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core::scoring::methods::PoissonBoltzmannEnergy Member List

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

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
cached_pose_by_state_core::scoring::methods::PoissonBoltzmannEnergymutableprivate
charged_chains_core::scoring::methods::PoissonBoltzmannEnergymutableprivate
charged_residues_core::scoring::methods::PoissonBoltzmannEnergymutableprivate
clone() const core::scoring::methods::PoissonBoltzmannEnergyvirtual
ContextIndependentLRTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentLRTwoBodyEnergy
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 core::scoring::methods::PoissonBoltzmannEnergyinlinevirtual
defines_intrares_energy_for_residue(conformation::Residue const &res) const core::scoring::methods::TwoBodyEnergyvirtual
defines_residue_pair_energy(pose::Pose const &pose, Size res1, Size res2) const core::scoring::methods::PoissonBoltzmannEnergyvirtual
defines_score_for_residue_pair(conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const core::scoring::methods::TwoBodyEnergyvirtual
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
EnergyMethod(EnergyMethod const &src)core::scoring::methods::EnergyMethod
epsilon_core::scoring::methods::PoissonBoltzmannEnergyprivate
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 core::scoring::methods::TwoBodyEnergyvirtual
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const core::scoring::methods::PoissonBoltzmannEnergyvirtual
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 core::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) const core::scoring::methods::TwoBodyEnergyvirtual
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 core::scoring::methods::TwoBodyEnergyvirtual
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const core::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const core::scoring::methods::EnergyMethodvirtual
fixed_residue_core::scoring::methods::PoissonBoltzmannEnergyprivate
indicate_required_context_graphs(utility::vector1< bool > &) const core::scoring::methods::PoissonBoltzmannEnergyvirtual
long_range_type() const core::scoring::methods::PoissonBoltzmannEnergyvirtual
LongRangeTwoBodyEnergy(EnergyMethodCreatorOP creator)core::scoring::methods::LongRangeTwoBodyEnergy
method_type() const core::scoring::methods::ContextIndependentLRTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const core::scoring::methods::EnergyMethodvirtual
parent typedefcore::scoring::methods::PoissonBoltzmannEnergy
PBLifetimeCache typedefcore::scoring::methods::PoissonBoltzmannEnergy
PBLifetimeCacheOP typedefcore::scoring::methods::PoissonBoltzmannEnergy
poisson_boltzmann_potential_core::scoring::methods::PoissonBoltzmannEnergymutableprivate
PoissonBoltzmannEnergy()core::scoring::methods::PoissonBoltzmannEnergy
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const core::scoring::methods::EnergyMethodvirtual
protein_position_equal_within(pose::Pose const &pose1, pose::Pose const &pose2, Size atom_num, Real tolA) const core::scoring::methods::PoissonBoltzmannEnergyprivate
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(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_pair_opportunity(pose::Pose const &pose) const core::scoring::methods::TwoBodyEnergyvirtual
residue_in_chains(conformation::Residue const &rsd, utility::vector1< Size > chains) const core::scoring::methods::PoissonBoltzmannEnergy
residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const core::scoring::methods::PoissonBoltzmannEnergyvirtual
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
revamp_weight_by_burial(conformation::Residue const &rsd, pose::Pose const &pose) const core::scoring::methods::PoissonBoltzmannEnergy
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) 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 &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, 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 &, utility::vector1< bool > const &, utility::vector1< bool > const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_scoring(pose::Pose &pose, ScoreFunction const &) const core::scoring::methods::PoissonBoltzmannEnergyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const core::scoring::methods::TwoBodyEnergyvirtual
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
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 resid) const core::scoring::methods::EnergyMethodvirtual
use_extended_intrares_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
use_extended_residue_pair_energy_interface() const core::scoring::methods::TwoBodyEnergyvirtual
version() const core::scoring::methods::PoissonBoltzmannEnergyprivatevirtual
~ContextIndependentLRTwoBodyEnergy()core::scoring::methods::ContextIndependentLRTwoBodyEnergyvirtual
~EnergyMethod()core::scoring::methods::EnergyMethodvirtual
~LongRangeTwoBodyEnergy()core::scoring::methods::LongRangeTwoBodyEnergyvirtual
~TwoBodyEnergy()core::scoring::methods::TwoBodyEnergyvirtual