Here is a list of all file members with links to the files they belong to:
- m -
- M
: test_rose.cc
, flail.cc
- m_inv_gen()
: RDCTest.cc
- M_iter
: frag2profile.cc
- MacAppIconData
: boinc_mac_app_icon.hh
- mad()
: gpu_mat_vec.hh
- main()
: adding_peptoids.cc
, sym_fixbb.cc
, dna_motifs_collector.cc
, ligand_motifs.cc
, motif_dna_packer_design.cc
, pdb2motiffile.cc
, buried_polar_finder.cc
, InterfaceMutMaker.cc
, min_pack_min.cc
, peptide_minimizer.cc
, simple_interfaceanalyzer.cc
, PDB_diagnostic.cc
, RDC_test.cc
, RBSegMove_test_viewer.cc
, RBSegMove_test.cc
, UBQ_UBQ_E2.cc
, sasa_qd.cc
, LoopAnalyzer.cc
, HECT_ubq.cc
, HECT_all.cc
, ForgetPDBInfo.cc
, FloppyTail_loop.cc
, Extender.cc
, TestLoophash.cc
, loophash_createfiltereddb.cc
, create_disulfide_fa_angle_statistics.cc
, SmotifPairRmsdCalculatorGPU.CC
, SmotifHasher.cc
, SewingAssembler.cc
, SewAppend.cc
, PrepareGraphNodes.cc
, NodePairRmsdCalculator.cc
, mpi_helixAssembly.cc
, MotifFinder.cc
, ModelTrimmer.cc
, model_dumper.cc
, xml_task_printer.cc
, InterfaceStrandFinderMover.cc
, HelixAssemblyDesigner.cc
, HelicalPdbGenerator.cc
, HelicalAssembly.cc
, FragmentDumper.cc
, FoldTreeOutputter.cc
, CompareBundleToNative.cc
, BundlePairRmsdCalculatorGPU.cc
, BundlePairRmsdCalculator.cc
, BundleDumper.cc
, metropolis_hastings.cc
, hotspot_stub_constraint_test.cc
, py_rosetta_test.cc
, PDBTest.cc
, OptionsTest.cc
, JSON_Demo.cc
, hal.cc
, hal-demo.cc
, GA.cc
, ComparingTracerExample.cc
, ColorsDemo.cc
, cloud_demo.cc
, struct_frag.cc
, PyEnTest.cc
, score_sidechain_sasa.cc
, print_disulfide_scorefunctions.cc
, pcs_score_select_helices.cc
, pcs_score_select.cc
, pcs_score_residues.cc
, pcs_score_individual_residues.cc
, pcs_fragments_to_distances_wRMS.cc
, pcs_fragments_to_distances2.cc
, pcs_fragments_to_distances.cc
, pcs_distances_for_fragpicker.cc
, for_dkim.cc
, complex_interface_optimize.cc
, TestTopologySampler.cc
, LoophashFilter.cc
, tmalign_cluster.cc
, score_hotspot_cst.cc
, read_pose_jump_orientation_repack.cc
, match_disulfide_to_scaffold.cc
, lowresdock_patchdock_hotspot_cst.cc
, generate_hbond_geometry.cc
, docking_parallel.cc
, docking_inputpatchdock_mpi.cc
, compute_Irmsd.cc
, AlanineScanner.cc
, cluster_hotspot_docking.cc
, bb_cluster.cc
, recon_mpi.cc
, msd_jd2.cc
, msd.cc
, minimization_test.cc
, find_consensus_mutations.cc
, TracerTest.cc
, SharedPtrDemo.cc
, PyMOLDemo.cc
, holes.cc
, CXdock.cc
, crossmatch_d2.cc
, crossmatch_3e.cc
, crossmatch.cc
, coiled_coil_zn.cc
, coiled_coil.cc
, cluster_cyc_disulf.cc
, bpy.cc
, atom_type_rdf.cc
, atom_design.cc
, holes_daball_input.cc
, cxdock_sheet.cc
, whitney_specificity_switch.cc
, whitney_repack_input.cc
, whitney_rebuild_ankyrin.cc
, whitney_prepare_native.cc
, whitney_local_backrub.cc
, whitney_identify_epitope.cc
, test_hpool.cc
, test_cluster.cc
, test_cen_rot.cc
, test_bbmc.cc
, params_opt.cc
, disulf_frag_match.cc
, r_count_neighbours.cc
, fnd_dutton.cc
, flail.cc
, fabio.cc
, dxdock.cc
, dump_res.cc
, dubois_graft.cc
, dubois.cc
, dock_asym.cc
, disulf_stat.cc
, disulf_frag_search.cc
, pairwise_fa_energy.cc
, designability_stats.cc
, design_frags.cc
, design_DL.cc
, d3_bpy_linker.cc
, cycsamp.cc
, cycgly_target.cc
, cycgly_superimpose.cc
, cycgly_canonical.cc
, cycgly_bbg8t3a.cc
, CXdock_TMP.cc
, PCA_internal_test.cc
, test_makebundle_mover.cc
, test_KIC_betapeptide.cc
, test_D_scoring.cc
, test_cyclic_rama.cc
, tensorflow_test1.cc
, symmetrize_rotlib.cc
, symmetrize_old_ramamap.cc
, symmetrize_new_ramamap.cc
, symmetrize_3d_ramamap.cc
, plot_scoreterm.cc
, PCA_visualizer.cc
, test_makebundlehelix_mover.cc
, make_truecyclicpeptide.cc
, make_mainchain_potential.cc
, make_ideal_betapeptide.cc
, make_helicalbundle.cc
, make_betahelicalbundle.cc
, fit_helixparams.cc
, design_truecycpeptide_fromstub.cc
, design_cycpeptide_MPI.cc
, cycpep_analysis.cc
, bettercluster.cc
, tseng_minimize.cc
, test_trRosetta.cc
, general_pair_counting.cc
, gen_cav_ball.cc
, fa_to_cenrot_score.cc
, decoys_frag_quality.cc
, cyclic_sampler.cc
, cenrot_bbsc_demo.cc
, calc_stress_tensor.cc
, long_loop.cc
, graphics_demo.cc
, test_trRosettaProtocolMover.cc
, test_trRosettaConstraintGenerator.cc
, ThreeHelixBundleFinder.cc
, test_tensorflow_graph_convolutional_nn.cc
, test_sidechainKIC.cc
, test_rosetta_thread_manager_basic_API.cc
, test_rosetta_thread_manager_advanced_API.cc
, test_pose_copy.cc
, test_multithreaded_ramapp_load.cc
, test_multithreaded_pdb_load.cc
, test_multithreaded_packing_performance.cc
, test_multithreaded_ig_correctness.cc
, test_metalloproteins.cc
, ragul_get_ligand_sasa.cc
, membrane_foldtree2.cc
, membrane_foldtree.cc
, local_minimize.cc
, load_membrane_pose.cc
, embed_mp_pose_from_topo.cc
, check_rotation.cc
, simon_darc_minimize.cc
, sarah_get_pharmacophores.cc
, ragul_test_darc.cc
, ragul_rosetta_dump_pdb.cc
, ragul_get_molecular_surface.cc
, membrane_info.cc
, ragul_get_ligand_hbonds.cc
, ragul_get_delphi_phimap.cc
, ragul_get_connolly_surface.cc
, ragul_get_aa_code.cc
, ragul_find_all_hbonds.cc
, ragul_darc_run_with_delphi.cc
, ragul_darc_optimize_weights.cc
, ragul_darc_minimize.cc
, ragul_calculate_residue_rmsd.cc
, ragul_calculate_ligand_rmsd.cc
, ragul_analyze_tcr_interface.cc
, mpscore_integrate.cc
, membrane_sampling.cc
, membrane_relax2.cc
, membrane_relax.cc
, membrane_docking.cc
, membrane_ddG.cc
, mpframework_integration.cc
, membrane_scorefxn.cc
, membrane_fa_scorefxn.cc
, make_canonical_helix.cc
, visualize_membrane.cc
, virtual_residue_trees.cc
, get_rna_ring_sasa.cc
, mpframework_score.cc
, mp_sfxn_integration.cc
, mp_scoring_feature_reporter.cc
, membrane_sfxn.cc
, membrane_rsd_energy_breakdown.cc
, pymol_viewer_test.cc
, mpframework_time_bchmk.cc
, mpframework_integration.cc
, mp_database_check.cc
, membrane_pose_test.cc
, membrane_integration.cc
, r_pdb2top.cc
, optE_simple.cc
, Superimpose_Pdbs.cc
, sasa_interface.cc
, multidomain_switch.cc
, r_trjconv.cc
, r_tempered_sidechains.cc
, r_score_rdc.cc
, r_score.cc
, r_rmsf.cc
, r_play_with_etables.cc
, design_glycans.cc
, r_parse_foldtree.cc
, r_mpi.cc
, r_min_check.cc
, r_local_rdc.cc
, r_frag_quality.cc
, r_frag_picker.cc
, r_fold_cst.cc
, r_dock_tempered.cc
, r_cst_tool.cc
, r_coupled_sidechain.cc
, dxdock_movie.cc
, symtest.cc
, get_rna_pharmacophore_with_water.cc
, get_rna_pharmacophore.cc
, get_pharmacophore_without_bound_rna.cc
, gen_rna_pharmacophore.cc
, cstmin.cc
, elec_dens_rot_recov.cc
, batchrelax_mpi.cc
, helical_param.cc
, build_repeats.cc
, zf_relax.cc
, test1.cc
, mutate_repack.cc
