- t -
- t
: cal_env.m
, draw_gen_env_dep_pair_decompose.m
, gen_vdw_radius_soft.m
- tag
: Tag.cc
- TD
: TwoChainInterface.cc
, TwoChainTenANeighbors.cc
- td
: analyze_dna.cc
, dimer_relax.cc
, dna_relax.cc
, zf_relax.cc
- template_interface
: david_pocket_align_and_save.cc
- tetrahedral_angle_sumsq_cutoff
: zinc2_homodimer_setup.cc
- th1_table
: load_angle_r_table.m
- th2_table
: load_angle_r_table.m
- thickness
: mp_parameters.cc
- THR
: draw_gen_env_dep_pair_decompose.m
, gen_vdw_radius.m
, load_pair_env_table.m
, load_angle_r_table.m
, gen_env_dep_pair_decompose.m
, gen_env_dep_pair.m
, gen_env_dep_orient_draw.m
, gen_env_dep_orient_decompose.m
, gen_env_dep_orient.m
, load_pair_env_table_ref.m
, load_pair_env_table.m
, cal_env.m
, draw_matrix.m
, draw_gen_env_dep_pair.m
, draw_gen_env_dep_orient_decompose.m
- TI
: TwoChainInterface.cc
, TwoChainTenANeighbors.cc
- ti
: zf_relax.cc
, dna_relax.cc
, dna_spec_test.cc
, dimer_relax.cc
, analyze_dna.cc
- tlc
: get_dihedral_peptide.cc
- TM
: OptionsTest.cc
, TracerTest.cc
- top
: Tag.cc
- toRelax_poseOP
: minimalCstRelax.cc
- TR
: test_trRosettaProtocolMover.cc
, symmetrize_old_ramamap.cc
, test_trRosettaConstraintGenerator.cc
, test_trRosetta.cc
, test_tensorflow_graph_convolutional_nn.cc
, test_multithreaded_ramapp_load.cc
, test_multithreaded_pdb_load.cc
, test_multithreaded_packing_performance.cc
, test_multithreaded_ig_correctness.cc
, test_makebundlehelix_mover.cc
, test_makebundle_mover.cc
, tensorflow_test1.cc
, symmetrize_rotlib.cc
, graphics_demo.cc
, long_loop.cc
, cenrot_bbsc_demo.cc
, cenrot_jd2.cc
, cyclic_sampler.cc
, fa_to_cenrot_score.cc
, gen_cav_ball.cc
, general_pair_counting.cc
, test_bbmc.cc
, test_cen_rot.cc
, test_cluster.cc
, whitney_identify_epitope.cc
, peptide_minimizer.cc
, whitney_local_backrub.cc
, mpi_helixAssembly.cc
, simple_interfaceanalyzer.cc
, sym_fixbb.cc
, xml_task_printer.cc
, BundleDumper.cc
, BundlePairRmsdCalculator.cc
, BundlePairRmsdCalculatorGPU.cc
, CompareBundleToNative.cc
, HelicalAssembly.cc
, InterfaceStrandFinderMover.cc
, loophash_createfiltereddb.cc
, model_dumper.cc
, ModelTrimmer.cc
, MotifFinder.cc
, symmetrize_new_ramamap.cc
, NodePairRmsdCalculator.cc
, PrepareGraphNodes.cc
, SewAppend.cc
, SewingAssembler.cc
, SmotifHasher.cc
, SmotifPairRmsdCalculatorGPU.CC
, tseng_minimize.cc
, cycpep_analysis.cc
, fit_helixparams.cc
, make_mainchain_potential.cc
, plot_scoreterm.cc
, symmetrize_3d_ramamap.cc
, genI213_2dsf.cc
, dxdock_movie.cc
, FunGroupTK.cc
, FunGroupTK_test.cc
, gen3bpy.cc
, gen_d2.cc
, gen_d2_3his_ooc.cc
, gen_d2_4his.cc
, gen_d2_hhhc.cc
, gen_disulf_homodimer.cc
, gen_homo_hc.cc
, gen_xtal_dimer_from_trimer.cc
, genI213.cc
, genI213_2comp.cc
, dxdock.cc
, genI213_gensym.cc
, genI213_nocontacts.cc
, genmatch.cc
, genmatch_3bpy.cc
, genmatch_d6_bhhcg.cc
, genmatch_d6_bpy.cc
, genmatch_m8.cc
, genP23.cc
, gensym_3bpy_from_dimer.cc
, gentetra.cc
