|
| bool | draw = False |
| | main More...
|
| |
| float | cutoff = 2.0 |
| |
| | restype = sys.argv[1] |
| |
| | ncluster = int(sys.argv[2]) |
| |
| string | inpfile = "./split/" + restype + ".dat" |
| |
| | inp = open(inpfile, 'r') |
| |
| | lines = inp.readlines() |
| |
| | skip = int(len(lines)/10000) |
| |
| list | xyzlist = [] |
| |
| list | intlist = [] |
| |
| list | bblist = [] |
| |
| | dats = line.split() |
| |
| | dis = float(dats[0]) |
| |
| | ang = float(dats[1]) |
| |
| | dih = float(dats[2]) |
| |
| | psi = float(dats[3]) |
| |
| | phi = float(dats[4]) |
| |
| | x = dis*sin(ang)*cos(dih) |
| |
| | y = dis*sin(ang)*sin(dih) |
| |
| | z = dis*cos(ang) |
| |
| | data = vstack(xyzlist) |
| | cluster, find the centroid More...
|
| |
| | save_data = data |
| |
| string | fn = "refine/" + restype + ".xyz" |
| |
| def | centroids = load_centroid_xyz(fn, ncluster) |
| |
| | _ |
| |
| | idx |
| |
| | dist |
| |
| | nd = len(data) |
| |
| | savend = nd |
| |
| list | colorlist = ['r', 'b', 'g', 'y', 'c', 'm', 'k', 'w', 'r'] |
| |
| list | marklist = ['o', '^', '+', '>', (5,2), (5,0)] |
| |
| | fig = plt.figure() |
| |
| | ax = fig.add_subplot(111, projection='3d') |
| |
| float | R = 2.0 |
| |
| list | c = colorlist[i] |
| |
| string | m = '.' |
| |
| | flag = i |
| | !!! note: it's too slow, use bined rho as an approximation Step 0 lambda_i for each data phis = np.zeros([savend]) psis = np.zeros([savend]) for nd in xrange(savend): all data phis[nd] = bblist[nd][1] psis[nd] = bblist[nd][0] More...
|
| |
| | xs = save_data[flag, 0] |
| |
| | ys = save_data[flag, 1] |
| |
| | zs = save_data[flag, 2] |
| |
| | n = len(xs) |
| |
| | s |
| |
| | marker |
| |
| | r = sqrt(x*x+y*y+z*z) |
| |
| | t = arccos(z/r) |
| |
| | p = arctan2(y,x) |
| |
| | u |
| |
| | v |
| |
| | color |
| |
| int | kappa_scale = 50 |
| | Adaptive Kernel Desity Estimate. More...
|
| |
| int | kappa = sqrt(savend)/kappa_scale |
| |
| list | prhos = [] |
| |
| list | rhos = [] |
| |
| list | ncs = [] |
| |
| list | phis = [] |
| |
| list | psis = [] |
| |
| | xphi = np.linspace(-180, 180, 36, endpoint=False) |
| | check: make sure the def is compatable with pbc !!! More...
|
| |
| | ypsi = np.linspace(-180, 180, 36, endpoint=False) |
| |
| | philst = np.zeros([n]) |
| |
| | psilst = np.zeros([n]) |
| |
| int | tn = 0 |
| |
| | rho = np.zeros([36,36]) |
| |
| | dphis = philst - phi |
| |
| | dpsis = psilst - psi |
| |
| def | kphis = ksr(dphis,sqrt(n)/kappa_scale) |
| |
| def | kpsis = ksr(dpsis,sqrt(n)/kappa_scale) |
| |
| | rho_dat = np.zeros([savend]) |
| |
| | all_phi = np.zeros([savend]) |
| |
| | all_psi = np.zeros([savend]) |
| |
| | psi_bin |
| |
| | phi_bin |
| |
| | log_rho = np.log(rho_dat) |
| |
| | log_g = np.sum(log_rho)/savend |
| |
| | lambda_i = np.exp( (log_g - log_rho)/2 ) |
| |
| int | kappa_i = kappa / lambda_i |
| |
| | surf |
| |
| | Pr = np.zeros([ncluster]) |
| |
| | sumP = np.zeros([36,36]) |
| |
| list | Pr_pp = [] |
| |
| list | prpp = rhos[i]*Pr[i]/sumP |
| |
| list | dis_lst = [] |
| |
| list | ang_lst = [] |
| |
| list | dih_lst = [] |
| |
| list | vdis_lst = [] |
| |
| list | vang_lst = [] |
| |
| list | vdih_lst = [] |
| |
| | lambda_mat = np.zeros([36,36]) |
| |
| | g = exp(log_g) |
| |
| | kappa_lst = np.zeros([n]) |
| |
| | dis_mat = np.zeros([36,36]) |
| |
| | ang_mat = np.zeros([36,36]) |
| |
| | dih_mat = np.zeros([36,36]) |
| |
| | vdis_mat = np.zeros([36,36]) |
| |
| | vang_mat = np.zeros([36,36]) |
| |
| | vdih_mat = np.zeros([36,36]) |
| |
| def | kernel = kpsis*kphis |
| |
| | denominator = np.sum(kernel) |
| |
| | ddis = dis - dis_mat[x,y] |
| |
| | dang = ang - ang_mat[x,y] |
| |
| | ddih = dih - dih_mat[x,y] |
| |
| float | rr2dd = 1.0 |
| |
| list | dihval = dih_lst[nc][phi_bin, psi_bin]*180/pi |
| |
| list kmeans_adaptive_kernel_density_bb_dependent_rotlib.n = len(xs) |