, simple_dna_regression_test.cc
, repeat_demo.cc
, motif_scan.cc
, dna_spec_test.cc
, dna_relax.cc
, dna_design_test.cc
, dimer_relax.cc
, capri15.cc
, analyze_dna.cc
, parin_test.cc
, silly_tag_stuff.cc
, bcl_type_check.cc
, atom_tree_check.cc
, ZincMatchFilter.cc
, SurfaceGroups.cc
, NeighborMatch.cc
, MetalInterfaceStructureCreator.cc
, stepwise_template_test.cc
, stepwise_lores_test.cc
, stepwise_loop_test.cc
, stepwise_helix_test.cc
, stepwise_centroid_test.cc
, bootstrap_bcl_types.cc
, screen_phosphates.cc
, rna_test.cc
, rna_protein_test.cc
, rna_assemble_test.cc
, read_tensor.cc
, rb_entropy.cc
, protein_helix_assemble.cc
, polar_pdbstats.cc
, pdbstats_test.cc
, pdbstats_rnahelix.cc
, pack_polar_hydrogens.cc
, hydrophobic_patch_stats_calculator.cc
, create_disulfide_database.cc
, create_disulfide_angle_statistics.cc
, create_disulfide_alldata.cc
, compute_disulfide_matching_score.cc
, calc_pair_stats.cc
, score_protein_ligand_interactions.cc
, generate_matcher_constraints.cc
, calibrate_pdb_via_sidechain_optimization.cc
, surfacescore.cc
, surface_optE_parallel.cc
, rss_energy_calculator.cc
, pack_phosphates.cc
, find_position_matches_using_inverse_rotamers.cc
, analyze_ddG.cc
, rts_check.cc
, rosetta_retype_check.cc
, restype_kin_output.cc
, molfile_read_test.cc
, ligand_rpkmin_jd1.cc
, ligand_dock_jd1.cc
, extract_atomtree_diffs_jd1.cc
, crash_report_test.cc
, color_by_lipid_type.cc
, score_jd2_replonly.cc
, replonly.cc
, place_fragments_into_density.cc
, fastrelax_replonly.cc
, cal_overlap_scores.cc
, cal_nonoverlap_scores.cc
, assemble_placed_fragments.cc
, version_mpscorefxn.cc
, mp_rsd_energies.cc
, find_optimal_hydrophobic_thk.cc
, enumerate_rotamers.cc
, density_res_zscores.cc
, visualize_membrane.cc
, version_mpscorefxn.cc
, translate_view_membrane.cc
, translate_membrane_pose.cc
, transform_into_membrane.cc
, transform_into_mem.cc
, test_mp_rmsd.cc
, sample_tilt_protocol.cc
, read_pose_from_seq.cc
, read_mp_pose_from_seq.cc
, read_mp_pose.cc
, homolog_finder_farna.cc
, morph_pdbs.cc
, mg_lores_pdbstats.cc
, mg_hires_pdbstats.cc
, loop_closure_test.cc
, turner_rules_test_WORKS.cc
, turner_rules_test.cc
, TRIAL_protein_helix_assemble.cc
, stepwise_test.cc
, OLD_TRIAL_protein_helix_assemble.cc
, erraser_monte_carlo.cc
, add_delete_monte_carlo.cc
, create_disulfide_distance_statistics.cc
, get_info.cc
, generalize_gaussian_chain_func_test.cc
, gcc185_test.cc
, entropy_test.cc
, easy_target_test.cc
, dna_test.cc
, coarse_rna_test.cc
, check_cubic_conv.cc
, block_stack_test.cc
, benzene_test.cc
, helix_from_sequence.cc
, mp_viewer.cc
, mp_transform.cc
, mp_symdock.cc
, mp_span_from_pdb.cc
, mp_seqrecov.cc
, mp_range_relax.cc
, mp_mutate_relax.cc
, mp_lipid_acc.cc
, mp_domain_assembly.cc
, mp_dock_setup.cc
, mp_dock.cc
, membrane_abinitio2.cc
, match.cc
, gen_lig_grids.cc
, gen_apo_grids.cc
, mg_modeler.cc
, transform_loodo.cc
, loopmodel.cc
, loodo.cc
, select_best_unique_ligand_poses.cc
, ligand_rpkmin.cc
, ligand_dock.cc
, extract_atomtree_diffs.cc
, UnfoldedStateEnergyCalculator.cc
, make_exemplar.cc
, pH_protocol.cc
, pepspec_anchor_dock.cc
, pepspec.cc
, packstat.cc
, peptoid_design.cc
, oop_design.cc
, hbs_design.cc
, r_noe_assign.cc
, ligand_transform_with_pcs.cc
, calc_nmr_tensor.cc
, revold.cc
, MakeRotLib.cc
, mutate.cc
, incorporate_motifs.cc
, extract_motifs.cc
, remove_duplicate_motifs.cc
, ligand_discovery_search_protocol.cc
, identify_ligand_motifs.cc
, determine_real_motifs.cc
, make_motif_tables.cc
, minimize_ppi.cc
, minimize.cc
, pmut_scan_parallel.cc
, fit_helix_in_map.cc
, drrafter_error_estimation.cc
, docking_protocol.cc
, docking_prepack_protocol.cc
, zinc_heterodimer_design.cc
, zinc2_homodimer_setup.cc
, zinc2_homodimer_design.cc
, zinc1_homodimer_setup.cc
, zinc1_homodimer_design.cc
, supercharge.cc
, sequence_recovery.cc
, dump_capped_residue.cc
, mpi_msd.cc
, fixbb.cc
, create_clash-based_repack_shell.cc
, beta_peptide_modeling.cc
, minimize_with_cst.cc
, ensemble_generator_score12_sidechain_ver2.cc
, ddg_monomer.cc
, cartesian_ddg.cc
, theta_ligand.cc
, make_ray_files.cc
, DARC.cc
, BuildPeptide.cc
, sewing_hasher.cc
, validate_database.cc
, generate_database_cache.cc
, AnchorFinder.cc
, AnchoredPDBCreator.cc
, AnchoredDesign.cc
, idealize_jd2.cc
, hydrate.cc
, helical_bundle_predict.cc
, fragment_picker.cc
, FlexPepDocking.cc
, pocket_measure.cc
, FiberDiffractionFreeSet.cc
, extract_pdbs.cc
, enzyme_design.cc
, CstfileToTheozymePDB.cc
, sim_cryo.cc
, mr_protocols.cc
, grower_prep.cc
, dgdp.cc
, density_tools.cc
, denovo_density.cc
, segment_file_generator.cc
, trRosetta.cc
, tcrmodel.cc
, SymDock.cc
, surface_docking.cc
, struc_set_fragment_picker.cc
, stepwise.cc
, resample_full_model.cc
, swa_rna_util.cc
, swa_rna_main.cc
, swa_protein_main.cc
, build_full_model.cc
, vip.cc
, zinc_statistic_generator.cc
, metal_site_finder.cc
, generate_starting_zinc_sites.cc
, backside_hbond_finder.cc
, edge_file_generator.cc
, sequence_tolerance.cc
, FloppyTail.cc
, doug_dock_design_min_mod2_cal_cal.cc
, UBQ_Gp_LYX-Cterm.cc
, UBQ_Gp_CYD-CYD.cc
, UBQ_E2_thioester.cc
, test_non-canonical_connectivities.cc
, main.cpp
, diffbinder.cpp
, main.cpp
, test_SiteConstraint.cc
, test_RingConformationMover.cc
, ca_to_allatom.cc
, test_explicit_membrane_input.cc
, test_EnergyMethodOptions.cc
, test_coenzymes.cc
, test_CCD_loop_closure.cc
, test_CarbohydrateInfo.cc
, test_carbohydrate_scoring.cc
, test_carbohydrate_docking.cc
, test_C-terminal_conjugation.cc
, torsional_potential_corrections.cc
, optE_parallel.cc
, relax.cc
, nucleobase_sample_around.cc
, cs_rosetta_rna.cc
, analyze_base_pairing.cc
, rna_thread_and_minimize.cc
, rna_thread.cc
, rna_design.cc
, rna_denovo.cc
, erraser_minimizer.cc
, erraser2.cc
, restype_converter.cc
, remodel.cc
, rna_cluster.cc
, recon.cc
, recces.cc
, thermal_sampler.cc
, recces_turner.cc
, phosphorylation.cc
, N-terminal_acetylation.cc
, glycosyltransfer.cc
, DNA_methylation.cc
, MakeSegmentFile.cc
, pocket_suggest_target_residues_by_ddg.cc
, pocket_relax.cc
, rna_suitename.cc
, homodimer_maker.cc
, homodimer_design.cc
, exposed_strand_finder.cc
, rosettaDNA.cc
, validate_rosetta_script.cc
, rosetta_scripts_jd3.cc
, rosetta_scripts.cc
, revert_design_to_native.cc
, parse_rosetta_script.cc
, multistage_rosetta_scripts.cc
, rnp_ddg.cc
, simple_cycpep_predict.cc
, rna_score.cc
, rna_predict_chem_map.cc
, rna_motif.cc
, rna_minimize.cc
, rna_idealize.cc
, rna_helix.cc
, rna_graft.cc
, rna_features.cc
, rna_extract.cc