, gentetra_bpy_from_znhis.cc
, gentetra_from_trimer.cc
, ragul_test_darc.cc
, cycgly_bbg8t3a.cc
, whitney_repack_input.cc
, whitney_specificity_switch.cc
, holes.cc
, atom_design.cc
, bpy.cc
, coiled_coil.cc
, coiled_coil_zn.cc
, crossmatch.cc
, crossmatch_3e.cc
, crossmatch_d2.cc
, CXdock.cc
, cxdock_sheet.cc
, CXdock_TMP.cc
, whitney_prepare_native.cc
, cycgly_canonical.cc
, cycgly_superimpose.cc
, cycgly_target.cc
, cycsamp.cc
, d3_bpy_linker.cc
, design_DL.cc
, gpu_cbdock.cc
, disulf_stat.cc
, dock_asym.cc
, dubois.cc
, dubois_graft.cc
, dump_res.cc
, mp_rsd_energies.cc
, membrane_sampling.cc
, read_mp_pose.cc
, read_mp_pose_from_seq.cc
, read_pose_from_seq.cc
, sample_tilt_protocol.cc
, test_mp_rmsd.cc
, transform_into_membrane.cc
, translate_membrane_pose.cc
, translate_view_membrane.cc
, visualize_membrane.cc
, color_by_lipid_type.cc
, enumerate_rotamers.cc
, find_optimal_hydrophobic_thk.cc
, membrane_relax2.cc
, cal_nonoverlap_scores.cc
, cal_overlap_scores.cc
, place_fragments_into_density.cc
, score_jd2_replonly.cc
, density_res_zscores.cc
, block_stack_test.cc
, check_cubic_conv.cc
, generalize_gaussian_chain_func_test.cc
, homolog_finder_farna.cc
, pack_phosphates.cc
, pack_polar_hydrogens.cc
, rb_entropy.cc
, pymol_viewer_test.cc
, transform_into_mem.cc
, sarah_get_pharmacophores.cc
, simon_darc_minimize.cc
, check_rotation.cc
, embed_mp_pose_from_topo.cc
, membrane_foldtree.cc
, membrane_foldtree2.cc
, membrane_info.cc
, membrane_integration.cc
, membrane_pose_test.cc
, mp_database_check.cc
, mpframework_integration.cc
, mpframework_time_bchmk.cc
, read_tensor.cc
, membrane_rsd_energy_breakdown.cc
, membrane_sfxn.cc
, mp_scoring_feature_reporter.cc
, mp_sfxn_integration.cc
, mpframework_score.cc
, mpscore_integrate.cc
, virtual_residue_trees.cc
, visualize_membrane.cc
, make_canonical_helix.cc
, membrane_fa_scorefxn.cc
, membrane_scorefxn.cc
, membrane_ddG.cc
, PDB_diagnostic.cc
, find_consensus_mutations.cc
, minimization_test.cc
, msd.cc
, msd_jd2.cc
, recon_mpi.cc
, bb_cluster.cc
, cluster_hotspot_docking.cc
, generate_hbond_geometry.cc
, lowresdock_patchdock_hotspot_cst.cc
, match_disulfide_to_scaffold.cc
, score_hotspot_cst.cc
, tmalign_cluster.cc
, AlanineScanner.cc
, PyMOLDemo.cc
, Extender.cc
, FloppyTail_loop.cc
, HECT.hh
, LoopAnalyzer.cc
, sasa_qd.cc
, UBQ_UBQ_E2.cc
, RBSegMove_test.cc
, RBSegMove_test_viewer.cc
, dna_motifs_collector.cc
, motif_dna_packer_design.cc
, buried_polar_finder.cc
, InterfaceMutMaker.cc
, find_position_matches_using_inverse_rotamers.cc
, screen_phosphates.cc
, stepwise_lores_test.cc
, MetalInterfaceStructureCreator.cc
, NeighborMatch.cc
, SurfaceGroups.cc
, ZincMatchFilter.cc
, atom_tree_check.cc
, bcl_type_check.cc
, molfile_read_test.cc
, restype_kin_output.cc
, rosetta_retype_check.cc
, rts_check.cc
, analyze_ddG.cc
, min_pack_min.cc
, hydrophobic_patch_stats_calculator.cc
, rss_energy_calculator.cc