Referenced by PoseWrap.absrms_to_orig_subsubs(), SphereNode.add_neighbor(), align_pdbs(), align_pdbs_function(), align_pose_general(), allifnone(), dsRNA_grow.append_Aform_residue(), xtal_water_bunsat.apply(), LigChiMover.apply(), DuboisChiMover.apply(), MyRotMover.apply(), PhProtocol.apply(), RNA_ScoreMover.apply(), HDmakerMover.apply(), zinc1_homodimer_design.apply(), apply_mask(), utility.arg_greatest_several(), utility.arg_least_several(), aro_pack_output(), detail::bigint.assign(), assign_rigid_body_settings_to_clusters_test(), atom_tree_torsion_test(), atom_vdw_test(), numeric::interpolation::InterpolatedPotential< N >.axis_range(), benchmark_contacts(), benzene_pair_score_test(), detail::bigint.bigint(), numeric::interpolation::periodic_range::full.bilinearly_interpolated(), numeric::interpolation::periodic_range::half.bilinearly_interpolated(), numeric::interpolation::periodic_range::full.bin(), numeric::interpolation::periodic_range::half.bin(), numeric::model_quality.BlankMatrixMult(), numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), build_helix_test(), build_next_nucleotide_test(), build_on_helix(), abbinding.calc_energies_and_sasa(), calc_median(), calc_min(), calc_rmsd_test(), calculate_binding_energy(), calculate_moments(), calculate_pairwise_RMSD(), calculate_res_map(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), center_ca(), center_heavy(), centroid_rescore_test(), numeric::kinematic_closure.chainParams(), numeric::kinematic_closure::radians.chainParams(), numeric::kinematic_closure.chainTORS(), numeric::kinematic_closure::radians.chainTORS(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), check_alignment_RMSD_cutoff(), check_contact_and_output(), detail::dragonbox.check_divisibility_and_divide_by_pow5(), check_lengths(), check_multilinear_interpolation(), check_oxygen_contact_and_output(), check_protein_rna_clash(), check_redundant(), check_spline(), check_tensor(), chi_stats_test(), clone(), close_loops(), cluster_outfile_test_OLD(), cluster_rigid_body_settings_test(), coarse_frag_test(), coarse_rb_test(), detail.code_point_index(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), numeric::AverageLinkClusterer.comparator(), compute_windowed_rama(), compute_windowed_rmsd(), constraint_set_slice(), numeric::alignment.coordinate_array_rmsd(), copy_DOFS_local(), copy_rotamerized_torsions(), copy_virtual_variant_type(), numeric::statistics.corrcoef_with_provided_mean_and_std_dev(), detail.count_digits(), detail.count_digits< 4 >(), numeric::statistics.cov_with_provided_mean(), binder.cpp_python_operator(), create_base_pair_step_database_test(), create_rna_vall_torsions_test(), cst_relax_test(), define_states_test(), delta_chi_correction_test(), zinc2_homodimer_design.design_symmetric_homodimer_metal_interface(), design_test(), numeric::interpolation::spline::PolycubicSpline< N >.dFdall(), numeric::interpolation::spline::PolycubicSpline< N >.dFdxi(), dinucleotide_test(), diversify_sam_loop_test(), detail::dragonbox.divide_by_10_to_kappa_plus_1(), dna_chain_check(), dna_design_test(), dna_geometry(), dna_io_test(), dna_nbr_radii_test(), dna_stats(), dna_test(), do_color_by_score(), do_the_match(), dump_points_pdb(), each_aa_test(), easy_target_test(), energy_cluster(), env_sugar_test(), erraser_monte_carlo(), PerformanceBenchmark.execute(), utility::BitVector< B >.expand(), utility::BitVector< B >.expand_tight(), extract_pdbs_test(), figure_out_stems(), figure_out_which_sequence_is_template(), files_for_openMM_test(), detail.fill(), filter_combine_long_loop(), PhProtocol.finalize_res_list(), find_close_parents(), find_index(), fixH(), formatter< detail::bigint >.format(), format_to_n(), detail.format_uint(), format_int.format_unsigned(), frag_extract_test(), binder.function_arguments_for_lambda(), numeric.gcd(), ObjexxFCL.gcd(), generalize_gaussian_chain_func_test(), binder::Context.generate(), get_avrgcrd(), get_boltzmann_probabilities(), get_bps_tag(), numeric::interpolation::spline::PolycubicSpline< N >.get_deriv(), numeric::interpolation::spline::PolycubicSpline< 1 >.get_deriv(), numeric::interpolation::spline::PolycubicSpline< 2 >.get_deriv(), get_lj_atom_score(), get_loop_for_n_mer(), get_max_and_intervals(), get_median(), get_min_frag_rmsd(), get_moment_of_inertia(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_ncac(), numeric::interpolation.get_patch(), get_phi_psi_mm(), get_pose_and_numbering(), get_quota_per_silent(), get_random_bundle_ids(), TestQuickRelaxMover.get_repack_residues(), get_repl_xyz(), utility.get_resnum_and_chain_and_segid(), utility.get_resnum_and_chain_from_one_tag(), utility.get_resnum_and_segid(), utility.get_resnum_and_segid_from_one_tag(), get_ring_centroids_and_stubs(), get_sidechain_rmsd(), numeric::interpolation.get_val(), graft_pdb(), grid_matcher(), hbond_stats(), hermann_phase_two(), hermann_phase_two_minimize(), homolog_finder(), idealize_tf_pose(), numeric::geometry::hashing::SixDOffsetTree.init(), initialize_fa_rep(), initialize_for_grid_matcher(), initialize_native_pose(), initialize_sequence_mask(), input_subset_poses(), input_torsion_M_v_lists(), insert_chunk(), int2str(), int2string(), interface_repack_test(), numeric::interpolation::periodic_range::full.interpolated(), numeric::interpolation::periodic_range::half.interpolated(), ObjexxFCL.ints_of(), numeric::MathMatrix< T >.inverse_tridiagonal_matrix(), numeric::fourier::SHT.inverseSo3(), binder::Config.is_namespace_binding_requested(), binder::Config.is_namespace_skipping_requested(), is_new_cluster_center_second_stage(), is_subset(), jacobi(), juke_sam_test(), numeric::fourier.kf_factor(), numeric::fourier::kiss_dct_state.kiss_dct_state(), numeric::fourier.kiss_fft_next_fast_size(), numeric::fourier::kiss_fft_state.kiss_fft_state(), numeric::fourier::kiss_fftnd_state.kiss_fftnd_state(), numeric::fourier::kiss_fftndr_state.kiss_fftndr_state(), numeric::fourier.kiss_fftr_next_fast_size_real(), numeric::fourier::kiss_fftr_state.kiss_fftr_state(), numeric::fourier::kiss_fftsplit_state.kiss_fftsplit_state(), numeric::fourier::SO3coeffs.Legendre(), ligrot_test(), detail::fixed_buffer_traits.limit(), numeric::nls.lm_enorm(), numeric::nls.lm_lmdif(), numeric::nls.lm_lmpar(), numeric::nls.lm_qrfac(), numeric::nls.lm_qrsolv(), numeric::nls.lmmin(), numeric::geometry::hashing::SixDOffsetTree.lookup(), luxr_test(), m_inv_gen(), main(), utility.make_segtag_with_dashes(), make_symm_data(), utility.make_tag(), utility.make_tag_with_dashes(), make_your_own_alignment(), makemask(), numeric::model_quality.MatrixMult(), numeric::model_quality.maxsub(), minimize_pdb(), minimize_poses(), minimize_protocol(), minimizer_test(), mismatch_test(), ObjexxFCL.mod(), modeler_closure_test(), modeler_map_test(), morph_by_internal_coords(), morph_pdbs_test(), motif_scan(), ExposedStrandMover.move_superimpose(), numeric::interpolation.multilinear_interpolation(), multimodel_gdt(), detail::bigint.multiply(), mutate_and_score_RNP(), mutate_residues_wrapper(), my_main(), utility::options::OptionCollection.n_part_prefix_match(), ui::task::Task.name(), binder.namespace_from_named_decl(), ObjexxFCL::format.nl_if(), normalize_res_freqs(), nucleobase_probe_score_test(), o2prime_packer(), detail::int_writer< OutputIt, Char, UInt >.on_num(), numeric::interpolation::TempStruct< T, N >.operator()(), numeric::interpolation::TempStruct< T, 1 >.operator()(), detail::accumulator.operator+=(), detail::uint128_wrapper.operator+=(), ObjexxFCL::byte.operator<<(), ObjexxFCL::ubyte.operator<<(), detail::bigint.operator<<=(), ObjexxFCL::byte.operator>>(), ObjexxFCL::ubyte.operator>>(), optimize_weights(), output_benchmark_stuff(), output_chi_stats(), output_constraints(), output_general_base_pair_steps(), output_strand1_strand2_info(), output_sugar_geometry_parameters(), output_sugar_internal_dof(), output_torsion_list(), output_torsion_M_v_lists(), pack_phosphates(), parse_pathway_test(), pass_VDW_replusion_screen_fast(), SphereSample.pdb_from_level(), pdb_stats(), pdb_to_silent_file(), pdbstats_test(), basic::sampling::orientations::Permute.Permute(), numeric::interpolation.polycubic_interpolate_catmull_rom(), pose2bin(), post_rebuild_bulge_assembly(), predict_chem_map_test(), utility::options::OptionCollection.prefix(), prepare_full_length_start_model(), prepare_start_model(), dsRNA_grow.prepend_Aform_residue(), print_all_torsions_test(), print_hbonds_test(), print_secstruct_test(), process_ss_str(), protein_helix_test(), ui::util::TreeNodeModel< T >::Node.push_back(), put_constraints_on_helix(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), numeric::linear_algebra.qzhes(), numeric::linear_algebra.qzit(), numeric::linear_algebra.qzval(), numeric::linear_algebra.qzvec(), rb_entropy_test(), read_alignment_fasta_file(), read_fragdata(), read_frags(), read_RDC_file(), SphereSample.read_sphere_data(), numeric.read_tensor_from_file(), read_tensor_test(), register_options(), numeric::RemainderSelector< T, bool >.remainder(), numeric::RemainderSelector< T, true >.remainder(), ObjexxFCL::RemainderSelector< T, bool >.remainder(), ObjexxFCL::RemainderSelector< T, true >.remainder(), basic_string_view< Char >.remove_prefix(), detail::dragonbox.remove_trailing_zeros(), replace_torsion_angles(), myspace.report_data(), rescore_test(), detail::arg_formatter_base< OutputIt, Char, ErrorHandler >.reserve(), detail.reserve(), numeric::fourier::kiss_fft_state.resize(), numeric::fourier::kiss_dct_state.resize(), numeric::fourier::kiss_fftsplit_state.resize(), numeric::fourier::kiss_fftr_state.resize(), numeric::fourier::kiss_fftnd_state.resize(), numeric::fourier::kiss_fftndr_state.resize(), reverse(), reverse_rbs_test(), numeric::linear_algebra.rgg(), rhiju_pdbstats(), PoseWrap.rms_to_orig_subsubs(), abbinding.rmsd_frmk_chothia_num_ab(), rna_assemble_test(), rna_backbone_rebuild_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_chain_closure_test(), rna_idealize_test(), rna_protein_pdbstats_test(), rna_protein_rb_test(), RNA_ScoreMover.RNA_ScoreMover(), rna_sequence_recovery_metrics(), rna_stack_pdbstats_from_pose(), rna_stats_test(), numeric::xyzTransform< T >.rt6(), run(), ScoreFragmentSetMover.run(), FragmentAssemblyMover.run(), ConsensusFragmentMover.run(), SolutionRescoreMover.run(), core::pack::annealer::FixbbSimAnnealer.run(), run_parallel_docking(), sample_rna_dofs_new(), sample_trp_test(), sample_trp_tyr_test(), SphereSample.sanity_check(), sasa_test(), scmove_residue(), screen_phosphates(), dsRNA_grow.set_Aform_torsions(), set_helix_torsions(), setup_alignment_map(), setup_atom_id_map(), setup_backbone_atoms(), setup_copy_DOF_input(), setup_crazy_fold_tree(), setup_domain_list(), setup_heavy_atoms(), setup_hydrophobic_cbetas(), setup_mask(), setup_pose(), setup_rhiju_fold_tree(), setup_rna_base_pair_constraints(), sicdock_thread_num(), sidechain_sample(), simple_opte_test(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), detail::dragonbox.small_division_by_pow10(), small_min_test(), solve_one_class(), utility::options::OptionCollection.space_prefixed(), spec_test(), spinner_test(), numeric::interpolation::spline.spline_interpolate(), numeric::interpolation::spline.spline_second_derivative(), detail::bigint.square(), ss_ds_ts_assign_test(), detail::bigint.subtract_aligned(), utility::options::OptionCollection.suffix(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), superimpose_pdb(), superimpose_tmalign(), numeric::linear_algebra.svdcmp(), svm_load_model(), ObjexxFCL::format.SW(), swa_rna_sample(), utility::options::OptionCollection.tab_prefixed(), tar_motif_test(), numeric::kinematic_closure.test_chainParams(), numeric::kinematic_closure.test_chainTORS(), numeric::kinematic_closure.test_chainXYZ(), test_chi_xform(), numeric::kinematic_closure.test_dixon(), test_MAT_VEC(), test_numerical_deriv(), detail.to_pointer(), numeric::fourier.transpose_so3(), utility::options::OptionCollection.trim(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), utility::options::OptionCollection.trimmed(), two_base_pairs_test(), two_base_pairs_via_loop_closure_test(), unvirtualize_phosphates(), ui::task::Updater.update_data_ready(), ui::task::Node.update_from_json(), vary_geometry_backbone(), vary_geometry_RNA(), vary_geometry_sidechains(), numeric::geometry.vector_normal_to_ring_plane_of_best_fit(), vformat_to_n(), numeric::statistics.w(), numeric::fourier::SO3coeffs.wignerSynthesis(), numeric::fourier::SO3coeffs.wignerSynthesisDiffSign(), numeric::fourier::SO3coeffs.wignerSynthesisSameSign(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >.write(), detail.write_buffer(), zf_relax_test(), and zf_test().