, rna_database.cc
, pentcb_design.cc
, rsd_canonical_units.cc
, rescore_i213.cc
, rblinker2_test.cc
, rblinker2_overlay_bound.cc
, rblinker2.cc
, rblinker.cc
, metric.cc
, filter.cc
, print_dunscores.cc
, pilot_packstat.cc
, pentcb_test.cc
, sasa_test.cc
, pentcb.cc
, pack_stat_energy.cc
, pack_ddg.cc
, organopv.cc
, nisod.cc
, motif_denovo_hb.cc
, mkresfile_i213.cc
, minimize_cavities.cc
, minimize.cc
, match_disulf.cc
, make_symmetric_task_test.cc
, tcdock.cc
, ward_design.cc
, test_sucker_energy.cc
, test_string.cc
, test_rose.cc
, test_loop_hash.cc
, test_leerichards.cc
, test_kc.cc
, test_ikrs_flymake.cc
, test_ikrs2.cc
, test_ikrs.cc
, test.cc
, isct_test.cc
, symdock_hybrid_cc3.cc
, symdock_hybrid.cc
, symdock_enum_3_1.cc
, sup_test.cc
, spiro.cc
, sphere_hierarchy.cc
, smhybrid.cc
, sicdock.cc
, sf4_hash.cc
, score_pdbs.cc
, scheme_v0_score.cc
, gen_trimer_disulf.cc
, genmatch_m8.cc
, genmatch_d6_bpy.cc
, genmatch_d6_bhhcg.cc
, genmatch_3bpy.cc
, genmatch.cc
, genI213_nocontacts.cc
, genI213_gensym.cc
, genI213_2dsf.cc
, genI213_2comp.cc
, genI213.cc
, gen_xtal_dimer_from_trimer.cc
, genP23.cc
, gen_homo_hc.cc
, gen_disulf_homodimer.cc
, gen_d2_hhhc.cc
, gen_d2_4his.cc
, gen_d2_3his_ooc.cc
, gen_d2.cc
, gen_cyc_gly_cst.cc
, gen_cyc_gly.cc
, gen3bpy.cc
, FunGroupTK_test.cc
, FunGroupTK.cc
, gpu_test_Mxform.cc
, IKFGDB.cc
, hubfragdesign.cc
, hubdenovo.cc
, hubabinitio.cc
, holes_training_data.cc
, holes_test.cc
, holes_pbpdb.cc
, holes2_training_data.cc
, heterodock.cc
, helix_assembly.cc
, hczndimer.cc
, will_mutalyze.cc
, gpu_test.cc
, gpu_score.cc
, gpu_linker.cc
, gpu_cpu_speedtest.cc
, gpu_cbdock.cc
, getDistConstraints.cc
, gentetra_from_trimer.cc
, gentetra_bpy_from_znhis.cc
, gentetra.cc
, gensym_3bpy_from_dimer.cc
, antibody_graft.cc
, dock_glycans.cc
, calculate_sasa.cc
, minirosetta_graphics.cc
, minirosetta.cc
, backrub.cc
, snugdock.cc
, packing_angle.cc
, identify_cdr_clusters.cc
, antibody_numbering_converter.cc
, antibody_legacy.cc
, antibody_H3.cc
, glycan_clash_check.cc
, antibody_designer.cc
, antibody_CR_paratope.cc
, antibody.cc
, SID_ERMS_prediction.cc
, shobuns.cc
, score_jd2.cc
, score.cc
, sc.cc
, ResidueDisorder.cc
, residue_energy_breakdown.cc
, report_hbonds_for_plugin.cc
, full_length_model.cc
, count_cycpep_sequences.cc
, coupled_moves.cc
, constel.cc
, validate_silent.cc
, template_features.cc
, super_aln.cc
, spheregrinder.cc
, score_aln2.cc
, score_aln.cc
, partial_thread.cc
, iterhybrid_selector.cc
, per_residue_solvent_exposure.cc
, fix_alignment_to_match_pdb.cc
, fast_gap.cc
, cluster_alns.cc
, avrg_silent.cc
, combine_silent.cc
, energy_based_clustering.cc
, cluster.cc
, pose_from_saccharide_sequence.cc
, GlycanDock.cc
, glycan_info.cc
, mp_transition_bfactor.cc
, combine_silent_test.cc
, AbinitioClassic.cc
, plot_hb.cc
, PB_potential.cc
, challenge.cc
, vllb.cc
, ufv.cc
, buns_report.cc
, dna_motif_matcher.cc
, graft_ligand.cc
, set_radius.cc
, design_contrast_and_statistic.cc
, mp_optimize_geometry_params.cc
, FiberDiffractionTest.cc
, test_threaded_scoring.cc
, test_surf_vol.cc
, sym_multicomp_test.cc
, yeates_align.cc
, xyzStripeHash_test.cc
, xyzStripeHash_dump.cc
, willmatch_d6_bpy.cc
, willmatch_chorismate.cc
, willmatch_2d6_bhe.cc
, batch_distances.cc
, per_residue_energies.cc
, PeptideDeriver.cc
, parcs_ccs_calc.cc
, InterfaceAnalyzer.cc
, interface_energy.cc
, HDXEnergy.cc
, fast_clustering.cc
, ensemble_analysis.cc
, cst_info.cc
, contactMap.cc
, cl_complex_rescore.cc
, for_tim.cc
, atom_energy_breakdown.cc
, AbinitioRelax.cc
, pad_helices.cc
, r_rmsf.cc
, fasta2pdb.cc
, extract_replica.cc
, extract_CA_coords.cc
, mucintypeglycosylation.cc
, extract_pdbs_test.cc
, design_contrast_test.cc
, hierarchical_clustering.cc
, betacat_movie.cc
, tnm_sampler.cc
, SaxsSampler.cc
, RotateSAXS.cc
, RescoreSAXS.cc
, RescorePDDF.cc
, linker_sampler.cc
, ComputeSAXSSpectrum.cc
, call_saxs_score.cc
, assemble_domains_with_saxs_jd2.cc
, IndirectSorter.cc
, Cu_binder_model.cc
, rescore_fragments.cc
, quotapicker_demo.cc
, PickSSE.cc
, picker.cc
, fragmentpicker_integration_demo.cc
, diverse_fragments.cc
, filters_in_abrelax.cc
, Features.cc
, welde_chains.cc
, TryScoreFilter.cc
, read_profile.cc
, peptoid_rotamer_prediction_benchmark.cc
, adapt_rotamers.cc
, reportFragments.cc
, flexibleLoopDesign.cc
, test_chain_sequence.cc
, simple_relax.cc
, score_min_rtmin_test.cc
, rotamer_prediction_benchmark.cc
, pymolmovertest.cc
, peptoid_rotlib_test3.cc
, peptoid_rotlib_test2.cc
, peptoid_rotlib_test1.cc
, RDCTest.cc
, peptoid_movie.cc
, number_of_residuetypes.cc
, noah_score_interface.cc
, make_peptoid_sequence.cc
, make_peptoid.cc
, get_dihedral_peptoid.cc
, get_dihedral_peptide.cc
, Cyclize.cc
, cyclic_peptoid_peptide_test1.cc
, cyclic_pack.cc
, make_peptoid.cc
, angle_stats.cc
, score_nonlocal_frags.cc
, extended_chain.cc
, decoy_features.cc
, convert_to_centroid.cc
, mmtfs2mmtf.cc
, mmtf2pdb.cc
, sidechain_min.cc
, LoopExtend.cc
, loop_minimize.cc
, kinematic_relax_test.cc
, generate_matcher_constraints.cc
, strand_pairings.cc
, make_retroinverso.cc
, sequencerecovery.cc
, generate_orbital_statistics.cc
, mm_params.cc
, ig_dump.cc
, cterdesign.cc
, backrub_pilot.cc
, windowed_rmsd.cc
, windowed_rama.cc
, star_abinitio.cc
, sheet_translate.cc
, DisulfideTest.cc
, print_options.cc
, GunnTest.cc
, DumpConstraints.cc
, DisulfideBondEnergy.cc
, DetailedScores.cc
, CreatePose.cc
, convert_frags.cc
, call_rdc.cc
, call_mover.cc
, AllCrmsd.cc
, DomainAssemblerNDocker.cc
, adenosine_stack_test.cc
, CustomAbinitio.cc
, simpleScore.cc
, RotamerDump.cc
, roc_test.cc
, roc_optimizer.cc
, process_mdl.cc
, params_tester.cc
, ligands_to_database.cc
, ligand_score.cc
, generate_ligand_start_position_file.cc
, david_align_and_recompute_score_and_rmsd.cc
, david_find_pocket_exemplar.cc
, david_find_exemplar.cc
, david_find_contacts.cc
, david_find_complex_contacts.cc
, david_find_best_pocket.cc
, david_find_best_contact_pocket.cc
, david_fill_gaps.cc
, david_extract_domain.cc
, david_extract_dinucleotide_musashi_reference.cc
, david_darc_multirun.cc
, david_align_append_and_recompute_score_and_rmsd.cc
, david_find_pocket_stabilizing_mutations.cc
, heme_replace.cc
, heme_binding.cc
, torsion_types.cc
, ligand_docking_hbonds.cc
, cryst_hbonds.cc
, align_substructure.cc
, RedesignXtal_Test.cc
, RedesignXtal_Silent.cc
, DenovoProteinDesign_Test.cc
, AbInitio_MPI.cc
, score_silent.cc
, mpi_refinement.cc
, test_LH.cc
, test_bbmc.org.cc
, test_bbmc.cc
, switch_fa.cc
