy_methods::FA_GrpElecEnergyprivate
context_minstrength_core::energy_methods::FA_GrpElecEnergyprivate
ContextDependentTwoBodyEnergy(EnergyMethodCreatorOP creator)core::scoring::methods::ContextDependentTwoBodyEnergy
coulomb() const core::energy_methods::FA_GrpElecEnergyinlineprotected
coulomb_core::energy_methods::FA_GrpElecEnergyprivate
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(core::scoring::EnergyMap const &) const overridecore::energy_methods::FA_GrpElecEnergyinlinevirtual
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::energy_methods::FA_GrpElecEnergyvirtual
divides_backbone_and_sidechain_energetics() const core::scoring::methods::ShortRangeTwoBodyEnergyvirtual
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
eval_atom_derivative(id::AtomID const &, pose::Pose const &, kinematics::DomainMap const &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap const &, Vector &, Vector &) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
eval_context_derivatives(conformation::Residue const &rsd1, FAElecContextDataCOP data, core::scoring::EnergyMap const &, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs) const core::energy_methods::FA_GrpElecEnergyprivate
eval_intrares_derivatives(conformation::Residue const &rsd, core::scoring::ResSingleMinimizationData const &, pose::Pose const &pose, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &atom_derivs) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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_n(Real const cendist, Real &dn_drij, bool const eval_deriv) const core::energy_methods::FA_GrpElecEnergyprivate
eval_residue_pair_derivatives(conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData const &, pose::Pose const &pose, core::scoring::EnergyMap const &weights, utility::vector1< core::scoring::DerivVectorPair > &r1_atom_derivs, utility::vector1< core::scoring::DerivVectorPair > &r2_atom_derivs) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
evaluate_rotamer_background_energies(conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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, core::scoring::ScoreFunction const &, core::scoring::EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
exclude_DNA_DNA_core::energy_methods::FA_GrpElecEnergyprivate
exclude_monomer_core::energy_methods::FA_GrpElecEnergyprivate
exclude_protein_protein_core::energy_methods::FA_GrpElecEnergyprivate
exclude_RNA_RNA_core::energy_methods::FA_GrpElecEnergyprivate
FA_GrpElecEnergy(core::scoring::methods::EnergyMethodOptions const &options)core::energy_methods::FA_GrpElecEnergy
FA_GrpElecEnergy(FA_GrpElecEnergy const &src)core::energy_methods::FA_GrpElecEnergy
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 &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
get_count_pair_function(Size const, Size const, pose::Pose const &, core::scoring::ScoreFunction const &) const core::energy_methods::FA_GrpElecEnergy
get_count_pair_function(conformation::Residue const &rsd1, conformation::Residue const &rsd2) const core::energy_methods::FA_GrpElecEnergy
get_intrares_countpair(conformation::Residue const &, pose::Pose const &, core::scoring::ScoreFunction const &) const core::energy_methods::FA_GrpElecEnergy
groupelec() const core::energy_methods::FA_GrpElecEnergyinlineprotected
groupelec_core::energy_methods::FA_GrpElecEnergyprivate
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
initialize()core::energy_methods::FA_GrpElecEnergy
method_type() const overridecore::scoring::methods::ContextDependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &pose) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
monomer_test(Size irsd, Size jrsd) const core::energy_methods::FA_GrpElecEnergyprivate
ncb_maxburial_core::energy_methods::FA_GrpElecEnergyprivate
ncb_minburial_core::energy_methods::FA_GrpElecEnergyprivate
nres_monomer_core::energy_methods::FA_GrpElecEnergymutableprivate
parent typedefcore::energy_methods::FA_GrpElecEnergy
precalc_context(pose::Pose &pose, FAElecContextDataOP data) const core::energy_methods::FA_GrpElecEnergyprivate
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
residue_pair_energy_ext(conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::scoring::ResPairMinimizationData const &, pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &emap) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
score_types() const core::scoring::methods::EnergyMethodinline
set_nres_mono(core::pose::Pose const &pose) const core::energy_methods::FA_GrpElecEnergyprivate
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, core::scoring::ScoreFunction const &scfxn) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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, core::scoring::ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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, core::scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData &) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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, core::scoring::ScoreFunction const &scfxn) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
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 &, Size) const overridecore::energy_methods::FA_GrpElecEnergyvirtual
use_extended_intrares_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() const overridecore::energy_methods::FA_GrpElecEnergyvirtual
version() const overridecore::energy_methods::FA_GrpElecEnergyprivatevirtual
~ContextDependentTwoBodyEnergy() overridecore::scoring::methods::ContextDependentTwoBodyEnergy
~ShortRangeTwoBodyEnergy() overridecore::scoring::methods::ShortRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy
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