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Rosetta
2021.16
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Rosetta
2021.16
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This is the complete list of members for core::energy_methods::ProQ_Energy, including all inherited members.
| all_inputs_ProQ2_ | core::energy_methods::ProQ_Energy | private |
| all_inputs_ProQM_ | core::energy_methods::ProQ_Energy | private |
| atom13(conformation::Residue const &rsd, Size atom_i) const | core::energy_methods::ProQ_Energy | private |
| atom13_0(conformation::Residue const &rsd, Size atom_i) const | core::energy_methods::ProQ_Energy | private |
| atom_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const | core::energy_methods::ProQ_Energy | private |
| atomic_interaction_cutoff() const override | core::energy_methods::ProQ_Energy | virtual |
| calculate_feature_vector(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &feature_vector) const | core::energy_methods::ProQ_Energy | private |
| calculate_feature_vector_proq2(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &feature_vector) const | core::energy_methods::ProQ_Energy | private |
| calculateZ(pose::Pose &pose, ObjexxFCL::FArray1D< Real > &Z) const | core::energy_methods::ProQ_Energy | private |
| clone() const override | core::energy_methods::ProQ_Energy | virtual |
| crd(pose::Pose &pose, Size i, Size j) const | core::energy_methods::ProQ_Energy | private |
| defines_high_order_terms(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| EnergyMethod(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | |
| entropy_ | core::energy_methods::ProQ_Energy | private |
| entropy_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=11) const | core::energy_methods::ProQ_Energy | private |
| 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::EnergyMethod | virtual |
| finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_after_minimizing(pose::Pose &pose) const | core::scoring::methods::EnergyMethod | virtual |
| finalize_total_energy(pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn, core::scoring::EnergyMap &totals) const override | core::energy_methods::ProQ_Energy | virtual |
| grsa_sc_feature(pose::Pose &pose, utility::vector1< Real > &rsd_sasa_rel, ObjexxFCL::FArray2D< Real > &vec, Size index) const | core::energy_methods::ProQ_Energy | private |
| gss_sc_feature(pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, Size index) const | core::energy_methods::ProQ_Energy | private |
| indicate_required_context_graphs(utility::vector1< bool > &) const override | core::energy_methods::ProQ_Energy | inlinevirtual |
| initialize() | core::energy_methods::ProQ_Energy | private |
| method_type() const override | core::scoring::methods::WholeStructureEnergy | virtual |
| minimize_in_whole_structure_context(pose::Pose const &) const | core::scoring::methods::EnergyMethod | virtual |
| nres_ | core::energy_methods::ProQ_Energy | private |
| output_local_prediction(pose::Pose &pose, ObjexxFCL::FArray1D< Real > &proq, std::string name) const | core::energy_methods::ProQ_Energy | private |
| parent typedef | core::energy_methods::ProQ_Energy | |
| potential_ | core::energy_methods::ProQ_Energy | private |
| prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const | core::scoring::methods::EnergyMethod | virtual |
| prob_profile_ | core::energy_methods::ProQ_Energy | private |
| profile_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=3) const | core::energy_methods::ProQ_Energy | private |
| profile_index_to_aa(int i) const | core::energy_methods::ProQ_Energy | private |
| ProQ_Energy() | core::energy_methods::ProQ_Energy | |
| ProQ_Energy(ProQ_Energy const &src) | core::energy_methods::ProQ_Energy | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | core::scoring::methods::EnergyMethod | virtual |
| prsa_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=1) const | core::energy_methods::ProQ_Energy | private |
| read_acc(std::string accfile) | core::energy_methods::ProQ_Energy | private |
| read_mpSA(std::string mpSAfile) | core::energy_methods::ProQ_Energy | private |
| read_profiles_and_entropy(std::string profile, std::string mtxfile) | core::energy_methods::ProQ_Energy | private |
| read_ss2(std::string ss2file) | core::energy_methods::ProQ_Energy | private |
| read_zpred(std::string zpredfile) | core::energy_methods::ProQ_Energy | private |
| requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const | core::scoring::methods::EnergyMethod | virtual |
| res6(conformation::Residue const &rsd) const | core::energy_methods::ProQ_Energy | private |
| res6(char const aa) const | core::energy_methods::ProQ_Energy | private |
| res_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const | core::energy_methods::ProQ_Energy | private |
| rsa_class_pred_ | core::energy_methods::ProQ_Energy | private |
| rsa_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, utility::vector1< Real > &rsd_sasa_rel, int const pos, Size index, int windowsize=1) const | core::energy_methods::ProQ_Energy | private |
| rsa_pred_ | core::energy_methods::ProQ_Energy | private |
| rsa_sc_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, utility::vector1< Real > &rsd_sasa_rel, int const pos, Size index, int windowsize=21) const | core::energy_methods::ProQ_Energy | private |
| scaled_logodds_profile_ | core::energy_methods::ProQ_Energy | private |
| score_types() const | core::scoring::methods::EnergyMethod | inline |
| set_score_types(EnergyMethodCreatorOP creator) | core::scoring::methods::EnergyMethod | protected |
| setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const | core::scoring::methods::EnergyMethod | virtual |
| setup_for_scoring(pose::Pose &pose, core::scoring::ScoreFunction const &scorefxn) const override | core::energy_methods::ProQ_Energy | virtual |
| 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::EnergyMethod | virtual |
| show_additional_info(std::ostream &, pose::Pose &, bool) const | core::scoring::methods::EnergyMethod | virtual |
| ss1_ | core::energy_methods::ProQ_Energy | private |
| ss_feature(pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=1) const | core::energy_methods::ProQ_Energy | private |
| ss_pred_ | core::energy_methods::ProQ_Energy | private |
| ss_sc_feature(pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=21) const | core::energy_methods::ProQ_Energy | private |
| stride_feature(pose::Pose &pose, core::scoring::dssp::Dssp &ss, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=11) const | core::energy_methods::ProQ_Energy | private |
| sum_profile(Size k, ObjexxFCL::FArray1D< Real > &vec) const | core::energy_methods::ProQ_Energy | private |
| surf_feature(pose::Pose &pose, utility::vector1< Real > &rsd_sasa_rel, ObjexxFCL::FArray2D< Real > &vec, Size index, int windowsize=21) const | core::energy_methods::ProQ_Energy | private |
| termini_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index, int windowsize=23) const | core::energy_methods::ProQ_Energy | private |
| topology_ | core::energy_methods::ProQ_Energy | private |
| topology_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const | core::energy_methods::ProQ_Energy | private |
| update_residue_for_packing(pose::Pose &, Size resid) const | core::scoring::methods::EnergyMethod | virtual |
| version() const override | core::energy_methods::ProQ_Energy | virtual |
| WholeStructureEnergy(EnergyMethodCreatorOP) | core::scoring::methods::WholeStructureEnergy | |
| z_feature(pose::Pose &pose, ObjexxFCL::FArray1D< Real > &Z, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const | core::energy_methods::ProQ_Energy | private |
| z_pred_ | core::energy_methods::ProQ_Energy | private |
| zpred_feature(pose::Pose &pose, ObjexxFCL::FArray2D< Real > &vec, int const pos, Size index) const | core::energy_methods::ProQ_Energy | private |
| ~WholeStructureEnergy() override | core::scoring::methods::WholeStructureEnergy | inline |
1.8.7