| AA typedef | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| aa() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inline |
| ANGLE_DELTA | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| assign_chi_for_interpolated_rotamer(PackedDunbrackRotamer< T, N, Real > const &interpolated_rotamer, conformation::Residue const &rsd, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| assign_random_rotamer(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center, Size &packed_rotno) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| assign_random_rotamer_with_bias(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| BB_BINRANGE | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| best_rotamer_energy(conformation::Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| bin_angle(Real const angle_start, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inline |
| bin_angle(Real const angle_start, utility::vector1< core::Size > const &bin_equivs, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inline |
| BIN_EQUIVALENTS | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| bin_rotameric_chi(Real chi, Size which_chi) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inline |
| build_rotamers(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, rotamers::RotamerVector &rotamers, PackedDunbrackRotamer< T, N, Real > const &interpolated_rotamer) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| bump_check(core::conformation::ResidueCOP rotamer, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| bump_filter(RotamerVector &rotamers, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| canonical_aa_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| canonicals_use_voronoi_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| chisamples_for_rotamer_and_chi(chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T, N > const &rotamer_data, utility::vector1< Real > const &extra_steps, utility::vector1< Real > &total_chi, utility::vector1< int > &total_rot, utility::vector1< Real > &total_ex_steps, utility::vector1< Real > &chisample_prob) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protectedvirtual |
| COEF_DELTA | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| compute_proton_chi_samplings(chemical::ResidueType const &concrete_residue, pack::task::ResidueLevelTask const &rlt, bool buried) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| correct_rotamer_well_order_on_read_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| correct_termini_derivatives(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| create_rotamers_from_chisets(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< ChiSetOP > const &chi_set_vector, rotamers::RotamerVector &rotamers) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| current_rotamer(RotamerVector &rotamers, core::Size resid, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| declare_all_existing_rotwells_encountered() | core::pack::dunbrack::SingleResidueDunbrackLibrary | protected |
| dun02() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| dun_entropy_correction() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| emergency_rotamer(RotamerVector &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| ENERGY_DELTA | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| enumerate_chi_sets(chemical::ResidueType const &rsd_type, pack::task::PackerTask const &task, Size const seqpos, bool buried, RotamericData< T, N > const &rotamer_data, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, utility::vector1< ChiSetOP > &chi_set_vector) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| eval_rotameric_energy_deriv(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| expand_proton_chis(utility::vector1< utility::vector1< core::Real > > const &sampling, chemical::ResidueType const &concrete_residue, core::Size max_rotamers=5000) const | core::pack::rotamers::SingleResidueRotamerLibrary | virtual |
| fill_rotamer_vector(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, rotamers::RotamerVector &rotamers) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| find_another_representative_for_unlikely_rotamer(conformation::Residue const &rsd, pose::Pose const &pose, Size4 &rotwell) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| get_all_rotamer_samples(Real5 bbs) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_bb_bins(utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > &bb_bin, utility::fixedsizearray1< Size, N > &bb_bin_next, utility::fixedsizearray1< Real, N > &bb_alpha) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| get_bb_bins(utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > &bb_bin) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| get_bb_bins(utility::vector1< core::Real > const &bbs, utility::vector1< core::Size > &bb_bin) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| get_IV_from_rsd(core::Size bbn, conformation::Residue const &rsd, pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| get_IVs_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| get_phi_from_rsd(conformation::Residue const &rsd) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protectedvirtual |
| get_probability_for_rotamer(utility::fixedsizearray1< Real, N > bbs, Size rot_ind) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_probability_for_rotamer(Real phi, Real psi, Size rot_ind) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_psi_from_rsd(conformation::Residue const &rsd) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protectedvirtual |
| get_rotamer(utility::fixedsizearray1< Real, N > bbs, Size rot_ind) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_rotamer(Real phi, Real psi, Size rot_ind) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_rotamer_from_chi(ChiVector const &chi, RotVector &rot) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| get_rotamer_from_chi_static(ChiVector const &chi, Size4 &rot) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| get_rotamer_from_chi_static(Real4 const &chi, Size4 &rot) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| get_rotamer_from_chi_static_voronoi(ChiVector const &chi, core::Size &rot, core::conformation::Residue const &rsd, core::pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| increment_tensor_index_recursively(utility::fixedsizearray1< Size,(N+1) > &bb_bin, utility::fixedsizearray1< Size,(N+1) > const &bb_bin_maxes, core::Size const recursion_level) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| initialize_bicubic_splines() | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| interpolate_rotamers(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, Size packed_rotno, PackedDunbrackRotamer< T, N, Real > &interpolated_rotamer) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| interpolate_rotamers(RotamerLibraryScratchSpace &scratch, Size packed_rotno, utility::fixedsizearray1< Size, N > const &bb_bin, utility::fixedsizearray1< Size, N > const &bb_bin_next, utility::fixedsizearray1< Real, N > const &bb_alpha, PackedDunbrackRotamer< T, N, Real > &interpolated_rotamer, ChiVector const &chi=ChiVector(T, 0.0), bool const use_chi=false) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| IVs | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| make_conditional_packed_rotno_index(Size const original_bb_index, Size const bb_index, Size const packed_rotno, ChiVector const &chi, bool const use_chi) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| mark_rotwell_exists(utility::vector1< Size > const &rotwell) | core::pack::dunbrack::SingleResidueDunbrackLibrary | protected |