| kmeans_adaptive_kernel_density_bb_dependent_rotlib.p = arctan2(y,x) |
Referenced by add_fa_cst(), SphereNode.add_parent(), binder.add_relevant_include_for_decl(), ConstraintConfig.add_sym_cst(), add_symm_sf4(), add_symm_zns(), advance_to(), align_sf4(), align_zns(), numeric::BodyPosition< T >.apply(), OutputCenrotIntCoord.apply(), RepackCenrotMover.apply(), SmoothFragRepackMover.apply(), RescoreCenrot.apply(), RepackMinCenrotMover.apply(), ConstraintConfig.apply_bb_csts(), ConstraintConfig.apply_cen_csts(), ConstraintConfig.apply_csts(), ConstraintConfig.apply_dcsts(), ConstraintConfig.apply_fa_csts(), ObjexxFCL::CArray< T >.assign(), ObjexxFCL::CArrayP< T >.assign(), attach_abego_pools(), attach_simple_abego_pools(), binder.bind_function(), blosum_score_alignment(), Bola.Bola(), calc_c3_rmsd(), HPatchNPDCalculator.calculate(), HPatchByChainNPDCalculator.calculate(), NBuriedUnsatsCalcultor.calculate(), ObjexxFCL::CArray< T >.CArray(), ObjexxFCL::CArrayP< T >.CArrayP(), numeric::interpolation.catmull_rom_interpolate_basic(), HubDenovo.cen_fold(), center_ca(), center_heavy(), Tensor.check(), clashcheck(), clashcheckhalf(), numeric::geometry::BoundingBox< T >.contains(), create_ensemble(), create_random_pose(), cxdock_design(), ddg(), HubDenovo.design(), design(), design_cluster(), design_hits(), detect_neighbors(), do_two(), dock(), utility.down_cast(), dump_energy_kinemage(), dump_points_pdb(), dump_points_pdb_contacts(), dump_unique_atoms(), ui::task::Node.erase(), DisulfideBondEnergy.evaluate(), ObjexxFCL::format.F(), detail::fallback_uintptr.fallback_uintptr(), fastexp(), fastpow2(), basic::resource_manager::locator::FileStream.FileStream(), ui::task::Node.find(), find_clusters(), fit_centroid_to_the_best_rot(), fitfun(), ObjexxFCL.fixed_Fstring_of(), ObjexxFCL.fixed_string_of(), PyCallBack_aaa_A_double_t.foo(), for(), detail.format_uint(), ObjexxFCL.Fstring_of(), binder.function_arguments_for_py_overload(), ObjexxFCL.general_Fstring_of(), ObjexxFCL.general_string_of(), get_ABGEO_string(), get_best_rotamer_index(), get_coordinate_system(), get_ddg(), numeric::interpolation::spline::SplineGenerator.get_interpolator(), get_max_and_intervals(), get_ncac(), MPInterfaceStatistics.get_size(), get_surface_points(), gpu_refold_test(), gpu_score_test(), harvest_scores(), header(), numeric.hsv_to_rgb(), numeric::geometry::hashing::SixDOffsetTree.init(), numeric::interpolation::InterpolatedPotential< N >.InterpolatedPotential(), intersecting_bpy_axes(), intersecting_disulfide_axes(), numeric::BodyPosition< T >.inverse_transform(), numeric::BodyPosition< T >.inverse_transformed(), binder.is_bindable_raw(), is_near_C2Z_iface(), ui::task::TaskSyncer_TaskStrategy.is_syncing(), numeric::fourier.kf_bfly_generic(), numeric::fourier.kf_factor(), numeric::fourier.kf_work(), numeric::statistics.kl_divergence(), kono_sarai_stats(), kono_sarai_zscore(), numeric::BodyPosition< T >.left_transform_by(), numeric::BodyPosition< T >.left_transform_by_inverse_of(), line_cone_intersection(), PosePyObserver.link(), Link.Link(), numeric::geometry::hashing::SixDOffsetTree.lookup(), main(), detail.make_checked(), make_coiled_coil(), HubDenovo.make_start_pose(), makerots(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_equal_operator(), merge_motifs(), HubDenovo.min_as_poly_ala(), minimize_with_constraints(), motif_column_deviation(), multiclass_probability(), my_main(), ui::task::Node.node_index(), num_nbrs(), detail::int_writer< OutputIt, Char, UInt >.on_num(), numeric::BodyPosition< T >.operator()(), numeric::interpolation::TempStruct< T, N >.operator()(), numeric::interpolation::TempStruct< T, 1 >.operator()(), operator<<(), std.operator<<(), numeric.operator<<(), numeric::sphericalVector< T >.operator=(), numeric::xyzTriple< T >.operator=(), numeric::xyzVector< T >.operator=(), numeric.operator>>(), optimize_pose(), detail.parse_align(), detail.parse_format_string(), passes_quality_check(), pca_align_BROKEN(), SphereSample.pdb_from_level(), place_sf4(), place_zns(), ui::task::PNode.PNode(), numeric::linear_algebra.point_in_ellipse(), JDmover.print_features(), print_header(), process_the_pose(), ObjexxFCL::CArrayP< T >.Proxy(), ptr(), PYBIND11_MODULE(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), numeric.read_probabilities_or_die(), SphereSample.read_sphere_data(), DisulfideBondEnergy.rebuildAndDetectDisulfideBond(), referenceRDC(), refold_ros(), relax_cenrot_pose(), repack(), repack_cluster(), repack_iface(), numeric::MathNTensor< T, N >.replace_layer(), replace_nat_seq(), rescore_pose(), numeric::geometry::BoundingBox< T >.reset(), HubDenovo.reset_hub(), numeric::BodyPosition< T >.right_transform_by(), numeric::BodyPosition< T >.right_transform_by_inverse_of(), myMC.roll(), rotamerize_rna_test(), run(), run_mc(), SphereSample.sanity_check(), ObjexxFCL.scientific_Fstring_of(), ObjexxFCL.scientific_string_of(), ui::task::ProjectModel.set(), numeric::geometry::BoundingBox< T >.set_lower(), numeric::HomogeneousTransform< T >.set_point(), set_temp_based_on_ens_diversity(), numeric::geometry::BoundingBox< T >.set_upper(), protocols::abinitio::JumpSpecificAbrelax.setup_jumps(), numeric::fourier::SHT.setup_Pmls(), DomainDescription.sheet_match(), sicdock_thread_num(), sigmoid_train(), binder.simplify_std_class_name_raw(), detail.snprintf_float(), binder::Context.sort_binders(), sphere_coverage(), numeric::interpolation::spline.spline_second_derivative(), DomainDescription.ss_match(), binder.standard_name_raw(), store_energies(), ObjexxFCL.string_of(), utility.strip(), svm_load_model(), svm_predict_values(), svm_save_model(), svm_train(), DisulfideBondEnergy.tabulate(), ui::ui_lib_test.test(), TEST(), test_chi_xform(), test_find_neighbors(), test_refold(), utility::json_spirit.to_str(), detail.to_uintptr(), numeric::interpolation::spline::PolycubicSpline< N >.train(), numeric::BodyPosition< T >.transform(), numeric::BodyPosition< T >.transformed(), numeric::kinematic_closure::radians.triaxialCoefficients(), numeric::kinematic_closure.triaxialCoefficients(), detail::dragonbox.umul128_upper64(), PosePyObserver.unlink(), ui::task::Node.update_from_json(), ui::viewers::ScoreFileView.update_ui_from_file_data(), updateSSAtoms(), use_backrub(), detail::utf8_to_utf16.utf8_to_utf16(), weights(), detail::arg_formatter_base< OutputIt, Char, ErrorHandler >.write_pointer(), and xyz().