, surfacescore.cc
, calibrate_pdb_via_sidechain_optimization.cc
, generate_matcher_constraints.cc
, score_protein_ligand_interactions.cc
, hotspot_stub_constraint_test.cc
, struct_frag.cc
, cloud_demo.cc
, ColorsDemo.cc
, GA.cc
, PyEnTest.cc
, calc_nmr_tensor.cc
, mp_range_relax.cc
, mp_seqrecov.cc
, mp_span_from_pdb.cc
, mp_symdock.cc
, mp_transform.cc
, minimize.cc
, minimize_ppi.cc
, make_motif_tables.cc
, extract_motifs.cc
, incorporate_motifs.cc
, mutate.cc
, MakeRotLib.cc
, UnfoldedStateEnergyCalculator.cc
, mp_mutate_relax.cc
, ligand_transform_with_pcs.cc
, hbs_design.cc
, oop_design.cc
, peptoid_design.cc
, pepspec.cc
, pepspec_anchor_dock.cc
, pH_protocol.cc
, make_exemplar.cc
, pocket_relax.cc
, pocket_suggest_target_residues_by_ddg.cc
, MakeSegmentFile.cc
, recces_turner.cc
, recces.cc
, ligand_dock.cc
, FiberDiffractionFreeSet.cc
, BuildPeptide.cc
, FlexPepDocking.cc
, helical_bundle_predict.cc
, hydrate.cc
, AnchoredDesign.cc
, AnchoredPDBCreator.cc
, AnchorFinder.cc
, generate_database_cache.cc
, validate_database.cc
, sewing_hasher.cc
, revold.cc
, extract_atomtree_diffs.cc
, recon.cc
, select_best_unique_ligand_poses.cc
, loodo.cc
, loopmodel.cc
, transform_loodo.cc
, mg_modeler.cc
, gen_apo_grids.cc
, gen_lig_grids.cc
, helix_from_sequence.cc
, mp_dock.cc
, mp_dock_setup.cc
, mp_domain_assembly.cc
, mp_lipid_acc.cc
, CitationManager.cc
, zinc_statistic_generator.cc
, segment_file_generator.cc
, build_full_model.cc
, swa_protein_main.cc
, swa_rna_main.cc
, swa_rna_util.cc
, resample_full_model.cc
, stepwise.cc
, trRosetta.cc
, vip.cc
, torsional_potential_corrections.cc
, Citation.cc
, CitationCollection.cc
, metal_site_finder.cc
, UnpublishedModuleAuthor.cc
, UnpublishedModuleInfo.cc
, ForeignKey.cc
, Index.cc
, init_random_generator.cc
, RandomGeneratorSettings.cc
, RosettaTensorflowManager.cc
, RosettaTensorflowSessionContainer.cc
, util.cc
, RosettaThreadAllocation.cc
, RosettaThreadManager.cc
, RosettaThreadManagerInitializationTracker.cc
, rosettaDNA.cc
, remodel.cc
, restype_converter.cc
, erraser2.cc
, rna_denovo.cc
, rna_motif.cc
, rna_score.cc
, rnp_ddg.cc
, multistage_rosetta_scripts.cc
, parse_rosetta_script.cc
, revert_design_to_native.cc
, rosetta_scripts.cc
, rosetta_scripts_jd3.cc
, validate_rosetta_script.cc
, sim_cryo.cc
, exposed_strand_finder.cc
, homodimer_design.cc
, homodimer_maker.cc
, UBQ_E2_thioester.cc
, UBQ_Gp_CYD-CYD.cc
, UBQ_Gp_LYX-Cterm.cc
, doug_dock_design_min_mod2_cal_cal.cc
, FloppyTail.cc
, sequence_tolerance.cc
, edge_file_generator.cc
, backside_hbond_finder.cc
, generate_starting_zinc_sites.cc
, willmatch_chorismate.cc
, smhybrid.cc
, spiro.cc
, symdock_enum_3_1.cc
, symdock_hybrid.cc
, symdock_hybrid_cc3.cc
, tcdock.cc
, test_ikrs.cc
, test_ikrs2.cc
, test_ikrs_flymake.cc
, test_kc.cc
, ward_design.cc
, will_mutalyze.cc
, willmatch_2d6_bhe.cc
, sicdock.cc
, willmatch_d6_bpy.cc
, yeates_align.cc