, rotamer_energy.cc
, rotamer_clash.cc
, rescore_mutscan.cc
, refit_rotamer_prob.cc
, rama_energy.cc
, NMsearch.cc
, NMcorrelation.cc
, score_pdb.cc
, min_test_hpark.cc
, min_test.cc
, decompose_GDT.cc
, collect_rotamer_contacts.cc
, david_rotation_experiment.cc
, david_recompute_score_and_rmsd.cc
, david_pocket_compare.cc
, david_pocket_align_and_save.cc
, david_pocket2PDB.cc
, david_open_pocket.cc
, david_find_surface_residues.cc
, EnzdesFixBB.cc
, dsrna_grow.cc
, dock_pdb_into_density.cc
, cryst_gen.cc
, cryst_design.cc
, cen_relax.cc
, cart_refine.cc
, calc_ssm_energies.cc
, autorb.cc
, lsmgridprobe.cc
, dumpstubinteractions.cc
, SecondaryMatcher.cc
, extract_silent.cc
, check_burial.cc
, turner_two_chain.cc
, turner_test_one_chain.cc
, turner_test_double_helix.cc
, thermal_sampler_alpha.cc
, test.cc
, swa_rna_analytical_closure.cc
, rotamer_test.cc
, rna_pdb_scoring.cc
, non_natural_na.cc
, lariat_modeling.cc
, perturb_structure.cc
, create_constraints.cc
, CutOutDomain.cc
, spinlabel_activity.cc
, steric_fusion_scan.cc
, SmartSEWINGTester.cc
, concatenate_poses.cc
, relax_viewer.cc
, redesign_minimize_into_density.cc
, RBSegMove.cc
, rb_rms.cc
, pseudo_ca_trace.cc
, rmsd_partial_thread.cc
, per_atom_gradients.cc
, pdb_to_map.cc
, pdb_gen_cryst.cc
, multimodel_gdt.cc
, mirrorsymm_test.cc
, min_test.cc
, map_morph.cc
, make_rms_filtered_fragfile.cc
, fpd_symmTest.cc
, fasol_perres.cc
, pose_iteration.cc
, compare_rms_byres.cc
, BuildFloppyTail.cc
, barak_relax.cc
, barak.score.cc
, vancomycin.cc
, triazolamer_dock_design.cc
, triazolamer_creator.cc
, trial_rna_mutants.cc
, test_metapatch.cc
, test_d_l_readin.cc
, sec_struct_finder.cc
, compare_structures.cc
, polyaramid_test.cc
, peptoid_hbs.cc
, peptidomimetic_ensembles.cc
, mike_linker_test.cc
, make_ideal_a3b_fragment.cc
, make_a3b_bundle.cc
, macrocycle_sampling.cc
, indel.cc
, hal_rna_denovo.cc
, get_dihedral_b3aa.cc
, diversify_conotoxin.cc
, membrane_rescore.cc
, fold_from_loops_devel.cc
, fold_from_loops.cc
, tgtres_polar_sho_energies.cc
, sel_hbonds.cc
, nrg_res_set.cc
, list_cnl_ngbs.cc
, lig_polar_unsat.cc
, lig_polar_sat.cc
, lig_low_sasa.cc
, cnl_env_lost_hbs.cc
, bou-min-ubo-nrg-jump.cc
, cov_test.cc
, membrane_relax.cc
, membrane_highres_score.cc
, thread_sidechains.cc
, thread_bb.cc
, test_frags.barak.cc
, print_phipsi.cc
, phosphorylate_position.cc
, PeptideDeriver.cc
, overlay_sidechains.cc
, overlay_bb_bondangles.cc
, extend_range.cc
, SymmDataTest.cc
, mmt_msd.cc
, measure_lcaa_neighbor_radii.cc
, measure_catalytic_geometry.cc
, kellogg_ddg_jd3.cc
, interface_ddg_bind.cc
, flex_regions_alc.cc
, fixbb_jd3.cc
, find_buns.cc
, domain_assembly_jd2.cc
, apl_msd.cc
, analyze_rtmin_failures.cc
, mpi_msd.cc
, find_ligand_local_res.cc
, mixedMC.cc
, detect_tight_clusters.cc
, design_tight_clusters.cc
, space_fill_analysis.cc
, ligand_discovery_search_protocol.cc
, holes_identifier.cc
, rotamer_recovery.cc
, design_contrast_and_statistic.cc
, ddg_benchmark.cc
, performance_benchmark.cc
, MSA_design.cc
, cov_peptidomimetic_creator.cc
, cov_hbs.cc
, build_a3b.cc
, beta_314_vs_a3b.cc
, b3a_distro_kinemage.cc
, aramid_folding.cc
, aggregate_coarse_rna_vdw.cc
, a3b_test.cc
, a3b_hbs_dock_design.cc
, a3b_hbs_creator.cc
, multistate_design_ga.cc
, iterative_design.cc
, jd2_parser_DNAInt.cc
, spec_prof_compare.cc
, sequence_tolerance_mf.cc
, model_e2c_ubiquitin.cc
, zn_match_symmdock.cc
, version_scorefunction.cc
, sweep_respair_energies.cc
, relax_jd3.cc
, optest.cc
, mpi_test.cc
, domain_assemble.cc
, pep_ref.cc
, pep_rama.cc
, pep_prepspec.cc
, pep_prep.cc
, pep_paapp.cc
, pep_opt_parallel.cc
, pep_opt.cc
, pep_nrg.cc
, pep_gly.cc
, pep_analysis.cc
, hbscan.cc
, pep_spec.03-11.cc
, byres_data.cc
, simple_dna_regression_test.cc
, test_glycan_trees.cc
, basic_glycan_sampler.cc
, unalignedEvaluate.cc
, silents_to_ss.cc
, repeat_dock.cc
, predictedCstFilter.cc
, outputSasa.cc
, outputRama.cc
, outputLayerDesignBurial.cc
, close_loops_cart.cc
, medal_exchange.cc
, medal.cc
, maxsub.cc
, kcluster.cc
, jumping.cc
, helix_rotate.cc
, gdtha.cc
, fragment_rmsd.cc
, extend.cc
, dssp.cc
, close_loops_ccd.cc
, outputAbego.cc
, zinc_stat.cc
, loop_test.cc
, PCS_main.cc
, rotamer_repack.cc
, pepspec_anchor_dock.cc
, pepspec.cc
, pep_spec_flx.mov.cc
, pep_spec_flx.cc
, pep_spec.cc
, pep_spec.06-23.cc
, karen_compare_different_proteins.cc
, disulfide_handoff.cc
, disulfide_finder.cc
, disulfide_filter.cc
, create_disulf_file.cc
, convert.cc
, conserve_disulfides.cc
, jumpRT_test.cc
, bus_error.cc
, karen_pocket_save.cc
, karen_pocket_compare.cc
, karen_compare_pocket_rmsd.cc
, disulfide_scorer.cc
, VIP_app.cc
, ZincSiteEvaluator.cc
, ZincMinimize.cc
, zinc_helix_cap.cc
, xtal_water_bunsat.cc
, HbondZincHHHO.cc
, HbondZincBackbone.cc
, HbondZinc_ser.cc
, HbondZinc_allpolar.cc
, HbondZinc.cc
, BuriedUnsatPolarsFinder.cc
, convertFragmentType.cc
, minimalCstRelax.cc
, minimalCstHomology.cc
, hle_predict.cc
, fragments_to_ss.cc
, findNaturallyOccuringAlphaRepeats.cc
, filterImperfectAln.cc
, filterAlignments.cc
, extractNativeRepeats.cc
, evalRepeats.cc
, evalFullLength.cc
, dumpPhiPsiStats.cc
, r_check_chainbreak.cc
, contact_map_from_homologs.cc
, cluster_alns.cc
, calcFractionFolded.cc
, calc_ssm_energies_with_structure_profile.cc
, armEval.cc
, aln_to_disulf.cc
, abego_predict.cc
, test.cc
, pilot.cc
, rotamerize_disulfides.cc
, debug_labontes_current_work.cc
, pack.cc
, ligand_design.cc
, deepMove.cc
, scratch1.cc
, mutate_relax.cc
, test_sugar_torsion_getters_and_setters.cc
, test_ResidueProperties.cc
, test_glycan_linkages.cc
, load_crazy_sugars.cc
, glycomutagenesis.cc
, design_glycans.cc
, protonatePack.cc
, fragment_extract.cc
, pH_neighbor_pack.cc
, pH_docking.cc
, mtransferase.cc
, antibody_test.cc
, ab_binding.cc
, test_rna_protein.cc
, setup_coord_csts.cc
, score_rnp_lowres.cc
, score_rnp.cc
, move_jump.cc
, consolidate_clusters.cc
, test_scmcmover.cc
, test_canonical_mover.cc
, score_ddgs.cc
, sasa.cc
, monomer_ddg.cc
, minimize_with_cst.cc
, minimize_with_constraints.cc
, ensemble_generator_using_mover.cc
, ensemble_generator_score12_sidechain.cc
, ensemble_generator.cc
, create_hierarchy.cc
, get_rmsd.cc
, close_homolog_refinement.cc
, feature_schema_generator.cc
, CycPepMain.cc
, CycDsulf.cc
, SymmSilentFile.cc
, SymmAbrelax.cc
, undirected_graph.cc
, simpleScore.cc
, rmsd_calculator.cc
, readAndWrite.cc
, randomMove.cc
, native_ensemble.cc
, fragpdb.cc
, FastGap.cc
, elscripts.cc
, scaffold_matcher.cc
, oop_dock_design.cc
, oop_creator.cc