| memory_usage_dynamic() const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protectedvirtual |
| memory_usage_in_bytes() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | virtual |
| memory_usage_static() const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protectedvirtual |
| N_BB_BINS | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| n_chi_bins() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| n_packed_rots() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| n_possible_rots() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| n_rotamer_bins() const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| n_rotamer_bins_for_aa(chemical::ResidueType const &rt, RotVector &rot, bool const dun02=false) | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| n_rotamer_bins_for_aa(chemical::AA const aa, RotVector &rot) | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| n_rotamer_bins_for_aa_02(chemical::AA const aa, RotVector &rot) | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| n_rotameric_bins_for_aa(chemical::AA const aa, RotVector &rot, bool dun02) | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| nbb() const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| nchi() const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| noncanonicals_use_voronoi_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| operator=(SingleResidueDunbrackLibrary const &other)=delete | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| operator==(SingleResidueRotamerLibrary const &) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| packed_rotamer_2_regular_rotamer(PackedDunbrackRotamer< T, N, P > const &packedrot) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| packed_rotno_2_rotwell(Size const packed_rotno, utility::vector1< Size > &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| packed_rotno_2_rotwell(Size const packed_rotno, Size4 &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| packed_rotno_2_rotwell(Size const packed_rotno) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| packed_rotno_2_sorted_rotno() const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | inlineprotected |
| packed_rotno_2_sorted_rotno() | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | inlineprotected |
| packed_rotno_2_sorted_rotno_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| parent typedef | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| PEPTIDE_NEUTRAL_PHI | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| PEPTIDE_NEUTRAL_PSI | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| peptoid_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| peptoid_is_achiral_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| PEPTOID_NEUTRAL_OMG | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| PEPTOID_NEUTRAL_PHI | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| PEPTOID_NEUTRAL_PSI | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| PROB_DELTA | core::pack::dunbrack::SingleResidueDunbrackLibrary | static |
| prob_to_accumulate(Real, Real) | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| prob_to_accumulate_buried(Real) | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| prob_to_accumulate_nonburied(Real) | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| probability_to_accumulate_while_building_rotamers(bool buried) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| read_from_binary(utility::io::izstream &in) override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| read_from_file(utility::io::izstream &in, bool first_line_three_letter_code_already_read) | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| rotamer_energy(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| rotamer_energy_deriv(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| RotamericSingleResidueDunbrackLibrary(chemical::ResidueType const &rt, bool dun02, bool use_bicubic, bool entropy_correction, core::Real prob_buried, core::Real prob_nonburied, bool const reduced_resolution_library=false) | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| RotamericSingleResidueDunbrackLibraryParser class | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | friend |
| rotamers() const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | inlineprotected |
| rotamers() | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | inlineprotected |
| rotamers_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| rotno_2_packed_rotno(Size const rotno) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| rotno_2_rotwell(Size const rotno, utility::vector1< Size > &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| rotwell_2_packed_rotno(utility::vector1< Size > const &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| rotwell_2_packed_rotno(Size4 const &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| rotwell_2_rotno(utility::vector1< Size > const &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| rotwell_2_rotno(Size4 const &rotwell) const | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| set_n_chi_bins(utility::vector1< Size > const &) | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| setup_entropy_correction() | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| setup_entropy_correction() const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | protected |
| ShannonEntropy_n_derivs_ | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| SingleResidueDunbrackLibrary class | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | friend |
| core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary(SingleResidueDunbrackLibrary const &)=delete | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary(chemical::ResidueType const &rt, Size const n_rotameric_chi, bool dun02, bool use_bicubic, bool dun_entropy_correction, core::Real prob_buried, core::Real prob_nonburied) | core::pack::dunbrack::SingleResidueDunbrackLibrary | |
| SingleResidueRotamerLibrary() | core::pack::rotamers::SingleResidueRotamerLibrary | inline |
| use_bicubic() const | core::pack::dunbrack::SingleResidueDunbrackLibrary | inlineprotected |
| verify_bb_bins(utility::fixedsizearray1< Real, N > const &bbs, utility::fixedsizearray1< Size, N > const &bb_bin, utility::fixedsizearray1< Size, N > const &bb_bin_next) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| verify_phipsi_bins(Real phi, Real psi, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next) const | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | private |
| virtual_sidechain(RotamerVector const &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const | core::pack::rotamers::SingleResidueRotamerLibrary | |
| write_to_binary(utility::io::ozstream &out) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| write_to_file(utility::io::ozstream &out) const override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | virtual |
| ~RotamericSingleResidueDunbrackLibrary() override | core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > | |
| ~SingleResidueRotamerLibrary() override | core::pack::rotamers::SingleResidueRotamerLibrary | |
1.8.7