, sym_multicomp_test.cc
, dna_motif_matcher.cc
, ufv.cc
, vllb.cc
, challenge.cc
, PB_potential.cc
, combine_silent_test.cc
, design_contrast_and_statistic.cc
, design_contrast_test.cc
, extract_pdbs_test.cc
, organopv.cc
, gpu_score.cc
, gpu_test.cc
, gpu_test_Mxform.cc
, helix_assembly.cc
, heterodock.cc
, holes_test.cc
, hubdenovo.cc
, IKFGDB.cc
, isct_test.cc
, mkresfile_i213.cc
, motif_denovo_hb.cc
, motif_hash_util.cc
, nisod.cc
, pad_helices.cc
, pentcb.cc
, pentcb_design.cc
, pentcb_test.cc
, print_dunscores.cc
, rblinker.cc
, rblinker2.cc
, rblinker2_overlay_bound.cc
, rblinker2_test.cc
, rescore_i213.cc
, rsd_canonical_units.cc
, scheme_v0_score.cc
, sf4_hash.cc
, zinc1_homodimer_design.cc
, template_features.cc
, constel.cc
, coupled_moves.cc
, count_cycpep_sequences.cc
, simple_cycpep_predict.cc
, DARC.cc
, cartesian_ddg.cc
, ddg_monomer.cc
, minimize_with_cst.cc
, mpi_msd.cc
, pmut_scan_parallel.cc
, sequence_recovery.cc
, supercharge.cc
, spheregrinder.cc
, zinc1_homodimer_setup.cc
, zinc2_homodimer_design.cc
, zinc2_homodimer_setup.cc
, zinc_heterodimer_design.cc
, drrafter_error_estimation.cc
, fit_helix_in_map.cc
, dump_capped_residue.cc
, denovo_density.cc
, density_tools.cc
, dgdp.cc
, grower_prep.cc
, mr_protocols.cc
, SID_ERMS_prediction.cc
, cl_complex_rescore.cc
, cst_info.cc
, HDXEnergy.cc
, interface_energy.cc
, InterfaceAnalyzer.cc
, parcs_ccs_calc.cc
, PeptideDeriver.cc
, per_residue_solvent_exposure.cc
, report_hbonds_for_plugin.cc
, ResidueDisorder.cc
, score.cc
, score_jd2.cc
, shobuns.cc
, gpu_linker.cc
, antibody_CR_paratope.cc
, antibody_graft.cc
, antibody_H3.cc
, antibody_numbering_converter.cc
, packing_angle.cc
, glycan_clash_check.cc
, glycan_info.cc
, GlycanDock.cc
, pose_from_saccharide_sequence.cc
, energy_based_clustering.cc
, avrg_silent.cc
, iterhybrid_selector.cc
, create_disulf_file.cc
, HbondZinc_ser.cc
, HbondZincBackbone.cc
, HbondZincHHHO.cc
, xtal_water_bunsat.cc
, zinc_helix_cap.cc
, ZincMinimize.cc
, ZincSiteEvaluator.cc
, karen_compare_different_proteins.cc
, karen_compare_pocket_rmsd.cc
, karen_pocket_compare.cc
, karen_pocket_save.cc
, conserve_disulfides.cc
, convert.cc
, HbondZinc_allpolar.cc
, disulfide_filter.cc
, disulfide_finder.cc
, disulfide_handoff.cc
, disulfide_scorer.cc
, rotamerize_disulfides.cc
, calc_ssm_energies_with_structure_profile.cc
, extractNativeRepeats.cc
, repeat_dock.cc
, basic_glycan_sampler.cc
, test_glycan_trees.cc
, simple_dna_regression_test.cc
, byres_data.cc
, domain_assemble.cc
, cnl_env_lost_hbs.cc
, triazolamer_dock_design.cc
, vancomycin.cc
, barak_relax.cc
, BuildFloppyTail.cc
, compare_structures.cc
, extend_range.cc
, overlay_bb_bondangles.cc
, overlay_sidechains.cc
, PeptideDeriver.cc
, phosphorylate_position.cc
, thread_bb.cc
, thread_sidechains.cc
, bou-min-ubo-nrg-jump.cc
, hbscan.cc
, lig_low_sasa.cc
, lig_polar_sat.cc
, lig_polar_unsat.cc
, list_cnl_ngbs.cc
, nrg_res_set.cc