, ld_converter.cc
, inverse_rotlib_dump.cc
, cmaes_test.cc
, cmaes_minimizer_test.cc
, ShapeScoring.cc
, loophash_createfiltereddb.cc
, trajectory_movie.cc
, query_trajectory.cc
, KicSandbox.cc
, original_app.cc
, xyz_from_pose.cc
, vector_math.cc
, tracer.cc
, torsion_id.cc
, silent_output.cc
, score_function.cc
, reindexing_mover.cc
, khSandbox2.cc
, check_rnp_coarse.cc
, check_frag_rmsd.cc
, calculate_distances.cc
, analyze_docked_RNA_motifs.cc
, wat_distances.cc
, vsasa_pdbcode_res.cc
, vsasa_buns.cc
, template.cc
, sasa_buns.cc
, read_l_print_pdbinfo.cc
, khXtal_water_bunsat.cc
, burial_measure_centroid.cc
, khSandbox.cc
, hydrate.cc
, BuriedUnsatPolarsFinder3.cc
, BuriedUnsatPolarsFinder2.cc
, bur_nodon_tyr.cc
, buns.cc
, symfragrm.cc
, sixdtreeTEST.cc
, pose_serialize_test.cc
, lua_test.cc
, matdes_design.cc
, hemagg_trimer.cc
, elliptical_ip.cc
, PeptideDeriver.cc
, r_SymDock_viewer.cc
, r_segment_rdc.cc
, symdock_enum_3_1.cc
, symdock_enum.cc
, relax_building_block.cc
, matdes_mutalyze.cc
, matdes_dock.cc
, matdes_design_2comp.cc
, motif_dock.cc
, enumeration_test.cc
, design_symm_no_hack_elec.cc
, design_symm_110330_good.cc
, design_symm.cc
, design_symm.bak.110314.cc
, des_pos_ddG.cc
, coiled_coil_search.cc
, char_native.cc
, calc_ddG.cc
, params2pdb.cc
, inv_kin_lig_loop_design.cc
, pick_lowestscore_pose.cc
, test_mm.cc
, r_convert_frags.cc
, r_build_hotspot_loops.cc
, r_broker.cc
, r_assign_clusters.cc
, r_abrelax.cc
, FragsToAtomDist.cc
, cloud_app.cc
, score_delete_segments.cc
, sasa.cc
, rama.cc
, convert_pdb_to_silent_file.cc
, pick_bab.cc
, pair_distance.cc
, ncontact.cc
, make_frag_ssdep.cc
, make_blueprint.cc
, local_rmsd.cc
, frag2profile.cc
, foldptn.cc
, flxbb.cc
, fldsgn.cc
, cluster.cc
, alignanalyse.cc
, loophash_test.cc
, loophash_mpi.cc
, loophash_createdb.cc
, loophash_cenrelax.cc
, loophash_analyse.cc
, loophash.cc
, inlinetest.cc
, evolution.cc
, energy_diff.cc
, crossaln.cc
, batchrelax.cc
, make_cst.cc
, view_membrane_protein.cc
, mp_rsd_energies.cc
, membrane_symdocking.cc
, membrane_relax.cc
, membrane_ddG.cc
, load_membrane_pose.cc
, motif_ligand_packer_design.cc
, ligand_motifs.cc
, score_test.cc
, per_residue_solvent_exposure.cc
, burial_measure_sphere.cc
, testderiv.cc
, surface_docking.cc
, moves_test.cc
, monica_relax.cc
, dock_test.cc
, report_hbonds.cc
, hbonds_test.cc
, hbond_param_sweep.cc
, format_converter.cc
, features_database_schema.cc
, testmpi.cc
, testloop.cc
, test_sampling.cc
, silent2frag.cc
, silent2cst.cc
, shake.cc
, sctrials.cc
, rosetta_backend.cc
, relax_viewer.cc
, rama_test.cc
, minbench.cc
, mikejd2test.cc
, md.cc
, jseq.cc
, prof_search.cc
, pick_frags.cc
, phi_hack.cc
, per_residue_features.cc
, model_quality.cc
, min_cst.cc
, medal_test.cc
, mammoth_hack.cc
, make_profile.cc
, make_artificial_centroids.cc
, kdtree_disulf.cc
, remap_aln.cc
, jscore.cc
, jrelax.cc
, jidealize.cc
, jdock.cc
, jcluster.cc
, hybrid.cc
, filter_sequences.cc
, fast_cm.cc
, exhaustive_align.cc
, dp_align.cc
, distances.cc
, domains.cc
, jd2memtest.cc
, TwoChainTenANeighbors.cc
, TwoChainInterface.cc
, hshash_utils.cc
, hotspot_hash.cc
, hh_test.cc
, hbond_connect.cc
, test_serialize.cc
, swap_elements.cc
, fragment_sequence_quality.cc
, fragment_based_design.cc
, design_profile.cc
, detect_symmetry.cc
, thread_fast.cc
, superdev.cc
, super.cc
, sparta_superdev.cc
, simple_cm.cc
, silent_cst_quality.cc
, seqdb_stats.cc
, score_silent_cst.cc
, sc_interaction.cc
, tensorflow_manager_test1.cc
, test_symmetry.cc
, test_neighborhood_selector.cc
, model_antibody_basic.cc
, relax_cdrs.cc
, raw_pointers.cc
, prob_design_cdrs.cc
, graft_design_cdrs.cc
, cxdock.cc
, cxdesign.cc
, test_rosetta_thread_manager_preallocation.cc
, tensorflow_test2.cc
, class_tests.cc
, tensorflow_manager_multirun_test.cc
, tensorflow_manager_multi_input_test.cc
, measure_sequence_similarity_to_native.cc
, benchmark_k_medoids.cc
, select_best_unique_ligand_poses_jd1.cc
, redo_rms_atomtree_diffs.cc
, ligdock_confidence.cc
, ligand_evis.cc
, cluster_ligand_poses.cc
, testNM.cc
, testMD.cc
, burial.cc
, density_grid.cc
, cst_quality.cc
, cst_func.cc
, cs_align.cc
, copy_hack.cc
, constraints_viewer.cc
, constraints_matrix.cc
, compare_features.cc
, casp9_superdev.cc
, cartesian.cc
, ca_build.cc
, random_seed.cc
, build_template.cc
, boost_hacks.cc
, basic_thread.cc
, assemble_domains_jd2.cc
, anneal_align.cc
, angles.cc
, angle_recovery_stats.cc
, analyze_casp9.cc
, add_ligand.cc
, test_grafting.cc
, kick_cyclic_pose.cc
, canonical_sampling.cc
, broken_original_kick.cc
, broken_kick.cc
, boost_vector.cc
, boost_regex.cc
, boost_matrix.cc
, atoms_from_residues.cc
, atom_id_demo.cc
, sidechain_tests.cc
, backbone_tests.cc
, load_cyclic_pose.cc
, chain_break.cc
, SID_rescore.cc
, collect_features.cc
, topo_driver.cc
, inject_hash.cc
, motif_loop_build.cc
, srirupa_two_loops.cc
, srirupa_phosphoArg_build_rotamers.cc
, ragul_backbone_diversity.cc
, phosphoArg_minimize.cc
, phosphoArg_build_rotamers.cc
, old_test_geosol_minimization.cc
, kick_with_balance.cc
, jd2test.cc
, read_cutpoint.cc
, rama_function.cc
, rama_distribution.cc
, pose_from_silent.cc
, pose_from_residues.cc
, pose_from_pdb.cc
, pick_from_rama.cc
, partial_pose.cc
, local_options.cc
, kinematic_closure.cc
, calc_cdr_rmsd.cc
, kick_n_terminus.cc
, kic_rama_bias.cc
, kic_bug.cc
, jd2_state.cc
, hello_world.cc
, fold_tree.cc
, features_reporter.cc
, dof_translator.cc
, dihedral.cc
, database_sandbox.cc
, current_example.cc
, mp_find_interface.cc
, mpframework_test2.cc
, mpframework_test1.cc
, mpframework_test.cc
, mpfolding.cc
, mpdocking_setup.cc
, mpdocking.cc
, mp_relax_partners_separately.cc
, mp_quick_relax.cc
, mp_qrtest.cc
, mp_parameters.cc
, mp_find_interface_test.cc
, per_residue_sc_sasa.cc
, interface_statistics.cc
, input_from_cmd.cc
, add_membrane.cc
, antibody_metrics.cc
, use_asn_motifs.cc
, rotamerize.cc
, optE_test.cc
, snugdock.cc
, Ncaa_Crosslink.cc
, calc_irms_despite_mismatch.cc
, nadeem_find_destabilizing_mutation.cc
, hotspot_test.cc
, nadeem_compensatory_mutation.cc
, metrics_test.cc
, justin_local_backrub.cc
, justin_identify_holes.cc
, johnk_recompute_score_and_rmsd.cc
, johnk_parametrize_geometric_solvation.cc
, johnk_interface_recompute_score_and_rmsd.cc
, johnk_interface_geosol_minimization.cc
, johnk_gapless_threading.cc
, johnk_exact_geometric_solvation.cc
, johnk_docking_protocol.cc
, david_open_pocket.cc
, david_check_pocket.cc
, constellation_list.cc
, compute_ddgs.cc
