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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 protocols::energy_based_clustering::EnergyBasedClusteringProtocol, including all inherited members.
| ::EnergyBasedClusteringTests class | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | friend |
| add_cyclic_constraints(core::pose::Pose &mypose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| add_user_constraints(core::pose::Pose &mypose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| align_with_offset(core::pose::Pose &pose1, core::pose::Pose const &pose2, core::Size const offset, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| alignment_atoms_in_res(core::pose::Pose const &pose, core::Size const position) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| alignment_torsions_in_res(core::pose::Pose const &pose, core::Size const position) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| calc_dist(utility::vector1< core::Real > const &vect1, utility::vector1< core::Real > const &vect2, EBC_ClusterType const clustmode, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect1, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect2, core::Size const nresidues, core::pose::Pose const &firstpose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| calc_dist(utility::vector1< core::Real > const &vect1, utility::vector1< core::Real > const &vect2, EBC_ClusterType const clustmode, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect1, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect2, core::Size const nresidues, core::pose::Pose const &firstpose, core::Size &offset, core::Size &permutation) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| check_backbones_match(core::pose::Pose const &pose1, core::pose::Pose const &pose2) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| clone() const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | |
| constraints_file_contents_ | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| determine_ABOXYZ_bin(core::Real const &phi, core::Real const &psi, core::Real const &omega) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| do_ABOXYZ_bin_analysis(core::pose::Pose const &pose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| do_initial_import_and_scoring(core::Size &count, core::Real &lowestE, core::Size &lowestE_index, core::pose::Pose &firstpose, protocols::cyclic_peptide::CycpepSymmetryFilter const &symmfilter, utility::vector1< core::Real > &poseenergies, utility::vector1< utility::vector1< core::Real > > &posedata, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &alignmentdata, utility::vector1< utility::vector1< core::Real > > &dihedral_reconstruction_data, utility::vector1< std::string > &pose_binstrings, utility::vector1< core::Size > &cluster_assignments, utility::vector1< core::Size > &cluster_offsets, utility::vector1< core::Size > &cluster_oligomer_permutations, core::scoring::ScoreFunctionOP sfxn, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| do_option_checks() const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| EnergyBasedClusteringProtocol() | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | |
| EnergyBasedClusteringProtocol(EnergyBasedClusteringOptions const &options) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | |
| get_circular_permutation_first_in_alphabetical_order(std::string const &string_in) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| get_mirror_bin(char const bin_in) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| get_mirror_bin_sequence(std::string const &binstring_in, bool const circularly_permuted_for_alphabetization) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| get_start_and_end_aa(core::Size const chain_index, core::pose::Pose const &pose, core::Size &startaa, core::Size &endaa) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| get_start_and_end_indices(core::Size const chain_index, core::pose::Pose const &pose, core::Size &startindex, core::Size &endindex) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| go() | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | |
| is_all_alpha_aa_or_peptoid(core::pose::Pose const &pose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| is_in_list(core::Size const val, utility::vector1< core::Size > const &vallist) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | inlineprivate |
| make_disulfides(core::pose::Pose &mypose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| mutate_to_alanine(core::pose::Pose &mypose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| n_clusters_from_last_run() const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | inline |
| n_clusters_from_last_run_ | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| num_asymmetric_binstrings(std::set< std::string > const &binstrings, bool const circularly_permute) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| num_asymmetric_binstrings_with_mirror_counterpart_represented(std::set< std::string > const &binstrings, bool const circularly_permute) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| options_ | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| parse_extra_atom_list(utility::vector1< core::id::NamedAtomID > &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| permute_string(std::string const &string_in) | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | privatestatic |
| pose_from_posedata(core::pose::Pose const &inputpose, core::pose::Pose &outputpose, EBC_ClusterType const clustermode, utility::vector1< core::Real > const &posedata, utility::vector1< core::Real > const &reconstruction_data, bool const rebuild_all_in_dihedral_mode=false) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| register_options() | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | static |
| remove_extraneous_virtuals(core::pose::Pose &pose) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| set_up_scorefunction() const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| sort_cluster_list(utility::vector1< core::Size > &statelist, utility::vector1< core::Real > &poseenergies) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| storeposedata(core::pose::Pose const &pose, utility::vector1< core::Real > &posedata, utility::vector1< numeric::xyzVector< core::Real > > &alignmentdata, utility::vector1< core::Real > &dihedral_mode_reconstruction_data, EBC_ClusterType const clustermode, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| swap_alignment_vector(utility::vector1< numeric::xyzVector< core::Real > > const &parentvect, utility::vector1< numeric::xyzVector< core::Real > > &swappedvect, core::pose::Pose const &refpose, core::Size const permutation_number) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| swap_chains(core::pose::Pose ¤tpose, core::Size const permutation_number) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| use_in_rmsd(core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno, core::Size atomno, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| use_in_rmsd_offset(core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno2, core::Size atomno, core::Size const pose1_offset, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| use_this_atom(core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Size const atomno, std::string const &atname1, std::string const &atname2="") const | protocols::energy_based_clustering::EnergyBasedClusteringProtocol | private |
| ~EnergyBasedClusteringProtocol() override | protocols::energy_based_clustering::EnergyBasedClusteringProtocol |
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