, sel_hbonds.cc
, tgtres_polar_sho_energies.cc
, fold_from_loops.cc
, fold_from_loops_devel.cc
, iterative_design.cc
, BuriedUnsatPolarsFinder.cc
, HbondZinc.cc
, flexibleLoopDesign.cc
, betacat_movie.cc
, Cu_binder_model.cc
, cyclic_pack.cc
, Cyclize.cc
, get_dihedral_peptide.cc
, get_dihedral_peptoid.cc
, noah_score_interface.cc
, number_of_residuetypes.cc
, peptoid_movie.cc
, peptoid_rotamer_prediction_benchmark.cc
, pymolmovertest.cc
, score_min_rtmin_test.cc
, test_chain_sequence.cc
, tnm_sampler.cc
, reportFragments.cc
, adapt_rotamers.cc
, calc_ssm_energies.cc
, cen_relax.cc
, cryst_design.cc
, cryst_gen.cc
, dsrna_grow.cc
, fasol_perres.cc
, min_test.cc
, mirrorsymm_test.cc
, pdb_gen_cryst.cc
, perturb_structure.cc
, sidechain_min.cc
, pep_prep.cc
, pepspec.cc
, pepspec_anchor_dock.cc
, backrub_pilot.cc
, cterdesign.cc
, ig_dump.cc
, mm_params.cc
, sequencerecovery.cc
, make_retroinverso.cc
, angle_stats.cc
, generate_matcher_constraints.cc
, kinematic_relax_test.cc
, loop_minimize.cc
, test_metapatch.cc
, mmtf2pdb.cc
, mmtfs2mmtf.cc
, convert_to_centroid.cc
, decoy_features.cc
, extended_chain.cc
, score_nonlocal_frags.cc
, strand_pairings.cc
, DomainAssemblerNDocker.cc
, TryScoreFilter.cc
, hierarchical_clustering.cc
, call_saxs_score.cc
, linker_sampler.cc
- tr
: r_frag_picker.cc
, SecondaryMatcher.cc
, dumpstubinteractions.cc
, density_grid.cc
, fragment_sequence_quality.cc
, inject_hash.cc
, native_ensemble.cc
, cloud_app.cc
, FragsToAtomDist.cc
, r_assign_clusters.cc
, r_build_hotspot_loops.cc
, r_convert_frags.cc
, r_count_neighbours.cc
, r_cst_tool.cc
, EnzdesFixBB.cc
, r_frag_quality.cc
, r_local_rdc.cc
, r_min_check.cc
, r_mpi.cc
, r_parse_foldtree.cc
, r_pdb2top.cc
, r_play_with_etables.cc
, r_rmsf.cc
, r_score.cc
, r_score_rdc.cc
, closability_score.hh
, FragMonteCarlo.hh
, outputAbego.cc
, abego_predict.cc
, armEval.cc
, calcFractionFolded.cc
, contact_map_from_homologs.cc
, dumpPhiPsiStats.cc
, evalFullLength.cc
, evalRepeats.cc
, filterAlignments.cc
, filterImperfectAln.cc
, findNaturallyOccuringAlphaRepeats.cc
, hle_predict.cc
, minimalCstHomology.cc
, minimalCstRelax.cc
, min_pack_min.hh
, outputLayerDesignBurial.cc
, outputRama.cc
, outputSasa.cc
, predictedCstFilter.cc
, unalignedEvaluate.cc
, LoopExtend.cc
, ApplicationContext.cc
, DisulfideTest.cc
, DetailedScores.cc
, DumpConstraints.cc
, GunnTest.cc
, JumpSpecificAbrelax.cc
- TR
: a3b_hbs_dock_design.cc
, fixbb_jd3.cc
, kellogg_ddg_jd3.cc
, mmt_msd.cc
, mpi_msd.cc
, mpi_test.cc
, relax_jd3.cc
, zn_match_symmdock.cc
, sequence_tolerance_mf.cc
, spec_prof_compare.cc
, jd2_parser_DNAInt.cc
, MSA_design.cc
, multistate_design_ga.cc
, a3b_hbs_creator.cc
, domain_assembly_jd2.cc
, aggregate_coarse_rna_vdw.cc
, aramid_folding.cc
, b3a_distro_kinemage.cc
, beta_314_vs_a3b.cc
, cov_hbs.cc
, diversify_conotoxin.cc
, get_dihedral_b3aa.cc
, mike_linker_test.cc
, peptidomimetic_ensembles.cc