, chet_trp_to_gly.cc
, chet_report_rmsd.cc
, transform_into_membrane.cc
, spanfile_from_pdb.cc
, simple_rotamer_recovery.cc
, range_relax.cc
- main2()
: benchmark_k_medoids.cc
- main_local()
: struc_set_fragment_picker.cc
- make_1mer_frags()
: pepspec.cc
- make_active_site_grid()
: loodo.cc
- make_ala_interface
: homodimer_design.cc
- make_args_checked()
: core.h
- make_bb_grid()
: loodo.cc
- make_bonded_rna_move()
: capri15.cc
- make_coiled_coil()
: coiled_coil.cc
, coiled_coil_zn.cc
, nisod.cc
- make_correct_perturbation()
: broken_kick.cc
- make_disulfides()
: bettercluster.cc
- make_dna_only_pose()
: motif_scan.cc
- make_dock_olig()
: CXdock.cc
- make_etable()
: r_play_with_etables.cc
- make_float_sc_min_mover()
: smhybrid.cc
- make_format_args()
: core.h
- make_format_to_n_args()
: format.h
- make_frag_set()
: spiro.cc
, smhybrid.cc
, rblinker.cc
, frag_util.hh
, dubois.cc
, bpy.cc
, frag_util.hh
- make_frag_set_9mers()
: frag_util.hh
, smhybrid.cc
- make_fragments()
: torsional_potential_corrections.cc
- make_frags()
: pepspec.cc
- make_helix()
: coiled_coil.cc
, coiled_coil_zn.cc
, nisod.cc
- make_motif_task()
: scheme_v0_score.cc
- make_move_map()
: coiled_coil.cc
, coiled_coil_zn.cc
- make_mutation_tag()
: rnp_ddg.cc
- make_mutations()
: rnp_ddg.cc
- make_native_olig()
: CXdock.cc
- make_nmer()
: d3_bpy_linker.cc
- make_olig()
: heterodock.cc
- make_pathological_perturbation()
: broken_kick.cc
- make_pdb_atom()
: coiled_coil_search.cc
- make_pose()
: bpy.cc
, spiro.cc
, dubois.cc
- make_printf_args()
: printf.h
- make_rand_ss()
: dubois.cc
, bpy.cc
, spiro.cc
- make_rand_ss_h()
: smhybrid.cc
- make_rand_ss_hs()
: smhybrid.cc
- make_random_perturbation()
: kick_n_terminus.cc
- make_sequence_change()
: pep_prep.cc
, pepspec.cc
, pepspec_anchor_dock.cc
, phil.hh
, pepspec.cc
, pepspec_anchor_dock.cc
- make_sf()
: coiled_coil.cc
, coiled_coil_zn.cc
- make_single_res_pose()
: hczndimer.cc
- make_symm_data()
: coiled_coil.cc
, coiled_coil_zn.cc
, nisod.cc
- make_two_trimers()
: gen_trimer_disulf.cc
- make_wprintf_args()
: printf.h
- make_your_own_alignment()
: r_frag_picker.cc
- MakeCanonicalHelixCOP
: make_canonical_helix.cc
- MakeCanonicalHelixOP
: make_canonical_helix.cc
- makemask()
: cycgly_bbg8t3a.cc
, cycgly_target.cc
- makerots()
: hczndimer.cc
- makesplitwork()
: crossmatch.cc
, crossmatch_d2.cc
, genmatch.cc
, genmatch_m8.cc
- makesplitwork_3bpy()
: gen3bpy.cc
, gentetra_from_trimer.cc
, gentetra_bpy_from_znhis.cc
, gentetra.cc
, genmatch_m8.cc
, genmatch_3bpy.cc
, genmatch.cc
- Malloc
: Svm.cc
- manual_copy()
: undirected_graph.cc
- manual_refine()
: dgdp.cc
- map_morph()
: map_morph.cc
- map_sec()
: capri15.cc
- map_secstruct()
: capri15.cc
- margin()
: peptidomimetic_ensembles.cc
- mask_out_loop()
: easy_target_test.cc
- masslst
: fa_to_cenrot_score.cc
- Mat
: print_dunscores.cc
, gen_d2_3his_ooc.cc
, coiled_coil_zn.cc
, pentcb_test.cc
, pentcb.cc
, nisod.cc
, motif_hash_util.cc
, motif_denovo_hb.cc
, make_symmetric_task_test.cc
, isct_test.cc
, IKFGDB.cc
, heterodock.cc
, helix_assembly.cc
, hczndimer.cc
, genmatch_d6_bpy.cc
, gen_homo_hc.cc
, gen_d2_hhhc.cc
, gen_d2_4his.cc
, test_kc.cc
, sym_multicomp_test.cc
, yeates_align.cc
, willmatch_d6_bpy.cc
, willmatch_chorismate.cc
, willmatch_2d6_bhe.cc
, will_mutalyze.cc
, ward_design.cc
, test_loop_hash.cc
, sasa_test.cc
, test_ikrs_flymake.cc
, test_ikrs2.cc
, test_ikrs.cc
, symdock_hybrid_cc3.cc
, symdock_hybrid.cc
, symdock_enum_3_1.cc
, smhybrid.cc
, sic_fast_x.hh
, design_symm_no_hack_elec.cc
, symdock_enum_3_1.cc
, symdock_enum.cc
, relax_building_block.cc
, matdes_mutalyze.cc
, matdes_dock.cc
, matdes_design_2comp.cc
, matdes_design.cc
, enumeration_test.cc
, FunGroupTK_test.cc
, design_symm_110330_good.cc
, design_symm.cc
, design_symm.bak.110314.cc
, des_pos_ddG.cc
, coiled_coil_search.cc
, char_native.cc
, cxdock.cc
- mat
: draw_matrix.m
- Mat
: disulf_stat.cc
, atom_design.cc
, gen_d2.cc
, FunGroupTK.cc
, dxdock_movie.cc
, dump_res.cc
, dubois_graft.cc
, dubois.cc
, dock_asym.cc
, designability_stats.cc
, d3_bpy_linker.cc
, CXdock_TMP.cc
, CXdock.cc
, crossmatch_d2.cc
, crossmatch_3e.cc
, crossmatch.cc
, coiled_coil.cc
- match1
: zinc2_homodimer_setup.cc
- match2
: zinc2_homodimer_setup.cc
- match_main()
: match.cc
- MatchAlignerOP
: crossmatch.cc
, crossmatch_d2.cc
- MatchBaseCOP
: crossmatch.cc
, crossmatch_d2.cc
- MatchBaseOP
: crossmatch.cc
, crossmatch_d2.cc
- MatchPosition
: MetalInterface.hh
, zinc_heterodimer_design.cc
- Matf
: symdock_enum_3_1.cc
, sphere_hierarchy.cc
, pentcb_design.cc
, gpu_test_Mxform.cc
, gpu_test.cc
, gpu_score.cc
, dxdock.cc
, gpu_linker.cc
, cxdesign.cc
, symdock_enum.cc
, cxdock_sheet.cc
, symdock_enum_3_1.cc
- mathntensor_from_dist()
: aggregate_coarse_rna_vdw.cc
- Matrix
: mg_lores_pdbstats.cc
, rb_entropy.cc
, morph_pdbs.cc
, pdbstats_rnahelix.cc
, pdbstats_test.cc
, polar_pdbstats.cc
, protein_helix_assemble.cc
, rna_assemble_test.cc
, rna_protein_test.cc
, rna_test.cc
, stepwise_centroid_test.cc
, stepwise_helix_test.cc
, stepwise_loop_test.cc
, stepwise_template_test.cc
, transform_loodo.cc
, rna_thread.cc
, rna_thread_and_minimize.cc
, nucleobase_sample_around.cc
, rna_database.cc
, rna_features.cc
, rna_graft.cc
, swa_protein_main.cc
, swa_rna_main.cc
, swa_rna_util.cc
, loop_closure_test.cc
- matrix
: calc_pair_matrix.m
- Matrix
: adenosine_stack_test.cc
, non_natural_na.cc
, swa_rna_analytical_closure.cc
, turner_test_double_helix.cc
, turner_two_chain.cc
, cryst_reporters.hh
, convert_pdb_to_silent_file.cc
, parin_test.cc
, phil.hh
, benzene_test.cc
, dna_test.cc
, easy_target_test.cc
, entropy_test.cc
, add_delete_monte_carlo.cc
, erraser_monte_carlo.cc
, OLD_TRIAL_protein_helix_assemble.cc
, stepwise_test.cc
, TRIAL_protein_helix_assemble.cc
, turner_rules_test.cc
, turner_rules_test_WORKS.cc
, mg_hires_pdbstats.cc
, coarse_rna_test.cc
- matrix3f_to_xyzMatrix()
: extractNativeRepeats.cc
- max()
: Svm.cc
- MAX
: lmmin.cc
- MAX_ANG_METAL
: hczndimer.cc
- max_atom_hbonds()
: hbscan.cc
- MAX_CYS_RES
: CXdock.cc
, d3_bpy_linker.cc
, designability_stats.cc
, dxdock_movie.cc
, hczndimer.cc
, test_loop_hash.cc
- MAX_DIS_METAL
: hczndimer.cc
- max_E_allow
: exposed_strand_finder.cc
- MAX_HUMAN_READABLE_RECURSION_LEVELS
: util.cc
- max_line_len
: Svm.cc
- MAX_MULTIPLE
: test_rosetta_thread_manager_advanced_API.cc
- max_neighbors
: exposed_strand_finder.cc
- MAX_NRES
: d3_bpy_linker.cc
, test_loop_hash.cc
, hczndimer.cc
, dxdock_movie.cc
, designability_stats.cc
- MAX_ORDER