| kmeans_adaptive_kernel_density_bb_dependent_rotlib.v |
Referenced by basic::sampling::orientations::QuatSet.Add(), add(), ui::task::FunctorSequence.add_functor(), ui::task::FunctorASyncSequence.add_functor(), binder.add_relevant_includes(), allifnone(), angle_degrees(), ObjexxFCL::ChunkVector< T >.append(), utility::vectorL< L, T, A >.append(), utility::vectorL< L, bool, A >.append(), utility.argsort(), array2vecs(), ObjexxFCL::ChunkVector< T >.assign(), assign_rigid_body_settings_to_clusters_test(), numeric::VoxelArray< _Float, _Value >.at(), bk_test(), utility::graph.breadth_first_visit_prune(), basic::TracerImpl.calculate_tracer_level(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), check_6D_potential(), ObjexxFCL::ChunkVector< T >.ChunkVector(), utility::options::VectorOption_T_< K, T >.cl_value(), numeric::geometry::hashing::MinimalClashHash.clash(), numeric::geometry::hashing::xyzStripeHash.clash(), numeric::geometry::hashing::xyzStripeHash.clash_amount(), numeric::geometry::hashing::xyzStripeHash.clash_not_resid(), numeric::geometry::hashing::xyzStripeHash.clash_raw(), clashcheck(), clashcheckhalf(), numeric::xyzMatrix< T >.col(), numeric::xyzMatrix< T >.col_x(), numeric::xyzMatrix< T >.col_y(), numeric::xyzMatrix< T >.col_z(), VecMaxElement.convert(), VecMinElement.convert(), VecLen.convert(), VecMean.convert(), VecContains.convert(), MatchSet.cross(), numeric::xyzTriple< T >.cross(), numeric::xyzVector< T >.cross(), MatchSet.cross_homodimer(), numeric::xyzTriple< T >.cross_product(), numeric::xyzVector< T >.cross_product(), numeric::geometry::hashing::xyzStripeHash.debug_pdb(), utility::deep_copy_vector1< T >.deep_copy_vector1(), utility::graph.depth_first_visit_sort_impl(), numeric::xyzTriple< T >.distance(), numeric::xyzVector< T >.distance(), numeric::xyzTriple< T >.distance_squared(), numeric::xyzVector< T >.distance_squared(), numeric::xyzTriple< T >.dot(), numeric::xyzVector< T >.dot(), numeric::xyzTriple< T >.dot_product(), numeric::xyzVector< T >.dot_product(), Link.dump_pdb(), Bola.dump_pdb(), dumpcgo(), eq(), numeric::xyzTriple< T >.equal_length(), numeric::xyzVector< T >.equal_length(), ObjexxFCL::FArray< T >.FArray(), fastpow2(), files_for_openMM_test(), numeric::geometry::hashing::xyzStripeHash.fill_pairs(), find_middle_of_vector(), basic::TracerImpl.flush_all_channels(), utility::py.foo_all(), utility::py.foo_all_sp(), utility::py::Base.foo_value(), utility::py::Base.foo_value_sp(), utility.fractional_rank(), numeric::xyzTransform< T >.from_four_points(), numeric.from_json(), rosetta_binders.generic_add_on_binder_maybe_has_insertion_operator(), get_median(), get_rmsd(), get_rmsd_debug(), getclosest(), getline(), utility::tag::Tag.getTag(), harvest_scores(), has_element(), numeric::deriv.helper(), numeric.hsv_to_rgb(), basic::TracerImpl.in(), ui::network::IndexPack.IndexPack(), utility.indices1(), TCDock.init(), numeric::xyzTriple< T >.inner_product(), numeric::xyzVector< T >.inner_product(), input_torsion_M_v_lists(), numeric::xyzTransform< T >.intersect3D_2Planes(), intersecting_bpy_axes(), intersecting_disulfide_axes(), numeric::xyzTransform< T >.inv_xform(), utility.is_finite(), jacobi(), length2v(), lengthv(), line_cone_intersection(), rosetta_binders.list_add_on_binder(), rosetta_binders.list_add_on_binder_maybe_has_equal_operator(), numeric::xyzTriple< T >.longer(), numeric::xyzVector< T >.longer(), numeric::xyzTriple< T >.longer_or_equal(), numeric::xyzVector< T >.longer_or_equal(), m_inv_gen(), main(), utility::tools.make_vector(), utility::tools.make_vector1(), numeric::sphericalVector< T >.max(), numeric::xyzTriple< T >.max(), numeric::xyzVector< T >.max(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_copy_constructible(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_equal_operator(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_insertion_operator(), numeric::sphericalVector< T >.min(), numeric::xyzTriple< T >.min(), numeric::xyzVector< T >.min(), numeric::kinematic_closure.modp(), multxv(), myasserteq(), numeric::geometry::hashing::xyzStripeHash.nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.nbcount(), numeric::geometry::hashing::xyzStripeHash.nbcount_raw(), normalizevector(), numeric::xyzTriple< T >.not_equal_length(), numeric::xyzVector< T >.not_equal_length(), formatter< TupleT, Char, enable_if_t< fmt::is_tuple_like< TupleT >::value > >::format_each< FormatContext >.operator()(), CheeseFunction.operator()(), numeric::xyzMatrix< T >.operator*(), ObjexxFCL::ChunkVector< T >.operator+=(), numeric::sphericalVector< T >.operator+=(), numeric::xyzTriple< T >.operator+=(), numeric::xyzVector< T >.operator+=(), ObjexxFCL::ChunkVector< T >.operator-=(), numeric::sphericalVector< T >.operator-=(), numeric::xyzTriple< T >.operator-=(), numeric::xyzVector< T >.operator-=(), std.operator<<(), utility.operator<<(), utility::py.operator<<(), operator<<(), numeric.operator<<(), ObjexxFCL.operator<<(), basic::Report.operator<<(), basic::Reporter.operator<<(), ObjexxFCL::ChunkVector< T >.operator=(), utility::deep_copy_vector1< T >.operator=(), numeric::sphericalVector< T >.operator=(), utility::vector0< T, A >.operator=(), utility::vector0< bool, A >.operator=(), utility::vector1< T, A >.operator=(), utility::vector1< bool, A >.operator=(), utility::vectorL< L, T, A >.operator=(), utility::vectorL< L, bool, A >.operator=(), numeric::xyzTriple< T >.operator=(), numeric::xyzVector< T >.operator=(), operator>>(), numeric.operator>>(), ConstraintConfig.parse_config_file(), parse_into_stub(), parse_numbers(), pdb_to_silent_file_simple(), proj(), numeric::xyzTriple< T >.project_normal(), numeric::xyzVector< T >.project_normal(), numeric::xyzTriple< T >.project_parallel(), numeric::xyzVector< T >.project_parallel(), numeric::xyzTriple< T >.projected_normal(), numeric::xyzVector< T >.projected_normal(), numeric::xyzTriple< T >.projected_parallel(), numeric::xyzVector< T >.projected_parallel(), projperp(), pymol(), rand_Vec(), rand_Vec_condition(), random_element(), numeric::random::RandomGenerator.random_element(), randomly_shift_and_tilt_pose(), randomly_shift_and_tilt_poses(), randvec(), replace_torsion_angles(), ObjexxFCL::ChunkVector< T >.reshape(), rg2d(), rotx(), roty(), numeric::xyzMatrix< T >.row(), numeric::xyzMatrix< T >.row_x(), numeric::xyzMatrix< T >.row_y(), numeric::xyzMatrix< T >.row_z(), run(), core::pack::annealer::FixbbSimAnnealer.run(), numeric::sphericalVector< T >.scaled_add(), numeric::xyzTriple< T >.scaled_add(), numeric::xyzVector< T >.scaled_add(), numeric::sphericalVector< T >.scaled_assign(), numeric::xyzTriple< T >.scaled_assign(), numeric::xyzVector< T >.scaled_assign(), numeric::sphericalVector< T >.scaled_sub(), numeric::xyzTriple< T >.scaled_sub(), numeric::xyzVector< T >.scaled_sub(), rosetta_binders.set_add_on_binder(), basic::options.set_boolean_option(), basic::options.set_boolean_vector_option(), basic::options.set_file_option(), basic::options.set_file_vector_option(), basic::options.set_integer_option(), basic::options.set_integer_vector_option(), basic::options.set_path_option(), basic::options.set_path_vector_option(), basic::options.set_real_option(), basic::options.set_real_vector_option(), utility::options::OptionCollection.set_show_accessed_options_flag(), utility::options::OptionCollection.set_show_unused_options_flag(), basic::options.set_string_option(), basic::options.set_string_vector_option(), numeric::xyzTriple< T >.shorter(), numeric::xyzVector< T >.shorter(), numeric::xyzTriple< T >.shorter_or_equal(), numeric::xyzVector< T >.shorter_or_equal(), sicdock_thread_num(), Solver.Solve(), numeric::linear_algebra.svdcmp(), ObjexxFCL::ChunkVector< T >.swap(), ObjexxFCL::FArray1D< T >.swap(), ObjexxFCL::FArray2D< T >.swap(), ObjexxFCL::FArray3D< T >.swap(), ObjexxFCL::FArray4D< T >.swap(), ObjexxFCL::FArray5D< T >.swap(), ObjexxFCL::FArray6D< T >.swap(), ObjexxFCL::KeyFArray1D< T >.swap(), ObjexxFCL::KeyFArray2D< T >.swap(), ObjexxFCL::KeyFArray3D< T >.swap(), ObjexxFCL::KeyFArray4D< T >.swap(), ObjexxFCL::KeyFArray5D< T >.swap(), ObjexxFCL::KeyFArray6D< T >.swap(), utility::vectorL< L, T, A >.swap(), utility::vectorL< L, bool, A >.swap(), ObjexxFCL::FArray2< T >.swap2DB(), ObjexxFCL::FArray3< T >.swap3DB(), utility.swap4_aligned(), ObjexxFCL::FArray4< T >.swap4DB(), ObjexxFCL::FArray5< T >.swap5DB(), ObjexxFCL::FArray6< T >.swap6DB(), ObjexxFCL::FArray< T >.swapB(), TCDock.TCDock(), test_fake_silent(), test_GA(), test_MAT_VEC(), numeric.to_json(), numeric::HomogeneousTransform< T >.to_local_coordinate(), detail.unwrap(), ui::network::PathArgument.update_label_text(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.utility_vector_binder(), ui::network::StringArgument.value(), vecs2vv(), numeric::geometry.vector_normal_to_ring_plane_of_best_fit(), ui::task::Task.version(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.visit(), numeric::geometry::hashing::xyzStripeHash.visit(), numeric::geometry::hashing::xyzStripeHash.visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >.visit_lax(), wrap_CXXRecordDecl(), numeric.write_tensor_to_file(), numeric::xyzTransform< T >.xform(), numeric::xyzTransform< T >.xyzTransform(), rosetta_binders.xyzVector_add_on_binder(), zcyl_score(), and basic::TracerImpl.~TracerImpl().