, peptoid_hbs.cc
, sec_struct_finder.cc
, test_d_l_readin.cc
- tr
: struc_set_fragment_picker.cc
, LoophashFilter.cc
, TestTopologySampler.cc
, hczndimer.cc
, plot_hb.cc
, extract_CA_coords.cc
, extract_replica.cc
, fasta2pdb.cc
, r_rmsf.cc
, contactMap.cc
, ensemble_analysis.cc
, fast_clustering.cc
, enzyme_design.cc
, r_noe_assign.cc
- TR
: ragul_get_ligand_sasa.cc
, performance_benchmark.hh
, ddg_benchmark.cc
, design_contrast_and_statistic.cc
, rotamer_recovery.cc
, ligand_discovery_search_protocol.cc
, space_fill_analysis.cc
, design_tight_clusters.cc
, detect_tight_clusters.cc
, mixedMC.cc
, find_ligand_local_res.cc
, SymmDataTest.cc
, apl_msd.cc
, per_residue_solvent_exposure.cc
, move_jump.cc
, score_rnp.cc
, score_rnp_lowres.cc
, setup_coord_csts.cc
, ab_binding.cc
, antibody_test.cc
, mtransferase.cc
, pH_docking.cc
, pH_neighbor_pack.cc
, SymmAbrelax.cc
, SymmSilentFile.cc
, CycPepMain.cc
, burial_measure_centroid.cc
, check_rnp_coarse.cc
, motif_ligand_packer_design.cc
, membrane_ddG.cc
, membrane_relax.cc
, membrane_symdocking.cc
, mp_rsd_energies.cc
, batchrelax.cc
, energy_diff.cc
, loophash.cc
, loophash_analyse.cc
, loophash_cenrelax.cc
, loophash_createdb.cc
, loophash_test.cc
, minbench.cc
, BuriedUnsatPolarsFinder2.cc
, cmaes_test.cc
, inverse_rotlib_dump.cc
, ld_converter.cc
, oop_dock_design.cc
, scaffold_matcher.cc
, elscripts.cc
, FastGap.cc
, fragpdb.cc
, loophash_createfiltereddb.cc
, sixdtreeTEST.cc
, symfragrm.cc
, buns.cc
, bur_nodon_tyr.cc
, rama_test.cc
, BuriedUnsatPolarsFinder3.cc
, hydrate.cc
, khSandbox.cc
, khSandbox2.cc
, khXtal_water_bunsat.cc
, read_l_print_pdbinfo.cc
, sasa_buns.cc
, template.cc
, vsasa_pdbcode_res.cc
, wat_distances.cc
, analyze_docked_RNA_motifs.cc
, calculate_distances.cc
, build_repeats.cc
, make_blueprint.cc
, make_frag_ssdep.cc
, pair_distance.cc
, pick_bab.cc
, pick_lowestscore_pose.cc
, rama.cc
, sasa.cc
, score_delete_segments.cc
, sasa_interface.cc
, capri15.cc
, repeat_demo.cc
, simple_dna_regression_test.cc
, symtest.cc
, local_rmsd.cc
, helical_param.cc
, batchrelax_mpi.cc
, get_pharmacophore_without_bound_rna.cc
, get_rna_pharmacophore.cc
, get_rna_pharmacophore_with_water.cc
, get_rna_ring_sasa.cc
, ragul_darc_minimize.cc
, ragul_darc_run_with_delphi.cc
, ragul_find_all_hbonds.cc
, ragul_get_delphi_phimap.cc
, ragul_get_ligand_hbonds.cc
, ragul_rosetta_dump_pdb.cc
, matdes_design_2comp.cc
, rosetta_backend.cc
, sctrials.cc
, report_hbonds.cc
, calc_ddG.cc
, char_native.cc
, coiled_coil_search.cc
, des_pos_ddG.cc
, design_symm.bak.110314.cc
, design_symm.cc
, design_symm_110330_good.cc
, design_symm_no_hack_elec.cc
, enumeration_test.cc
, matdes_design.cc
, SmartSEWINGTester.cc
, matdes_dock.cc
, matdes_mutalyze.cc
, relax_building_block.cc
, symdock_enum.cc
, symdock_enum_3_1.cc
, PeptideDeriver.cc
, elliptical_ip.cc
, hemagg_trimer.cc
, motif_dock.cc
, flxbb.cc
, foldptn.cc