: sturm.hh
- max_RMSD
: exposed_strand_finder.cc
- MAX_SOLN
: sturm.hh
- MAXCAVN
: gen_cav_ball.cc
, gen_apo_grids.cc
- MAXPOW
: sturm.hh
- MAXRES
: cycsamp.cc
- MAXRESD
: gen_cav_ball.cc
, gen_apo_grids.cc
- maxsub_align()
: mammoth_hack.cc
- maybe_throw_on_next_assertion_failure()
: backtrace.cc
, backtrace.hh
- mc
: test_bbmc.cc
, test_bbmc.org.cc
, test_bbmc.cc
- MC_run()
: turner_two_chain.cc
, rb_entropy.cc
, recces_turner.cc
, recces.cc
- mean()
: james_util.hh
, drrafter_error_estimation.cc
- measure_disorder()
: ResidueDisorder.cc
- measure_rotamer_recovery()
: sequencerecovery.cc
, sequence_recovery.cc
, mp_seqrecov.cc
- measure_sequence_recovery()
: mp_seqrecov.cc
, sequence_recovery.cc
, optE_test.cc
, bur_nodon_tyr.cc
, sequencerecovery.cc
- mem_tr
: r_abrelax.cc
- membrane_center_protein_core()
: set_radius.cc
- MembraneDockingMoverOP
: membrane_docking.cc
- MembraneMinMoverCOP
: local_minimize.cc
- MembraneMinMoverOP
: local_minimize.cc
- MembraneRelaxMoverCOP
: membrane_relax2.cc
- MembraneRelaxMoverOP
: membrane_relax.cc
, membrane_relax2.cc
- MembraneSampleMoverCOP
: membrane_sampling.cc
- MembraneSampleMoverOP
: membrane_sampling.cc
- MembraneSfxnMoverOP
: membrane_fa_scorefxn.cc
, membrane_scorefxn.cc
- MembraneTransformMoverCOP
: transform_into_mem.cc
, translate_membrane_pose.cc
- MembraneTransformMoverOP
: translate_membrane_pose.cc
, transform_into_mem.cc
- MembraneViewMoverCOP
: check_rotation.cc
, pymol_viewer_test.cc
, visualize_membrane.cc
, translate_view_membrane.cc
- MembraneViewMoverOP
: check_rotation.cc
, pymol_viewer_test.cc
, visualize_membrane.cc
, translate_view_membrane.cc
- memory_buffer
: format.h
- merge_motifs()
: make_motif_tables.cc
- MET
: gen_env_dep_orient.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
, load_pair_env_table.m
, cal_env.m
, draw_matrix.m
, draw_gen_env_dep_pair_decompose.m
, draw_gen_env_dep_pair.m
, draw_gen_env_dep_orient_decompose.m
- metal
: MetalInterface.hh
, zinc_heterodimer_design.cc
- metal_dist_cutoff
: BuriedUnsatPolarsFinder2.cc
- MetalSiteFinderMoverCOP
: metal_site_finder.cc
- MetalSiteFinderMoverOP
: metal_site_finder.cc
- methane_pair_score_test()
: adenosine_stack_test.cc
- metropolis_criterion()
: design_truecycpeptide_fromstub.cc
- mg_hires_pdbstats_from_pose()
: mg_hires_pdbstats.cc
- mg_modeler_test()
: mg_modeler.cc
- mg_pdbstats_from_pose()
: mg_lores_pdbstats.cc
- mg_pdbstats_test()
: mg_hires_pdbstats.cc
, mg_lores_pdbstats.cc
- micelle_raidus_from_protein_core()
: set_radius.cc
- MikeLinkerMoverCOP
: mike_linker_test.cc
- MikeLinkerMoverOP
: mike_linker_test.cc
- min()
: Svm.cc
- MIN
: lmmin.cc
- MIN_DIS_METAL_SEP
: hczndimer.cc
- min_energy()
: score_protein_ligand_interactions.cc
- MIN_HELEX_RES
: dxdock_movie.cc
, hczndimer.cc
, d3_bpy_linker.cc
, CXdock.cc
- min_index()
: score_ddgs.cc
- min_mod()
: cryst_gen.cc
, pdb_gen_cryst.cc
- MIN_NBR_COUNT
: hczndimer.cc
- MinCenrotMoverOP
: cenrot_jd2.cc
- minimize()
: genmatch_3bpy.cc
, genmatch.cc
, gen_disulf_homodimer.cc
, gen_d2_hhhc.cc
, gen_d2_4his.cc
, gen_d2_3his_ooc.cc
, gen_d2.cc
, gen_cyc_gly_cst.cc
, gentetra_from_trimer.cc
, gen_cyc_gly.cc
, genmatch_m8.cc
, gentetra.cc
, gentetra_bpy_from_znhis.cc
, organopv.cc
, pentcb_design.cc
, smhybrid.cc
, spiro.cc
, ward_design.cc
, will_mutalyze.cc
, dubois.cc
, dubois_graft.cc
, des_pos_ddG.cc
, design_symm.bak.110314.cc
, design_symm.cc
, design_symm_110330_good.cc
, design_symm_no_hack_elec.cc
, matdes_design.cc
, cxdesign.cc
, matdes_design_2comp.cc
, matdes_mutalyze.cc
, coiled_coil.cc
, coiled_coil_zn.cc
, crossmatch.cc
, crossmatch_d2.cc
, cycgly_bbg8t3a.cc
, cycgly_canonical.cc
, cycgly_target.cc
, cycsamp.cc
, bpy.cc
- minimize_all_sidechains()
: rotamer_repack.cc
- minimize_and_score()
: turner_test_double_helix.cc
- minimize_helix()
: OLD_TRIAL_protein_helix_assemble.cc
- minimize_pdb()
: parin_test.cc
- minimize_poses()
: turner_rules_test.cc
- minimize_protocol()
: easy_target_test.cc
- minimize_ref_weights()
: pep_opt.cc
, pep_opt_parallel.cc
- minimize_sidechain()
: rotamer_repack.cc
- minimize_test()
: beta_peptide_modeling.cc
- minimize_to_close()
: repeat_dock.cc
- minimize_with_constraints()
: ensemble_generator.cc
, ensemble_generator_score12_sidechain.cc
, minimize_with_cst.cc
, ensemble_generator_score12_sidechain_ver2.cc
, minimize_with_cst.cc
- Minimizer_dfpmin_
: performance_benchmark.cc
- minimizer_test()
: stepwise_test.cc
- MinimizerBenchmark_dfpmin
: Minimizer.bench.hh
- MinimizerBenchmark_dfpmin_armijo
: Minimizer.bench.hh
- MinimizerBenchmark_dfpmin_armijo_
: performance_benchmark.cc
- MinimizerBenchmark_dfpmin_armijo_nonmonotone
: Minimizer.bench.hh
- MinimizerBenchmark_dfpmin_armijo_nonmonotone_
: performance_benchmark.cc
- MINNRES
: gen_apo_grids.cc
- MinToolMoverCOP
: r_min_check.cc
- MinToolMoverOP
: r_min_check.cc
- mirror_bin()
: cycgly_bbg8t3a.cc
, cycgly_target.cc
- misc
: Tag.cc
- mismatch_test()
: coarse_rna_test.cc
- mm_pack_test()
: test1.cc
- Mod()
: atom_id_demo.cc
- mod360()
: cycgly_canonical.cc
, gen_cyc_gly.cc
, cycsamp.cc
, cycgly_target.cc
, cycgly_bbg8t3a.cc
- MODE()
: crash_report.cc
- modeler_closure_test()
: loop_closure_test.cc
- modeler_map_test()
: coarse_rna_test.cc
- modelSSLoop()
: CycDsulf.cc
- modify_foldtree()
: membrane_foldtree2.cc
, membrane_foldtree.cc
- ModuleGetter
: T43.stl.pybind11_include_stl.ref.cpp
, T31.include_for_class.ref.cpp
, T32.call_guard.ref.cpp
, T33.buffer_protocol.ref.cpp
, T40.stl.ref.cpp
, T42.stl.names.map.ref.cpp
, T42.stl.names.multi.ref.cpp
, T42.stl.names.multimap.ref.cpp
, T42.stl.names.multiset.ref.cpp
, T42.stl.names.ref.cpp
, T42.stl.names.set.ref.cpp
, T50.add_on_binder.ref.cpp
, T50.namespace_binder.ref.cpp
, T60.custom_shared.ref.cpp
, T60.pybind11.ref.cpp
, T70.module_local.ref.cpp
, T70.options.ref.cpp
, T71.module_local.ref.cpp
, T80.custom_trampoline.ref.cpp
, T81.custom_trampoline_with_args.ref.cpp
, T20.template.variadic.ref.cpp
, T30.include.ref.cpp
, T00.basic.ref.cpp
, T01.enum.ref.cpp
, T02.function.ref.cpp
, T05.default.ref.cpp
, T07.class.match_args.ref.cpp
, T07.class.ref.cpp
, T08.constructor.ref.cpp
, T09.overload.ref.cpp
, T10.inheritance.ref.cpp
, T11.override.ref.cpp
, T10.virtual_inheritance.ref.cpp
, T20.template.ref.cpp
, T17.anonymous.ref.cpp
, T15.inner_class.ref.cpp
, T15.copy.ref.cpp
, T15.inner_class.fwd.ref.cpp
, T12.insertion_operator.ref.cpp
, T12.operator.ref.cpp
- ModuleType
: InstantiateModules.bench.hh
- molten_get_vallfrags()
: loodo.cc
- MONOCLINIC
