Rosetta
core::energy_methods::GenericBondedEnergy Member List

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

atomic_interaction_cutoff() constcore::energy_methods::GenericBondedEnergyinlinevirtual
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
clone() const overridecore::energy_methods::GenericBondedEnergyvirtual
ContextIndependentLRTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentLRTwoBodyEnergy
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(core::scoring::EnergyMap const &) const overridecore::energy_methods::GenericBondedEnergyinlinevirtual
defines_intrares_energy_for_residue(conformation::Residue const &res) constcore::scoring::methods::TwoBodyEnergyvirtual
defines_residue_pair_energy(pose::Pose const &, Size, Size) const overridecore::energy_methods::GenericBondedEnergyinlinevirtual
defines_score_for_residue_pair(conformation::Residue const &rsd1, conformation::Residue const &rsd2, bool res_moving_wrt_eachother=false) const overridecore::energy_methods::GenericBondedEnergyvirtual
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
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) constcore::scoring::methods::EnergyMethodvirtual
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::GenericBondedEnergyvirtual
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &emap) const overridecore::energy_methods::GenericBondedEnergyvirtual
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, core::scoring::ResSingleMinimizationData const &, core::scoring::ResSingleMinimizationData const &, core::scoring::ResPairMinimizationData const &min_data, 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::GenericBondedEnergyvirtual
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) constcore::scoring::methods::TwoBodyEnergyvirtual
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) constcore::scoring::methods::TwoBodyEnergyvirtual
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) constcore::scoring::methods::TwoBodyEnergyvirtual
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
GenericBondedEnergy(GenericBondedEnergy const &src)core::energy_methods::GenericBondedEnergy
GenericBondedEnergy(core::scoring::methods::EnergyMethodOptions const &eopt)core::energy_methods::GenericBondedEnergy
has_atomistic_energies() constcore::scoring::methods::EnergyMethodvirtual
has_atomistic_pairwise_energies() constcore::scoring::methods::EnergyMethodvirtual
indicate_required_context_graphs(utility::vector1< bool > &) const overridecore::energy_methods::GenericBondedEnergyvirtual
long_range_type() const overridecore::energy_methods::GenericBondedEnergyvirtual
LongRangeTwoBodyEnergy(EnergyMethodCreatorOP creator)core::scoring::methods::LongRangeTwoBodyEnergy
method_type() const overridecore::scoring::methods::ContextIndependentLRTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const overridecore::energy_methods::GenericBondedEnergyinlinevirtual
parent typedefcore::energy_methods::GenericBondedEnergy
potential_core::energy_methods::GenericBondedEnergyprivate
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) constcore::scoring::methods::EnergyMethodvirtual
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, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &emap) const overridecore::energy_methods::GenericBondedEnergyvirtual
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_full() constcore::energy_methods::GenericBondedEnergyinline
score_full_core::energy_methods::GenericBondedEnergyprivate
score_hybrid() constcore::energy_methods::GenericBondedEnergyinline
score_hybrid_core::energy_methods::GenericBondedEnergyprivate
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, core::scoring::ScoreFunction const &sfxn) const overridecore::energy_methods::GenericBondedEnergyvirtual
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, core::scoring::ScoreFunction const &sfxn) const overridecore::energy_methods::GenericBondedEnergyvirtual
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
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
version() const overridecore::energy_methods::GenericBondedEnergyvirtual
~ContextIndependentLRTwoBodyEnergy() overridecore::scoring::methods::ContextIndependentLRTwoBodyEnergy
~LongRangeTwoBodyEnergy() overridecore::scoring::methods::LongRangeTwoBodyEnergy
~TwoBodyEnergy() overridecore::scoring::methods::TwoBodyEnergy