, frag2profile.cc
, test_symmetry.cc
, benchmark_k_medoids.cc
, measure_sequence_similarity_to_native.cc
, tensorflow_manager_multi_input_test.cc
, tensorflow_manager_multirun_test.cc
, tensorflow_manager_test1.cc
, tensorflow_test2.cc
, test_rosetta_thread_manager_preallocation.cc
, FixbbSimAnnealer.cc
, cxdesign.cc
, cxdock.cc
, AddFrameworkProfilesOperation.cc
, AntibodyDesignMoverGenerator.cc
, test_neighborhood_selector.cc
, test_bbmc.org.cc
, class_tests.cc
, test_grafting.cc
, detect_symmetry.cc
, domains.cc
, fragment_based_design.cc
, swap_elements.cc
, test_serialize.cc
, hbond_connect.cc
, hh_test.cc
, hotspot_hash.cc
, hshash_utils.cc
, jd2test.cc
, calc_cdr_rmsd.cc
, david_extract_domain.cc
, cmaes_minimizer_test.cc
, concatenate_poses.cc
, steric_fusion_scan.cc
, AbInitio_MPI.cc
, align_substructure.cc
, cryst_hbonds.cc
, ligand_docking_hbonds.cc
, torsion_types.cc
, heme_binding.cc
, heme_replace.cc
, david_align_and_recompute_score_and_rmsd.cc
, david_align_append_and_recompute_score_and_rmsd.cc
, david_extract_dinucleotide_musashi_reference.cc
, ShapeScoring.cc
, david_fill_gaps.cc
, david_find_best_contact_pocket.cc
, david_find_complex_contacts.cc
, david_find_contacts.cc
, david_find_exemplar.cc
, david_find_pocket_stabilizing_mutations.cc
, david_find_surface_residues.cc
, david_pocket2PDB.cc
, david_pocket_align_and_save.cc
, david_pocket_compare.cc
, david_recompute_score_and_rmsd.cc
, test_bbmc.cc
, srirupa_two_loops.cc
, johnk_interface_geosol_minimization.cc
, johnk_interface_recompute_score_and_rmsd.cc
, johnk_parametrize_geometric_solvation.cc
, johnk_recompute_score_and_rmsd.cc
, justin_identify_holes.cc
, justin_local_backrub.cc
, nadeem_compensatory_mutation.cc
, nadeem_find_destabilizing_mutation.cc
, old_test_geosol_minimization.cc
, phosphoArg_build_rotamers.cc
, phosphoArg_minimize.cc
, ragul_backbone_diversity.cc
, srirupa_phosphoArg_build_rotamers.cc
, antibody_metrics.cc
, SID_rescore.cc
, kick_cyclic_pose.cc
, load_cyclic_pose.cc
, backbone_tests.cc
, sidechain_tests.cc
, atoms_from_residues.cc
, kic_rama_bias.cc
, kick_with_balance.cc
, pose_from_residues.cc
, tracer.cc
, xyz_from_pose.cc
, original_app.cc
, johnk_exact_geometric_solvation.cc
, calc_irms_despite_mismatch.cc
, add_membrane.cc
, input_from_cmd.cc
, interface_statistics.cc
, mp_find_interface.cc
, mp_find_interface_test.cc
, mp_parameters.cc
, mp_qrtest.cc
, mp_quick_relax.cc
, mp_relax_partners_separately.cc
, mpdocking.cc
, mpdocking_setup.cc
, mpfolding.cc
, mpframework_test.cc
, mpframework_test1.cc
, mpframework_test2.cc
, per_residue_sc_sasa.cc
, range_relax.cc
, simple_rotamer_recovery.cc
, spanfile_from_pdb.cc
, transform_into_membrane.cc
, chet_report_rmsd.cc
, chet_trp_to_gly.cc
, constellation_list.cc
, johnk_gapless_threading.cc
- tr2
: tj_util.hh
- TR2
: buried_polar_finder.cc
, InteractionGraph.bench.hh
- TR_
: OptionsTest.cc
, TracerTest.cc
