| AA typedef | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| aa() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inline |
| assign_chi_for_interpolated_rotamer(PackedDunbrackRotamer< T, 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::RotamericSingleResiduePeptoidLibrary< T > | 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::RotamericSingleResiduePeptoidLibrary< T > | 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 | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| best_rotamer_energy(conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | 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::SingleResiduePeptoidLibrary | inline |
| bin_rotameric_chi(Real chi, Size which_chi) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inline |
| build_rotamers(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, 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, RotamerVector &rotamers, PackedDunbrackRotamer< T, Real > const &interpolated_rotamer) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| chisamples_for_rotamer_and_chi(chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T > 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::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| CIS_OMG_LOWER_RANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| CIS_OMG_UPPER_RANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| cis_packed_rotno_2_sorted_rotno_ | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| cis_rotamers_ | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| CIS_UPPER_TRANS_LOWER_SPLIT | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| correct_termini_derivatives(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| create_rotamers_from_chisets(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< ChiSetOP > const &chi_set_vector, RotamerVector &rotamers) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| declare_all_existing_rotwells_encountered() | core::pack::dunbrack::SingleResiduePeptoidLibrary | protected |
| dun02() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inlineprotected |
| enumerate_chi_sets(chemical::ResidueType const &rsd_type, pack::task::PackerTask const &task, Size const seqpos, bool buried, RotamericData< T > const &rotamer_data, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, utility::vector1< ChiSetOP > &chi_set_vector) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| eval_rotameric_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| fill_rotamer_vector(pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, 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, RotamerVector &rotamers) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| find_another_representative_for_unlikely_rotamer(conformation::Residue const &rsd, Size4 &rotwell) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| get_all_rotamer_samples(Real omg, Real phi, Real psi) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| get_omg_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| get_omgphipsi_bins(Real omg, Real phi, Real psi, Size &omgbin, Size &phibin, Size &psibin, Size &omgbin_next, Size &phibin_next, Size &psibin_next, Real &omg_alpha, Real &phi_alpha, Real &psi_alpha) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| get_omgphipsi_bins(Real omg, Real phi, Real psi, Size &omgbin, Size &phibin, Size &psibin) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| get_phi_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| get_probability_for_rotamer(Real omg, Real phi, Real psi, Size rot_ind) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| get_psi_from_rsd(conformation::Residue const &rsd, pose::Pose const &pose) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| get_rotamer(Real omg, Real phi, Real psi, Size rot_ind) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| get_rotamer_from_chi(ChiVector const &chi, RotVector &rot) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| get_rotamer_from_chi_static(ChiVector const &chi, Size4 &rot) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| get_rotamer_from_chi_static(Real4 const &chi, Size4 &rot) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| interpolate_rotamers(conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| interpolate_rotamers(typename ObjexxFCL::FArray4D< PackedDunbrackRotamer< T > > const &rotamers, ObjexxFCL::FArray4D< Size > const &packed_rotno_2_sorted_rotno, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, Size const omgbin, Size const phibin, Size const psibin, Size const omgbin_next, Size const phibin_next, Size const psibin_next, Real const omg_alpha, Real const phi_alpha, Real const psi_alpha, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| is_cis_omg(Real omg_angle) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | inlineprotected |
| is_trans_omg(Real omg_angle) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | inlineprotected |
| mark_rotwell_exists(utility::vector1< Size > const &rotwell) | core::pack::dunbrack::SingleResiduePeptoidLibrary | protected |
| memory_usage_dynamic() const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| memory_usage_in_bytes() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | virtual |
| memory_usage_static() const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedvirtual |
| n_chi_bins() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inlineprotected |
| N_OMG_BINS | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| n_packed_rots() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inlineprotected |
| N_PHI_BINS | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| n_possible_rots() const | core::pack::dunbrack::SingleResiduePeptoidLibrary | inlineprotected |
| N_PSI_BINS | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| n_rotamer_bins() const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| n_rotamer_bins_for_aa(chemical::AA const aa, RotVector &rot) | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| n_rotamer_bins_for_aa_02(chemical::AA const aa, RotVector &rot) | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| n_rotameric_bins_for_aa(chemical::AA const aa, RotVector &rot, bool dun02) | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| nchi() const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| NEUTRAL_OMG | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| NEUTRAL_PHI | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| NEUTRAL_PSI | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| OMG_BINRANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| packed_rotamer_2_regular_rotamer(PackedDunbrackRotamer< T, P > const &packedrot) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| packed_rotno_2_rotwell(Size const packed_rotno, utility::vector1< Size > &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| packed_rotno_2_rotwell(Size const packed_rotno, Size4 &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| packed_rotno_2_rotwell(Size const packed_rotno) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| packed_rotno_2_sorted_rotno(Real omg_angle) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| packed_rotno_2_sorted_rotno(Real omg_angle) | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| parent typedef | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| PHI_BINRANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| prob_to_accumulate(Real, Real) | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| prob_to_accumulate_buried(Real) | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| prob_to_accumulate_nonburied(Real) | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| probability_to_accumulate_while_building_rotamers(bool buried) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| PSI_BINRANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| read_from_binary(utility::io::izstream &in) | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| read_from_file(utility::io::izstream &in) | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| read_options() | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotamer_energy(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| rotamer_energy_deriv(conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| RotamericSingleResiduePeptoidLibrary() | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | |
| rotamers(Real omg_angle) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| rotamers(Real omg_angle) | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protected |
| rotno_2_packed_rotno(Size const rotno) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotno_2_rotwell(Size const rotno, utility::vector1< Size > &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotwell_2_packed_rotno(utility::vector1< Size > const &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotwell_2_packed_rotno(Size4 const &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotwell_2_rotno(utility::vector1< Size > const &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| rotwell_2_rotno(Size4 const &rotwell) const | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| RSD_OMG_INDEX | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| RSD_PHI_INDEX | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| RSD_PSI_INDEX | core::pack::dunbrack::SingleResiduePeptoidLibrary | static |
| set_n_chi_bins(utility::vector1< Size > const &) | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| SingleResiduePeptoidLibrary class | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | friend |
| core::pack::dunbrack::SingleResiduePeptoidLibrary::SingleResiduePeptoidLibrary(Size const n_rotameric_chi) | core::pack::dunbrack::SingleResiduePeptoidLibrary | |
| TRANS_OMG_LOWER_RANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| TRANS_OMG_UPPER_RANGE | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| trans_packed_rotno_2_sorted_rotno_ | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| trans_rotamers_ | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| TRANS_UPPER_CIS_LOWER_SPLIT | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | protectedstatic |
| verify_omgphipsi_bins(Real omg, Real phi, Real psi, Size const omgbin, Size const phibin, Size const psibin, Size const omgbin_next, Size const phibin_next, Size const psibin_next) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | private |
| write_to_binary(utility::io::ozstream &out) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| write_to_file(utility::io::ozstream &out) const | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| ~RotamericSingleResiduePeptoidLibrary() | core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T > | virtual |
| ~SingleResiduePeptoidLibrary() | core::pack::dunbrack::SingleResiduePeptoidLibrary | virtual |
| ~SingleResidueRotamerLibrary() | core::pack::dunbrack::SingleResidueRotamerLibrary | virtual |
1.8.7