: spacegroup.hh
- MoreHelp()
: main.cpp
- morph_by_internal_coords()
: morph_pdbs.cc
- morph_pdbs_test()
: morph_pdbs.cc
- Motif
: motif_scan.cc
- motif_column_deviation()
: motif_scan.cc
- motif_deviation()
: motif_scan.cc
- motif_distances()
: extract_motifs.cc
- motif_dna_packer_design()
: motif_dna_packer_design.cc
- motif_file
: segment_file_generator.cc
- motif_scan()
: motif_scan.cc
- motif_score_pose()
: scheme_v0_score.cc
- MotifColumn
: motif_scan.cc
- MotifDockOP
: motif_dock.cc
- motifs
: MakeSegmentFile.cc
- move_it()
: place_fragments_into_density.cc
- move_jump()
: sym_multicomp_test.cc
- move_pose()
: enumeration_test.cc
, matdes_dock.cc
- MPDomainAssemblyOP
: mp_domain_assembly.cc
- MPFindInterfaceTestMoverOP
: mp_find_interface_test.cc
- MPFoldingMoverOP
: mpfolding.cc
- MPframeworkTest1MoverOP
: mpframework_test1.cc
- MPframeworkTestMoverOP
: mpframework_test.cc
- MPI_ONLY
: assert.hh
, mpi_util.cc
- MPInterfaceStatisticsOP
: interface_statistics.cc
- MPLipidAccessibilityOP
: mp_lipid_acc.cc
- MPScoreFunctionFingerprintMoverOP
: version_mpscorefxn.cc
- ms_tr
: remove_duplicate_motifs.cc
, ligand_motifs.cc
- MSA_design()
: MSA_design.cc
- MSA_design_main()
: MSA_design.cc
- msd_base_doublet()
: turner_rules_test.cc
- msd_base_doublet_symmetric()
: turner_rules_test.cc
- mtransferaseOP
: mtransferase.cc
- MU
: plot_scoreterm.cc
- multfm()
: gpu_mat_vec.hh
- multfv()
: gpu_mat_vec.hh
- multiclass_probability()
: Svm.cc
- multimodel_gdt()
: multimodel_gdt.cc
- multiple_variant_type_test()
: parin_test.cc
- multivec2sf()
: params_opt.cc
- multmm()
: gpu_mat_vec.hh
- multmv()
: gpu_mat_vec.hh
- multxv()
: gpu_mat_vec.hh
- multxx()
: gpu_mat_vec.hh
- mut_index
: InterfaceMutMaker.cc
- mut_info()
: score_ddgs.cc
- mutate_and_score_RNP()
: rnp_ddg.cc
- mutate_random_residue()
: pep_spec_flx.cc
, pep_spec_flx.mov.cc
, pepspec.cc
- mutate_residue()
: swa_rna_util.cc
, generate_starting_zinc_sites.cc
, pack_ddg.cc
- mutate_residues_wrapper()
: swa_rna_util.cc
- mutate_to_ala()
: bettercluster.cc
, torsional_potential_corrections.cc
- mutate_to_sequence()
: design_cycpeptide_MPI.cc
- mutations
: cartesian_ddg.cc
, ddg_monomer.cc
- mvmul()
: RDCTest.cc
- MY__has_include
: backtrace.hh
- my_main()
: score_hotspot_cst.cc
, stepwise_helix_test.cc
, stepwise_loop_test.cc
, stepwise_lores_test.cc
, stepwise_template_test.cc
, calibrate_pdb_via_sidechain_optimization.cc
, complex_interface_optimize.cc
, compute_Irmsd.cc
, generate_hbond_geometry.cc
, relax_viewer.cc
, lowresdock_patchdock_hotspot_cst.cc
, stepwise_centroid_test.cc
, RBSegMove_test_viewer.cc
, graphics_demo.cc
, calc_stress_tensor.cc
, cenrot_jd2.cc
, cyclic_sampler.cc
, fa_to_cenrot_score.cc
, general_pair_counting.cc
, pairwise_fa_energy.cc
, test_bbmc.cc
, challenge.cc
, loop_closure_test.cc
, generalize_gaussian_chain_func_test.cc
, get_info.cc
, homolog_finder_farna.cc
, add_delete_monte_carlo.cc
, erraser_monte_carlo.cc
, OLD_TRIAL_protein_helix_assemble.cc
, stepwise_test.cc
, TRIAL_protein_helix_assemble.cc
, turner_rules_test.cc
, turner_rules_test_WORKS.cc
, antibody_designer.cc
, morph_pdbs.cc
, pack_phosphates.cc
, pack_polar_hydrogens.cc
, protein_helix_assemble.cc
, rb_entropy.cc
, read_tensor.cc
, rna_assemble_test.cc
, rna_test.cc
, screen_phosphates.cc
, silly_tag_stuff.cc
, rna_motif.cc
, cs_rosetta_rna.cc
, nucleobase_sample_around.cc
, rna_cluster.cc
, rna_database.cc
, rna_extract.cc
, rna_features.cc
, rna_graft.cc
, rna_helix.cc
, rna_idealize.cc
, rna_minimize.cc
, analyze_base_pairing.cc
, rna_predict_chem_map.cc
, rna_score.cc
, rna_suitename.cc
, rosetta_scripts.cc
, rosettaDNA.cc
, build_full_model.cc
, swa_protein_main.cc
, swa_rna_main.cc
, swa_rna_util.cc
, resample_full_model.cc
, pepspec.cc
, backrub.cc
, coupled_moves.cc
, simple_cycpep_predict.cc
, beta_peptide_modeling.cc
, docking_protocol.cc
, drrafter_error_estimation.cc
, fit_helix_in_map.cc
, mr_protocols.cc
, mg_modeler.cc
, membrane_abinitio2.cc
, stepwise.cc
, recces_turner.cc
, thermal_sampler.cc
, recces.cc
, erraser2.cc
, erraser_minimizer.cc
, rna_denovo.cc
, rna_design.cc
, rna_thread.cc
, rna_thread_and_minimize.cc
, cart_refine.cc
, adenosine_stack_test.cc
, non_natural_na.cc
, rna_pdb_scoring.cc
, rotamer_test.cc
, swa_rna_analytical_closure.cc
, thermal_sampler_alpha.cc
, turner_test_double_helix.cc
, turner_test_one_chain.cc
, turner_two_chain.cc
, autorb.cc
, sidechain_min.cc
, cen_relax.cc
, cryst_design.cc
, dsrna_grow.cc
, fasol_perres.cc
, fpd_symmTest.cc
, min_test.cc
, mirrorsymm_test.cc
, per_atom_gradients.cc
, perturb_structure.cc
, min_test.cc
, pep_spec.06-23.cc
, SymmDataTest.cc
, jd2_parser_DNAInt.cc
, aggregate_coarse_rna_vdw.cc
, aramid_folding.cc
, trial_rna_mutants.cc
, simple_dna_regression_test.cc
, byres_data.cc
, domain_assemble.cc
, hbscan.cc
, pep_prepspec.cc
, easy_target_test.cc
, pep_spec.cc
, pep_spec_flx.cc
, pep_spec_flx.mov.cc
, pepspec.cc
, rotamer_repack.cc
, loop_test.cc
, backrub_pilot.cc
, cterdesign.cc
, kinematic_relax_test.cc
, loop_minimize.cc
, mpframework_score.cc
, dna_design_test.cc
, dna_dr_test.cc
, dna_relax.cc
, dna_spec_test.cc
, motif_scan.cc
, simple_dna_regression_test.cc
, zf_relax.cc
, elec_dens_rot_recov.cc
, embed_mp_pose_from_topo.cc
, membrane_sfxn.cc
, test_bbmc.cc
, mpscore_integrate.cc
, read_mp_pose.cc
, read_mp_pose_from_seq.cc
, read_pose_from_seq.cc
, benzene_test.cc
, block_stack_test.cc
, check_cubic_conv.cc
, coarse_rna_test.cc
, dna_test.cc
, entropy_test.cc
, get_rmsd.cc
, dimer_relax.cc
, min_test_hpark.cc
, test_bbmc.org.cc
, medal_test.cc
, min_cst.cc
, sc_interaction.cc
, oop_dock_design.cc
, analyze_docked_RNA_motifs.cc
, check_frag_rmsd.cc
, fragment_extract.cc
, SymmAbrelax.cc
, SymmSilentFile.cc
, convert_pdb_to_silent_file.cc
, flxbb.cc
, r_fold_cst.cc
, r_play_with_etables.cc
, multidomain_switch.cc
, parin_test.cc
, analyze_dna.cc
, capri15.cc
- my_shared_ptr
: T60.custom_shared.hpp
, T61.smart_holder.hpp
- MyAppCOP
: features_reporter.cc
- MyAppOP
: features_reporter.cc
- myasserteq()
: gpu_mat_vec.hh
- myComparison()
: avrg_silent.cc
- mydumppdb()
: atom_design.cc
- MyFeaturesReporterCOP
: features_reporter.cc
- MyFeaturesReporterOP
: features_reporter.cc
- myoptH()
: crossmatch.cc
, willmatch_d6_bpy.cc
, willmatch_chorismate.cc
, willmatch_2d6_bhe.cc
, genmatch_m8.cc
, genmatch_d6_bpy.cc
, genmatch_d6_bhhcg.cc
, genmatch.cc
, crossmatch_d2.cc
- MYSQL_ONLY
: util.hh
- myuniform()
: test_leerichards.cc
- myxdis()
: heterodock.cc