- TR_apps_pilot_blivens_disulfides_hh
: disulfides.hh
- tr_clash_score
: clash_score.hh
- TR_EX
: get_dihedral_b3aa.cc
, get_dihedral_peptide.cc
, get_dihedral_peptoid.cc
- TR_IR
: get_dihedral_b3aa.cc
, get_dihedral_peptide.cc
, get_dihedral_peptoid.cc
- TR_level0
: test_rosetta_thread_manager_advanced_API.cc
- TR_level1
: test_rosetta_thread_manager_advanced_API.cc
, test_rosetta_thread_manager_basic_API.cc
- TR_level2
: test_rosetta_thread_manager_basic_API.cc
, test_rosetta_thread_manager_advanced_API.cc
- TR_level3
: test_rosetta_thread_manager_advanced_API.cc
, test_rosetta_thread_manager_basic_API.cc
- TR_main
: test_rosetta_thread_manager_advanced_API.cc
, test_rosetta_thread_manager_basic_API.cc
- TR_output
: test_rosetta_thread_manager_basic_API.cc
- tr_overlap_score
: overlap_score.hh
- TR_PCS_main
: PCS_main.cc
- TR_results
: measure_sequence_similarity_to_native.cc
- tr_rms_util
: rms_util.hh
- TR_unsat
: byres_data.cc
- tr_util
: util.hh
- TRA
: fold_from_loops_devel.hh
, fold_from_loops.hh
- trace
: RDCTest.cc
, diverse_fragments.cc
, fragmentpicker_integration_demo.cc
, picker.cc
, PickSSE.cc
, quotapicker_demo.cc
, rescore_fragments.cc
, fragment_picker.cc
- tracer
: r_trjconv.cc
- tracer_data_print
: simple_interfaceanalyzer.cc
, InterfaceAnalyzer.cc
- trAllCrmsd
: AllCrmsd.cc
- TRdebug
: peptide_minimizer.cc
, buried_polar_finder.cc
- trFilteredAbrelax
: filters_in_abrelax.cc
- trmain
: lua_test.cc
, pose_serialize_test.cc
- TRmin
: rotamer_repack.cc
- TRnat
: rotamer_repack.cc
- TRout
: exposed_strand_finder.cc
- TRP
: cal_env.m
, gen_vdw_radius.m
, load_pair_env_table.m
, load_angle_r_table.m
, gen_env_dep_pair_decompose.m
, gen_env_dep_pair.m
, gen_env_dep_orient_draw.m
, gen_env_dep_orient_decompose.m
, load_pair_env_table_ref.m
, gen_env_dep_orient.m
, draw_gen_env_dep_orient_decompose.m
, draw_gen_env_dep_pair.m
, draw_matrix.m
, load_pair_env_table.m
, draw_gen_env_dep_pair_decompose.m
- TRps
: pilot_packstat.cc
, packstat.cc
- trRescorePDDF
: Features.cc
, RescorePDDF.cc
- trRescoreSAXS
: ComputeSAXSSpectrum.cc
, RescoreSAXS.cc
- trRotateSAXS
: RotateSAXS.cc
- TRrtmin
: rotamer_repack.cc
- trSaxs
: SaxsSampler.cc
- TRscmove
: rotamer_repack.cc
- try
: cenrot_jd2.cc
- TS
: cryst_reporters.hh
- TSG
: spacegroup.hh
- tt
: zf_relax.cc
, test1.cc
, motif_scan.cc
, dna_spec_test.cc
, dna_relax.cc
, dna_design_test.cc
, dimer_relax.cc
, analyze_dna.cc
- TT
: ncontact.cc
, TwoChainTenANeighbors.cc
, TwoChainInterface.cc
- tt
: dna_dr_test.cc
- tw
: motif_scan.cc
, zf_relax.cc
, dna_relax.cc
, dimer_relax.cc
- TYR
: draw_matrix.m
, gen_vdw_radius.m
, load_pair_env_table.m
, load_angle_r_table.m
, gen_env_dep_pair_decompose.m
, gen_env_dep_pair.m
, gen_env_dep_orient_draw.m
, gen_env_dep_orient.m
, load_pair_env_table_ref.m
, load_pair_env_table.m
, cal_env.m
, draw_gen_env_dep_pair_decompose.m
, draw_gen_env_dep_pair.m
- TZ
: ca_to_allatom.cc
