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core::scoring::geometric_solvation::GeometricSolEnergy Member List

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

__pad0__core::scoring::geometric_solvation::GeometricSolEnergy
acceptorRes_occludingRes_geometric_sol_one_way(conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
acceptorRes_occludingRes_geometric_sol_RNA_intra(conformation::Residue const &rsd, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
atom_is_acceptor(conformation::Residue const &rsd, Size const atm) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
atom_is_donor(conformation::Residue const &rsd, Size const atm) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
atom_is_donor_h(conformation::Residue const &rsd, Size const atm) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
atom_is_heavy(conformation::Residue const &rsd, Size const atm) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
atomic_interaction_cutoff() const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
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
clone() const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
ContextDependentTwoBodyEnergy(EnergyMethodCreatorOP creator)core::scoring::methods::ContextDependentTwoBodyEnergy
correct_geom_sol_acceptor_base_core::scoring::geometric_solvation::GeometricSolEnergyprivate
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 &weights) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
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
dist_cut2_core::scoring::geometric_solvation::GeometricSolEnergyprivate
divides_backbone_and_sidechain_energetics() const core::scoring::methods::ShortRangeTwoBodyEnergyvirtual
donorRes_occludingRes_geometric_sol_one_way(conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
donorRes_occludingRes_geometric_sol_RNA_intra(conformation::Residue const &rsd, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergyprivate
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
EnergyMethod(EnergyMethod const &src)core::scoring::methods::EnergyMethod
eval_atom_derivative(id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
eval_atom_derivative_intra_RNA(id::AtomID const &atom_id, pose::Pose const &pose, EnergyMap const &weights, Vector &F1, Vector &F2) const core::scoring::geometric_solvation::GeometricSolEnergy
eval_atom_energy(id::AtomID const &atom_id, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergy
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 &, EnergyMap &emap) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
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::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 core::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 core::scoring::methods::ShortRangeTwoBodyEnergyvirtual
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
geometric_sol_scale_core::scoring::geometric_solvation::GeometricSolEnergyprivate
GeometricSolEnergy(methods::EnergyMethodOptions const &options)core::scoring::geometric_solvation::GeometricSolEnergy
GeometricSolEnergy(GeometricSolEnergy const &src)core::scoring::geometric_solvation::GeometricSolEnergy
get_acceptor_base_atm_xyz(conformation::Residue const &acc_rsd, Size const &acc_atm) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
get_atom_atom_geometric_solvation_for_acceptor(Size const &acc_atm, conformation::Residue const &acc_rsd, Size const &occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=hbonds::DUMMY_DERIVS) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
get_atom_atom_geometric_solvation_for_donor(Size const &don_h_atm, conformation::Residue const &don_rsd, Size const &occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=hbonds::DUMMY_DERIVS) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
get_water_cos(Vector const &base_atm_xyz, Vector const &polar_atm_xyz, Vector const &occluding_atm_xyz) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
hb_database_core::scoring::geometric_solvation::GeometricSolEnergyprivate
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
method_type() const core::scoring::methods::ContextDependentTwoBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const core::scoring::methods::EnergyMethodvirtual
occluded_water_hbond_penalty(bool const &is_donor, hbonds::HBEvalTuple const &hbond_eval_type, Vector const &polar_atm_xyz, Vector const &base_atm_xyz, Vector const &occluding_atm_xyz, Size const &polar_nb, Size const &occ_nb, bool const update_deriv=false, hbonds::HBondDerivs &deriv=hbonds::DUMMY_DERIVS) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
options_core::scoring::geometric_solvation::GeometricSolEnergyprivate
parent typedefcore::scoring::methods::ContextDependentTwoBodyEnergy
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) 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(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
res_res_geometric_sol_one_way(conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
residue_pair_energy(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
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
set_water_base_atm(Vector const &base_v, Vector const &atom_v, Vector const &water_v, Vector &water_base_v, Real const &xH, Distance const &bond_length) const core::scoring::geometric_solvation::GeometricSolEnergyinlineprivate
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &) const core::scoring::geometric_solvation::GeometricSolEnergyvirtual
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::geometric_solvation::GeometricSolEnergyvirtual
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
ShortRangeTwoBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ShortRangeTwoBodyEnergy
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
verbose_core::scoring::geometric_solvation::GeometricSolEnergyprivate
version() const core::scoring::geometric_solvation::GeometricSolEnergyprivatevirtual
~ContextDependentTwoBodyEnergy()core::scoring::methods::ContextDependentTwoBodyEnergyvirtual
~EnergyMethod()core::scoring::methods::EnergyMethodvirtual
~ShortRangeTwoBodyEnergy()core::scoring::methods::ShortRangeTwoBodyEnergyvirtual
~TwoBodyEnergy()core::scoring::methods::TwoBodyEnergyvirtual